add_helixer_workflow #555

rlibouba · 2024-10-08T13:55:29Z

Hello, I would like to propose this workflow in connection with the GTN "Genome annotation with Helixer".
Thank you. Have a nice day!

github-actions · 2024-10-08T14:15:04Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat' --species '' --gff-output-path '/tmp/tmpbjlbttns/job_working_directory/000/2/outputs/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:04:51.802616: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-08 14:04:52.493612: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-08 14:04:57.902564: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:04:58.111355: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:05:00.801827: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:05:03.411030: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:05:06.031928: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat',
 'gff_output_path': '/tmp/tmpbjlbttns/job_working_directory/000/2/outputs/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpufm2it1t
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.24 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.39 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpufm2it1t/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpufm2it1t/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat', 'timestamp': '2024-10-08 14:04:55.157284'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.06 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat in 0.07 hours. GFF file written to /tmp/tmpbjlbttns/job_working_directory/000/2/outputs/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat' genomeref.fa &&  gffread '/tmp/tmpbjlbttns/files/8/e/b/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
chr_replace	`None`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpbjlbttns/files/8/e/b/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpbjlbttns/job_working_directory/000/5/outputs/dataset_f1de88e0-4b00-4780-ba4d-165e1945ac11.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat' 2>&1 | tail -n +3 >> '/tmp/tmpbjlbttns/job_working_directory/000/5/outputs/dataset_f1de88e0-4b00-4780-ba4d-165e1945ac11.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpbjlbttns/job_working_directory/000/5/outputs/dataset_f1de88e0-4b00-4780-ba4d-165e1945ac11.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpbjlbttns/job_working_directory/000/5/outputs/dataset_1cde761f-2623-4b9e-a680-f4aa1cb6f650.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca_files &&  cp /tmp/tmpbjlbttns/job_working_directory/000/6/configs/tmp4o2spt0x /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca_files /tmp/tmpbjlbttns/job_working_directory/000/6/configs/tmp4o2spt0x &&  cp /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca_files/index.html /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

busco --in '/tmp/tmpbjlbttns/files/f/f/e/dataset_ffe630b0-92d0-4683-a1e0-1b22062a99d5.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - cca0f42c8fe97eb6
- history_state
  - error
- invocation_id
  - cca0f42c8fe97eb6
- invocation_state
  - scheduled
- workflow_id
  - cca0f42c8fe97eb6

github-actions · 2024-10-08T14:41:16Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat' --species '' --gff-output-path '/tmp/tmpjo038yv5/job_working_directory/000/2/outputs/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:35:08.583343: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-08 14:35:09.305046: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-08 14:35:14.833701: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:35:15.087517: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:35:17.511875: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:35:19.978380: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:35:22.485818: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat',
 'gff_output_path': '/tmp/tmpjo038yv5/job_working_directory/000/2/outputs/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpb13qee9_
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.25 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.40 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpb13qee9_/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpb13qee9_/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat', 'timestamp': '2024-10-08 14:35:12.001462'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat in 0.07 hours. GFF file written to /tmp/tmpjo038yv5/job_working_directory/000/2/outputs/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:36:49 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-08 14:32:47 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/08/2024 14:32:47 *****
2024-10-08 14:32:47 INFO:	Configuring BUSCO with local environment
2024-10-08 14:32:47 INFO:	Running genome mode
2024-10-08 14:33:01 INFO:	Input file is /tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat
2024-10-08 14:33:01 INFO:	No lineage specified. Running lineage auto selector.

2024-10-08 14:33:01 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-10-08 14:33:01 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:01 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:01 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-10-08 14:33:01 INFO:	Running 1 job(s) on bbtools, starting at 10/08/2024 14:33:01
2024-10-08 14:33:02 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-08 14:33:02 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-08 14:33:02 INFO:	Running Prodigal with genetic code 11 in single mode
2024-10-08 14:33:02 INFO:	Running 1 job(s) on prodigal, starting at 10/08/2024 14:33:02
2024-10-08 14:33:04 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-08 14:33:04 INFO:	Genetic code 11 selected as optimal
2024-10-08 14:33:04 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:04 INFO:	Running 194 job(s) on hmmsearch, starting at 10/08/2024 14:33:04
2024-10-08 14:33:06 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-10-08 14:33:07 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-10-08 14:33:07 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-10-08 14:33:08 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-10-08 14:33:09 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-10-08 14:33:10 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-10-08 14:33:11 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-10-08 14:33:12 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-10-08 14:33:13 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-10-08 14:33:13 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-10-08 14:33:13 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-10-08 14:33:13 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:13 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:14 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-10-08 14:33:14 INFO:	Skipping BBTools as already run
2024-10-08 14:33:14 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-08 14:33:14 INFO:	Running Prodigal with genetic code 4 in single mode
2024-10-08 14:33:14 INFO:	Running 1 job(s) on prodigal, starting at 10/08/2024 14:33:14
2024-10-08 14:33:16 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-08 14:33:16 INFO:	Genetic code 4 selected as optimal
2024-10-08 14:33:16 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:16 INFO:	Running 124 job(s) on hmmsearch, starting at 10/08/2024 14:33:16
2024-10-08 14:33:18 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-10-08 14:33:19 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-10-08 14:33:20 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-10-08 14:33:20 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-10-08 14:33:21 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-10-08 14:33:21 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-10-08 14:33:22 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-10-08 14:33:22 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-10-08 14:33:23 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-10-08 14:33:24 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-10-08 14:33:24 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-10-08 14:33:24 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-10-08 14:33:24 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-10-08 14:33:24 INFO:	Skipping BBTools as already run
2024-10-08 14:33:24 INFO:	Running 1 job(s) on makeblastdb, starting at 10/08/2024 14:33:24
2024-10-08 14:33:25 INFO:	Creating BLAST database with input file
2024-10-08 14:33:25 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-10-08 14:33:25 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-08 14:33:25 INFO:	Running 1 job(s) on tblastn, starting at 10/08/2024 14:33:25
2024-10-08 14:33:26 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-08 14:33:26 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-08 14:33:26 INFO:	Running Augustus prediction using fly as species:
2024-10-08 14:33:26 INFO:	Running 6 job(s) on augustus, starting at 10/08/2024 14:33:26
2024-10-08 14:33:29 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-08 14:33:31 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-08 14:33:34 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-08 14:33:37 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-08 14:33:38 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-08 14:33:40 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-08 14:33:40 INFO:	Extracting predicted proteins...
2024-10-08 14:33:40 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:40 INFO:	Running 6 job(s) on hmmsearch, starting at 10/08/2024 14:33:40
2024-10-08 14:33:40 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-08 14:33:40 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	37 exons in total
2024-10-08 14:33:41 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-10-08 14:33:41 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-10-08 14:33:41 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-10-08 14:33:41 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-08 14:33:41 INFO:	Running 1 job(s) on tblastn, starting at 10/08/2024 14:33:41
2024-10-08 14:33:51 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-08 14:33:51 INFO:	Converting predicted genes to short genbank files
2024-10-08 14:33:51 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 10/08/2024 14:33:51
2024-10-08 14:33:52 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-10-08 14:33:52 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-10-08 14:33:52 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-10-08 14:33:52 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-10-08 14:33:52 INFO:	Running 1 job(s) on new_species.pl, starting at 10/08/2024 14:33:52
2024-10-08 14:33:52 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-10-08 14:33:52 INFO:	Running 1 job(s) on etraining, starting at 10/08/2024 14:33:52
2024-10-08 14:33:53 INFO:	[etraining]	1 of 1 task(s) completed
2024-10-08 14:33:53 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-10-08 14:33:53 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-08 14:33:53 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-10-08 14:33:53 INFO:	Running 6 job(s) on augustus, starting at 10/08/2024 14:33:53
2024-10-08 14:33:57 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-08 14:33:58 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-08 14:34:00 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-08 14:34:04 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	Extracting predicted proteins...
2024-10-08 14:34:05 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:34:05 INFO:	Running 6 job(s) on hmmsearch, starting at 10/08/2024 14:34:05
2024-10-08 14:34:05 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	37 exons in total
2024-10-08 14:34:05 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-10-08 14:34:05 INFO:	eukaryota_odb10 selected

2024-10-08 14:34:05 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-10-08 14:34:05 INFO:	Extract markers...
2024-10-08 14:34:06 INFO:	Place the markers on the reference tree...
2024-10-08 14:34:06 INFO:	Running 1 job(s) on sepp, starting at 10/08/2024 14:34:06
2024-10-08 14:36:46 INFO:	[sepp]	1 of 1 task(s) completed
2024-10-08 14:36:46 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-10-08 14:36:46 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-10-08 14:36:46 INFO:	BUSCO analysis done with WARNING(s). Total running time: 225 seconds

***** Summary of warnings: *****
2024-10-08 14:33:01 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:01 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:13 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:13 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:24 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-10-08 14:36:46 INFO:	Results written in /tmp/tmpjo038yv5/job_working_directory/000/3/working/busco_galaxy
2024-10-08 14:36:46 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-08 14:36:46 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 127 4096 Oct  8 14:34 augustus_output
drwxr-xr-x 3 1001 127 4096 Oct  8 14:33 blast_output
drwxr-xr-x 5 1001 127 4096 Oct  8 14:33 busco_sequences
-rw-r--r-- 1 1001 127 5831 Oct  8 14:34 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Oct  8 14:33 hmmer_output
-rw-r--r-- 1 1001 127 3548 Oct  8 14:34 missing_busco_list.tsv
drwxr-xr-x 2 1001 127 4096 Oct  8 14:36 placement_files
-rw-r--r-- 1 1001 127 3180 Oct  8 14:34 short_summary.json
-rw-r--r-- 1 1001 127 1078 Oct  8 14:34 short_summary.txt
2024-10-08 14:36:47 INFO:	****************** Start plot generation at 10/08/2024 14:36:47 ******************
2024-10-08 14:36:47 INFO:	Load data ...
2024-10-08 14:36:47 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-10-08 14:36:47 INFO:	Generate the R code ...
2024-10-08 14:36:47 INFO:	Run the R code ...
2024-10-08 14:36:49 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-08 14:36:49 INFO:	Plot generation done. Total running time: 2.2741615772247314 seconds
2024-10-08 14:36:49 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat' genomeref.fa &&  gffread '/tmp/tmpjo038yv5/files/e/d/9/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
chr_replace	`None`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpjo038yv5/files/e/d/9/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpjo038yv5/job_working_directory/000/5/outputs/dataset_69b6a85e-92c1-4090-8121-98ab12b4837f.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat' 2>&1 | tail -n +3 >> '/tmp/tmpjo038yv5/job_working_directory/000/5/outputs/dataset_69b6a85e-92c1-4090-8121-98ab12b4837f.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpjo038yv5/job_working_directory/000/5/outputs/dataset_69b6a85e-92c1-4090-8121-98ab12b4837f.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpjo038yv5/job_working_directory/000/5/outputs/dataset_98d89ef3-b06b-4401-8b96-548b799b1166.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir -p /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770_files &&  cp /tmp/tmpjo038yv5/job_working_directory/000/6/configs/tmplvzmfsif /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770_files /tmp/tmpjo038yv5/job_working_directory/000/6/configs/tmplvzmfsif &&  cp /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770_files/index.html /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770.dat;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmpjo038yv5/files/3/b/6/dataset_3b6f8213-9133-4170-8728-7f7fd95294df.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 70a9d196ab7d53ba
- history_state
  - error
- invocation_id
  - 70a9d196ab7d53ba
- invocation_state
  - scheduled
- workflow_id
  - 70a9d196ab7d53ba

github-actions · 2024-10-08T14:43:00Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat' --species '' --gff-output-path '/tmp/tmp88q28s6d/job_working_directory/000/2/outputs/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:36:32.061351: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-08 14:36:32.737547: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-08 14:36:38.160538: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:36:38.374570: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:36:40.875694: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:36:43.349369: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:36:45.784360: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat',
 'gff_output_path': '/tmp/tmp88q28s6d/job_working_directory/000/2/outputs/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmp6vfv9bei
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.34 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.49 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmp6vfv9bei/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmp6vfv9bei/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat', 'timestamp': '2024-10-08 14:36:35.465286'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat in 0.07 hours. GFF file written to /tmp/tmp88q28s6d/job_working_directory/000/2/outputs/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:37:23 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-08 14:32:50 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/08/2024 14:32:50 *****
2024-10-08 14:32:50 INFO:	Configuring BUSCO with local environment
2024-10-08 14:32:50 INFO:	Running genome mode
2024-10-08 14:33:10 INFO:	Input file is /tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat
2024-10-08 14:33:10 INFO:	No lineage specified. Running lineage auto selector.

2024-10-08 14:33:10 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-10-08 14:33:10 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:10 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:10 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-10-08 14:33:10 INFO:	Running 1 job(s) on bbtools, starting at 10/08/2024 14:33:10
2024-10-08 14:33:12 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-08 14:33:12 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-08 14:33:12 INFO:	Running Prodigal with genetic code 11 in single mode
2024-10-08 14:33:12 INFO:	Running 1 job(s) on prodigal, starting at 10/08/2024 14:33:12
2024-10-08 14:33:14 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-08 14:33:14 INFO:	Genetic code 11 selected as optimal
2024-10-08 14:33:14 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:14 INFO:	Running 194 job(s) on hmmsearch, starting at 10/08/2024 14:33:14
2024-10-08 14:33:16 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-10-08 14:33:18 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-10-08 14:33:19 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-10-08 14:33:21 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-10-08 14:33:22 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-10-08 14:33:24 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-10-08 14:33:25 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-10-08 14:33:27 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-10-08 14:33:29 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-10-08 14:33:30 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-10-08 14:33:30 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-10-08 14:33:30 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:30 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:30 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-10-08 14:33:30 INFO:	Skipping BBTools as already run
2024-10-08 14:33:30 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-08 14:33:30 INFO:	Running Prodigal with genetic code 4 in single mode
2024-10-08 14:33:30 INFO:	Running 1 job(s) on prodigal, starting at 10/08/2024 14:33:30
2024-10-08 14:33:33 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-08 14:33:33 INFO:	Genetic code 4 selected as optimal
2024-10-08 14:33:33 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:33 INFO:	Running 124 job(s) on hmmsearch, starting at 10/08/2024 14:33:33
2024-10-08 14:33:35 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-10-08 14:33:36 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-10-08 14:33:37 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-10-08 14:33:38 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-10-08 14:33:39 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-10-08 14:33:40 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-10-08 14:33:42 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-10-08 14:33:43 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-10-08 14:33:44 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-10-08 14:33:44 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-10-08 14:33:44 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-10-08 14:33:44 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-10-08 14:33:44 INFO:	Skipping BBTools as already run
2024-10-08 14:33:44 INFO:	Running 1 job(s) on makeblastdb, starting at 10/08/2024 14:33:44
2024-10-08 14:33:45 INFO:	Creating BLAST database with input file
2024-10-08 14:33:45 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-10-08 14:33:45 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-08 14:33:45 INFO:	Running 1 job(s) on tblastn, starting at 10/08/2024 14:33:45
2024-10-08 14:33:47 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-08 14:33:47 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-08 14:33:47 INFO:	Running Augustus prediction using fly as species:
2024-10-08 14:33:47 INFO:	Running 6 job(s) on augustus, starting at 10/08/2024 14:33:47
2024-10-08 14:33:50 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-08 14:33:52 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-08 14:33:56 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-08 14:33:58 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-08 14:33:59 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-08 14:34:01 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-08 14:34:01 INFO:	Extracting predicted proteins...
2024-10-08 14:34:01 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:34:01 INFO:	Running 6 job(s) on hmmsearch, starting at 10/08/2024 14:34:01
2024-10-08 14:34:02 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	37 exons in total
2024-10-08 14:34:02 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-10-08 14:34:02 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-10-08 14:34:02 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-10-08 14:34:03 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-08 14:34:03 INFO:	Running 1 job(s) on tblastn, starting at 10/08/2024 14:34:03
2024-10-08 14:34:13 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-08 14:34:13 INFO:	Converting predicted genes to short genbank files
2024-10-08 14:34:13 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 10/08/2024 14:34:13
2024-10-08 14:34:14 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-10-08 14:34:14 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-10-08 14:34:14 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-10-08 14:34:14 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-10-08 14:34:14 INFO:	Running 1 job(s) on new_species.pl, starting at 10/08/2024 14:34:14
2024-10-08 14:34:14 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-10-08 14:34:14 INFO:	Running 1 job(s) on etraining, starting at 10/08/2024 14:34:14
2024-10-08 14:34:15 INFO:	[etraining]	1 of 1 task(s) completed
2024-10-08 14:34:15 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-10-08 14:34:15 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-08 14:34:15 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-10-08 14:34:15 INFO:	Running 6 job(s) on augustus, starting at 10/08/2024 14:34:15
2024-10-08 14:34:19 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-08 14:34:20 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-08 14:34:21 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-08 14:34:24 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-08 14:34:25 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-08 14:34:26 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-08 14:34:26 INFO:	Extracting predicted proteins...
2024-10-08 14:34:26 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:34:26 INFO:	Running 6 job(s) on hmmsearch, starting at 10/08/2024 14:34:26
2024-10-08 14:34:27 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	37 exons in total
2024-10-08 14:34:27 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-10-08 14:34:27 INFO:	eukaryota_odb10 selected

2024-10-08 14:34:27 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-10-08 14:34:28 INFO:	Extract markers...
2024-10-08 14:34:28 INFO:	Place the markers on the reference tree...
2024-10-08 14:34:28 INFO:	Running 1 job(s) on sepp, starting at 10/08/2024 14:34:28
2024-10-08 14:37:19 INFO:	[sepp]	1 of 1 task(s) completed
2024-10-08 14:37:19 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-10-08 14:37:19 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-10-08 14:37:19 INFO:	BUSCO analysis done with WARNING(s). Total running time: 249 seconds

***** Summary of warnings: *****
2024-10-08 14:33:10 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:10 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:30 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:30 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:44 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-10-08 14:37:19 INFO:	Results written in /tmp/tmp88q28s6d/job_working_directory/000/3/working/busco_galaxy
2024-10-08 14:37:19 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-08 14:37:19 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 127 4096 Oct  8 14:34 augustus_output
drwxr-xr-x 3 1001 127 4096 Oct  8 14:34 blast_output
drwxr-xr-x 5 1001 127 4096 Oct  8 14:33 busco_sequences
-rw-r--r-- 1 1001 127 5831 Oct  8 14:34 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Oct  8 14:34 hmmer_output
-rw-r--r-- 1 1001 127 3548 Oct  8 14:34 missing_busco_list.tsv
drwxr-xr-x 2 1001 127 4096 Oct  8 14:37 placement_files
-rw-r--r-- 1 1001 127 3180 Oct  8 14:34 short_summary.json
-rw-r--r-- 1 1001 127 1078 Oct  8 14:34 short_summary.txt
2024-10-08 14:37:20 INFO:	****************** Start plot generation at 10/08/2024 14:37:20 ******************
2024-10-08 14:37:20 INFO:	Load data ...
2024-10-08 14:37:20 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-10-08 14:37:20 INFO:	Generate the R code ...
2024-10-08 14:37:20 INFO:	Run the R code ...
2024-10-08 14:37:23 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-08 14:37:23 INFO:	Plot generation done. Total running time: 2.407008647918701 seconds
2024-10-08 14:37:23 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat' genomeref.fa &&  gffread '/tmp/tmp88q28s6d/files/8/9/8/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
chr_replace	`None`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmp88q28s6d/files/8/9/8/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp88q28s6d/job_working_directory/000/5/outputs/dataset_e47c29b1-9042-43f9-b0c0-ea6dcea5d212.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat' 2>&1 | tail -n +3 >> '/tmp/tmp88q28s6d/job_working_directory/000/5/outputs/dataset_e47c29b1-9042-43f9-b0c0-ea6dcea5d212.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp88q28s6d/job_working_directory/000/5/outputs/dataset_e47c29b1-9042-43f9-b0c0-ea6dcea5d212.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp88q28s6d/job_working_directory/000/5/outputs/dataset_3b701bcd-4d08-45ce-ac5c-5732fafb5ef4.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir -p /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98_files &&  cp /tmp/tmp88q28s6d/job_working_directory/000/6/configs/tmplj2vg_1i /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98_files /tmp/tmp88q28s6d/job_working_directory/000/6/configs/tmplj2vg_1i &&  cp /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98_files/index.html /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98.dat;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmp88q28s6d/files/e/3/a/dataset_e3a07acc-c042-4969-8b1c-a36255f09872.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 49a4bd8b99eb7f47
- history_state
  - error
- invocation_id
  - 49a4bd8b99eb7f47
- invocation_state
  - scheduled
- workflow_id
  - 49a4bd8b99eb7f47

github-actions · 2024-10-10T09:31:57Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat' --species '' --gff-output-path '/tmp/tmpcmf3ezyu/job_working_directory/000/2/outputs/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-10 09:24:32.475025: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-10 09:24:33.180938: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-10 09:24:38.730559: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 09:24:38.976324: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 09:24:41.578172: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 09:24:44.176115: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 09:24:46.786359: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat',
 'gff_output_path': '/tmp/tmpcmf3ezyu/job_working_directory/000/2/outputs/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpi3q8kbke
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.24 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.39 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpi3q8kbke/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpi3q8kbke/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat', 'timestamp': '2024-10-10 09:24:35.923143'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat in 0.07 hours. GFF file written to /tmp/tmpcmf3ezyu/job_working_directory/000/2/outputs/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-10 09:28:44 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-10 09:23:52 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/10/2024 09:23:52 *****
2024-10-10 09:23:52 INFO:	Configuring BUSCO with local environment
2024-10-10 09:23:52 INFO:	Running genome mode
2024-10-10 09:23:56 INFO:	Input file is /tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat
2024-10-10 09:23:56 INFO:	No lineage specified. Running lineage auto selector.

2024-10-10 09:23:56 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-10-10 09:23:56 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:23:56 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:23:56 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-10-10 09:23:56 INFO:	Running 1 job(s) on bbtools, starting at 10/10/2024 09:23:56
2024-10-10 09:23:58 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-10 09:23:58 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-10 09:23:58 INFO:	Running Prodigal with genetic code 11 in single mode
2024-10-10 09:23:58 INFO:	Running 1 job(s) on prodigal, starting at 10/10/2024 09:23:58
2024-10-10 09:24:01 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-10 09:24:01 INFO:	Genetic code 11 selected as optimal
2024-10-10 09:24:01 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 09:24:01 INFO:	Running 194 job(s) on hmmsearch, starting at 10/10/2024 09:24:01
2024-10-10 09:24:05 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-10-10 09:24:07 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-10-10 09:24:10 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-10-10 09:24:13 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-10-10 09:24:17 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-10-10 09:24:21 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-10-10 09:24:24 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-10-10 09:24:27 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-10-10 09:24:30 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-10-10 09:24:33 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-10-10 09:24:33 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-10-10 09:24:33 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:33 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:33 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-10-10 09:24:33 INFO:	Skipping BBTools as already run
2024-10-10 09:24:33 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-10 09:24:33 INFO:	Running Prodigal with genetic code 4 in single mode
2024-10-10 09:24:33 INFO:	Running 1 job(s) on prodigal, starting at 10/10/2024 09:24:33
2024-10-10 09:24:36 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-10 09:24:36 INFO:	Genetic code 4 selected as optimal
2024-10-10 09:24:36 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 09:24:37 INFO:	Running 124 job(s) on hmmsearch, starting at 10/10/2024 09:24:37
2024-10-10 09:24:39 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-10-10 09:24:41 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-10-10 09:24:43 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-10-10 09:24:45 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-10-10 09:24:47 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-10-10 09:24:49 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-10-10 09:24:51 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-10-10 09:24:53 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-10-10 09:24:55 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-10-10 09:24:57 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-10-10 09:24:57 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-10-10 09:24:57 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-10-10 09:24:57 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-10-10 09:24:57 INFO:	Skipping BBTools as already run
2024-10-10 09:24:57 INFO:	Running 1 job(s) on makeblastdb, starting at 10/10/2024 09:24:57
2024-10-10 09:24:58 INFO:	Creating BLAST database with input file
2024-10-10 09:24:58 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-10-10 09:24:58 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-10 09:24:58 INFO:	Running 1 job(s) on tblastn, starting at 10/10/2024 09:24:58
2024-10-10 09:25:00 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-10 09:25:00 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-10 09:25:00 INFO:	Running Augustus prediction using fly as species:
2024-10-10 09:25:00 INFO:	Running 6 job(s) on augustus, starting at 10/10/2024 09:25:00
2024-10-10 09:25:04 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-10 09:25:06 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-10 09:25:10 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-10 09:25:13 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-10 09:25:15 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-10 09:25:17 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-10 09:25:17 INFO:	Extracting predicted proteins...
2024-10-10 09:25:17 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 09:25:17 INFO:	Running 6 job(s) on hmmsearch, starting at 10/10/2024 09:25:17
2024-10-10 09:25:18 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-10 09:25:18 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-10 09:25:18 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-10 09:25:19 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-10 09:25:19 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-10 09:25:19 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-10 09:25:19 INFO:	37 exons in total
2024-10-10 09:25:19 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-10-10 09:25:19 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-10-10 09:25:19 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-10-10 09:25:20 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-10 09:25:20 INFO:	Running 1 job(s) on tblastn, starting at 10/10/2024 09:25:20
2024-10-10 09:25:32 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-10 09:25:32 INFO:	Converting predicted genes to short genbank files
2024-10-10 09:25:32 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 10/10/2024 09:25:32
2024-10-10 09:25:32 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-10-10 09:25:32 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-10-10 09:25:32 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-10-10 09:25:32 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-10-10 09:25:32 INFO:	Running 1 job(s) on new_species.pl, starting at 10/10/2024 09:25:32
2024-10-10 09:25:33 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-10-10 09:25:33 INFO:	Running 1 job(s) on etraining, starting at 10/10/2024 09:25:33
2024-10-10 09:25:34 INFO:	[etraining]	1 of 1 task(s) completed
2024-10-10 09:25:34 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-10-10 09:25:34 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-10 09:25:34 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-10-10 09:25:34 INFO:	Running 6 job(s) on augustus, starting at 10/10/2024 09:25:34
2024-10-10 09:25:39 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-10 09:25:40 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-10 09:25:42 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-10 09:25:45 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-10 09:25:47 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-10 09:25:48 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-10 09:25:48 INFO:	Extracting predicted proteins...
2024-10-10 09:25:48 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 09:25:48 INFO:	Running 6 job(s) on hmmsearch, starting at 10/10/2024 09:25:48
2024-10-10 09:25:49 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-10 09:25:49 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	37 exons in total
2024-10-10 09:25:50 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-10-10 09:25:50 INFO:	eukaryota_odb10 selected

2024-10-10 09:25:50 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-10-10 09:25:50 INFO:	Extract markers...
2024-10-10 09:25:50 INFO:	Place the markers on the reference tree...
2024-10-10 09:25:50 INFO:	Running 1 job(s) on sepp, starting at 10/10/2024 09:25:50
2024-10-10 09:28:39 INFO:	[sepp]	1 of 1 task(s) completed
2024-10-10 09:28:40 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-10-10 09:28:40 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-10-10 09:28:40 INFO:	BUSCO analysis done with WARNING(s). Total running time: 284 seconds

***** Summary of warnings: *****
2024-10-10 09:23:56 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:23:56 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:33 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:33 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:57 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-10-10 09:28:40 INFO:	Results written in /tmp/tmpcmf3ezyu/job_working_directory/000/3/working/busco_galaxy
2024-10-10 09:28:40 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-10 09:28:40 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 118 4096 Oct 10 09:25 augustus_output
drwxr-xr-x 3 1001 118 4096 Oct 10 09:25 blast_output
drwxr-xr-x 5 1001 118 4096 Oct 10 09:24 busco_sequences
-rw-r--r-- 1 1001 118 5831 Oct 10 09:25 full_table.tsv
drwxr-xr-x 4 1001 118 4096 Oct 10 09:25 hmmer_output
-rw-r--r-- 1 1001 118 3548 Oct 10 09:25 missing_busco_list.tsv
drwxr-xr-x 2 1001 118 4096 Oct 10 09:28 placement_files
-rw-r--r-- 1 1001 118 3180 Oct 10 09:25 short_summary.json
-rw-r--r-- 1 1001 118 1078 Oct 10 09:25 short_summary.txt
2024-10-10 09:28:41 INFO:	****************** Start plot generation at 10/10/2024 09:28:41 ******************
2024-10-10 09:28:41 INFO:	Load data ...
2024-10-10 09:28:41 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-10-10 09:28:41 INFO:	Generate the R code ...
2024-10-10 09:28:41 INFO:	Run the R code ...
2024-10-10 09:28:44 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-10 09:28:44 INFO:	Plot generation done. Total running time: 3.167226552963257 seconds
2024-10-10 09:28:44 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat' genomeref.fa &&  gffread '/tmp/tmpcmf3ezyu/files/2/4/d/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
chr_replace	`None`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpcmf3ezyu/files/2/4/d/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpcmf3ezyu/job_working_directory/000/5/outputs/dataset_260120ec-d58b-4412-b4f3-824af3309cea.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat' 2>&1 | tail -n +3 >> '/tmp/tmpcmf3ezyu/job_working_directory/000/5/outputs/dataset_260120ec-d58b-4412-b4f3-824af3309cea.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpcmf3ezyu/job_working_directory/000/5/outputs/dataset_260120ec-d58b-4412-b4f3-824af3309cea.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpcmf3ezyu/job_working_directory/000/5/outputs/dataset_28df8c72-84fa-457b-9115-852f805cf3c9.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir -p /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5_files &&  cp /tmp/tmpcmf3ezyu/job_working_directory/000/6/configs/tmptk4ctt_h /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5_files /tmp/tmpcmf3ezyu/job_working_directory/000/6/configs/tmptk4ctt_h &&  cp /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5_files/index.html /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5.dat;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmpcmf3ezyu/files/c/7/f/dataset_c7f57249-94f9-40c9-87b5-3359bbec2051.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - ff726b155b645e6d
- history_state
  - error
- invocation_id
  - ff726b155b645e6d
- invocation_state
  - scheduled
- workflow_id
  - ff726b155b645e6d

github-actions · 2024-10-10T17:26:10Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat' --species '' --gff-output-path '/tmp/tmp9tr0sopf/job_working_directory/000/2/outputs/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-10 17:16:31.094407: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-10 17:16:31.886043: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-10 17:16:37.746447: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 17:16:38.045402: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 17:16:40.463150: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 17:16:42.768220: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 17:16:45.359623: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat',
 'gff_output_path': '/tmp/tmp9tr0sopf/job_working_directory/000/2/outputs/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpp0uh165t
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.25 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.41 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.02 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpp0uh165t/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpp0uh165t/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat', 'timestamp': '2024-10-10 17:16:34.780739'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.09 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat in 0.07 hours. GFF file written to /tmp/tmp9tr0sopf/job_working_directory/000/2/outputs/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-10 17:20:58 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-10 17:16:16 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/10/2024 17:16:16 *****
2024-10-10 17:16:16 INFO:	Configuring BUSCO with local environment
2024-10-10 17:16:16 INFO:	Running genome mode
2024-10-10 17:16:18 INFO:	Input file is /tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat
2024-10-10 17:16:18 INFO:	No lineage specified. Running lineage auto selector.

2024-10-10 17:16:18 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-10-10 17:16:18 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:18 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:18 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-10-10 17:16:18 INFO:	Running 1 job(s) on bbtools, starting at 10/10/2024 17:16:18
2024-10-10 17:16:19 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-10 17:16:19 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-10 17:16:19 INFO:	Running Prodigal with genetic code 11 in single mode
2024-10-10 17:16:19 INFO:	Running 1 job(s) on prodigal, starting at 10/10/2024 17:16:19
2024-10-10 17:16:21 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-10 17:16:22 INFO:	Genetic code 11 selected as optimal
2024-10-10 17:16:22 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 17:16:22 INFO:	Running 194 job(s) on hmmsearch, starting at 10/10/2024 17:16:22
2024-10-10 17:16:24 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-10-10 17:16:25 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-10-10 17:16:27 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-10-10 17:16:28 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-10-10 17:16:30 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-10-10 17:16:32 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-10-10 17:16:33 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-10-10 17:16:35 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-10-10 17:16:36 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-10-10 17:16:38 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-10-10 17:16:38 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-10-10 17:16:38 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:38 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:38 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-10-10 17:16:38 INFO:	Skipping BBTools as already run
2024-10-10 17:16:38 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-10 17:16:38 INFO:	Running Prodigal with genetic code 4 in single mode
2024-10-10 17:16:38 INFO:	Running 1 job(s) on prodigal, starting at 10/10/2024 17:16:38
2024-10-10 17:16:41 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-10 17:16:41 INFO:	Genetic code 4 selected as optimal
2024-10-10 17:16:41 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 17:16:41 INFO:	Running 124 job(s) on hmmsearch, starting at 10/10/2024 17:16:41
2024-10-10 17:16:43 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-10-10 17:16:44 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-10-10 17:16:45 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-10-10 17:16:48 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-10-10 17:17:04 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-10-10 17:17:09 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-10-10 17:17:10 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-10-10 17:17:11 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-10-10 17:17:12 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-10-10 17:17:13 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-10-10 17:17:13 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-10-10 17:17:13 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-10-10 17:17:13 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-10-10 17:17:13 INFO:	Skipping BBTools as already run
2024-10-10 17:17:13 INFO:	Running 1 job(s) on makeblastdb, starting at 10/10/2024 17:17:13
2024-10-10 17:17:14 INFO:	Creating BLAST database with input file
2024-10-10 17:17:14 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-10-10 17:17:14 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-10 17:17:14 INFO:	Running 1 job(s) on tblastn, starting at 10/10/2024 17:17:14
2024-10-10 17:17:16 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-10 17:17:16 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-10 17:17:16 INFO:	Running Augustus prediction using fly as species:
2024-10-10 17:17:16 INFO:	Running 6 job(s) on augustus, starting at 10/10/2024 17:17:16
2024-10-10 17:17:20 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-10 17:17:23 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-10 17:17:27 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-10 17:17:30 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-10 17:17:32 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-10 17:17:34 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-10 17:17:34 INFO:	Extracting predicted proteins...
2024-10-10 17:17:34 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 17:17:35 INFO:	Running 6 job(s) on hmmsearch, starting at 10/10/2024 17:17:35
2024-10-10 17:17:35 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-10 17:17:35 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-10 17:17:35 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-10 17:17:35 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-10 17:17:36 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-10 17:17:36 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-10 17:17:36 INFO:	37 exons in total
2024-10-10 17:17:36 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-10-10 17:17:36 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-10-10 17:17:36 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-10-10 17:17:36 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-10 17:17:36 INFO:	Running 1 job(s) on tblastn, starting at 10/10/2024 17:17:36
2024-10-10 17:17:48 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-10 17:17:48 INFO:	Converting predicted genes to short genbank files
2024-10-10 17:17:48 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 10/10/2024 17:17:48
2024-10-10 17:17:49 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-10-10 17:17:49 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-10-10 17:17:49 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-10-10 17:17:49 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-10-10 17:17:49 INFO:	Running 1 job(s) on new_species.pl, starting at 10/10/2024 17:17:49
2024-10-10 17:17:49 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-10-10 17:17:49 INFO:	Running 1 job(s) on etraining, starting at 10/10/2024 17:17:49
2024-10-10 17:17:50 INFO:	[etraining]	1 of 1 task(s) completed
2024-10-10 17:17:50 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-10-10 17:17:50 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-10 17:17:50 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-10-10 17:17:50 INFO:	Running 6 job(s) on augustus, starting at 10/10/2024 17:17:50
2024-10-10 17:17:55 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-10 17:17:57 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-10 17:17:59 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-10 17:18:02 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-10 17:18:04 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	Extracting predicted proteins...
2024-10-10 17:18:06 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 17:18:06 INFO:	Running 6 job(s) on hmmsearch, starting at 10/10/2024 17:18:06
2024-10-10 17:18:06 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-10 17:18:07 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-10 17:18:07 INFO:	37 exons in total
2024-10-10 17:18:07 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-10-10 17:18:07 INFO:	eukaryota_odb10 selected

2024-10-10 17:18:07 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-10-10 17:18:07 INFO:	Extract markers...
2024-10-10 17:18:07 INFO:	Place the markers on the reference tree...
2024-10-10 17:18:07 INFO:	Running 1 job(s) on sepp, starting at 10/10/2024 17:18:07
2024-10-10 17:20:53 INFO:	[sepp]	1 of 1 task(s) completed
2024-10-10 17:20:53 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-10-10 17:20:53 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-10-10 17:20:53 INFO:	BUSCO analysis done with WARNING(s). Total running time: 276 seconds

***** Summary of warnings: *****
2024-10-10 17:16:18 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:18 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:38 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:38 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:17:13 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-10-10 17:20:53 INFO:	Results written in /tmp/tmp9tr0sopf/job_working_directory/000/3/working/busco_galaxy
2024-10-10 17:20:53 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-10 17:20:53 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 118 4096 Oct 10 17:18 augustus_output
drwxr-xr-x 3 1001 118 4096 Oct 10 17:17 blast_output
drwxr-xr-x 5 1001 118 4096 Oct 10 17:17 busco_sequences
-rw-r--r-- 1 1001 118 5831 Oct 10 17:18 full_table.tsv
drwxr-xr-x 4 1001 118 4096 Oct 10 17:17 hmmer_output
-rw-r--r-- 1 1001 118 3548 Oct 10 17:18 missing_busco_list.tsv
drwxr-xr-x 2 1001 118 4096 Oct 10 17:20 placement_files
-rw-r--r-- 1 1001 118 3180 Oct 10 17:18 short_summary.json
-rw-r--r-- 1 1001 118 1078 Oct 10 17:18 short_summary.txt
2024-10-10 17:20:55 INFO:	****************** Start plot generation at 10/10/2024 17:20:55 ******************
2024-10-10 17:20:55 INFO:	Load data ...
2024-10-10 17:20:55 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-10-10 17:20:55 INFO:	Generate the R code ...
2024-10-10 17:20:55 INFO:	Run the R code ...
2024-10-10 17:20:58 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-10 17:20:58 INFO:	Plot generation done. Total running time: 2.808326244354248 seconds
2024-10-10 17:20:58 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat' genomeref.fa &&  gffread '/tmp/tmp9tr0sopf/files/9/4/3/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
chr_replace	`None`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmp9tr0sopf/files/9/4/3/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp9tr0sopf/job_working_directory/000/5/outputs/dataset_dfdad63d-536e-45fb-90b7-c44715368ff6.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat' 2>&1 | tail -n +3 >> '/tmp/tmp9tr0sopf/job_working_directory/000/5/outputs/dataset_dfdad63d-536e-45fb-90b7-c44715368ff6.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp9tr0sopf/job_working_directory/000/5/outputs/dataset_dfdad63d-536e-45fb-90b7-c44715368ff6.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp9tr0sopf/job_working_directory/000/5/outputs/dataset_780a159f-dd83-4692-9bf6-086b9dc265d4.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir -p /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc_files &&  cp /tmp/tmp9tr0sopf/job_working_directory/000/6/configs/tmp0vtzdolc /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc_files /tmp/tmp9tr0sopf/job_working_directory/000/6/configs/tmp0vtzdolc &&  cp /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc_files/index.html /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc.dat;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmp9tr0sopf/files/e/4/1/dataset_e410dcf8-4da1-4afd-a5be-044716cbeadf.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 7a46bb8a29f136d4
- history_state
  - error
- invocation_id
  - 7a46bb8a29f136d4
- invocation_state
  - scheduled
- workflow_id
  - 7a46bb8a29f136d4

github-actions · 2024-10-15T15:38:57Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat' --species '' --gff-output-path '/tmp/tmp7vk7_3fs/job_working_directory/000/2/outputs/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-15 15:32:16.720998: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-15 15:32:17.434596: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-15 15:32:22.863717: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-15 15:32:23.114792: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-15 15:32:25.713627: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-15 15:32:28.307060: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-15 15:32:30.906081: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat',
 'gff_output_path': '/tmp/tmp7vk7_3fs/job_working_directory/000/2/outputs/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmp07e936s1
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.24 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.39 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmp07e936s1/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmp07e936s1/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat', 'timestamp': '2024-10-15 15:32:20.144514'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat in 0.07 hours. GFF file written to /tmp/tmp7vk7_3fs/job_working_directory/000/2/outputs/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat' genomeref.fa &&  gffread '/tmp/tmp7vk7_3fs/files/d/4/5/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
chr_replace	`None`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

ln -s '/tmp/tmp7vk7_3fs/files/d/4/5/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp7vk7_3fs/job_working_directory/000/5/outputs/dataset_5aefeac5-189f-4b20-b71a-1c09580791b4.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat' 2>&1 | tail -n +3 >> '/tmp/tmp7vk7_3fs/job_working_directory/000/5/outputs/dataset_5aefeac5-189f-4b20-b71a-1c09580791b4.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp7vk7_3fs/job_working_directory/000/5/outputs/dataset_5aefeac5-189f-4b20-b71a-1c09580791b4.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp7vk7_3fs/job_working_directory/000/5/outputs/dataset_9eea7fe3-531c-4933-8979-e2518f0ce22f.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec_files &&  cp /tmp/tmp7vk7_3fs/job_working_directory/000/6/configs/tmpn8ghbccm /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec_files /tmp/tmp7vk7_3fs/job_working_directory/000/6/configs/tmpn8ghbccm &&  cp /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec_files/index.html /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmp7vk7_3fs/files/2/1/a/dataset_21aa14b6-a430-4119-9915-bf8610175323.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 39f1166267c984e7
- history_state
  - error
- invocation_id
  - 39f1166267c984e7
- invocation_state
  - scheduled
- workflow_id
  - 39f1166267c984e7

github-actions · 2024-11-12T10:00:39Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	1
Error	0
Failure	0
Skipped	0

Passed Tests

✅ Galaxy-Workflow-annotation_helixer.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpmtie51tr/files/a/5/8/dataset_a5856987-f5d4-4efd-82b1-ff7fa5fb19a7.dat' --species '' --gff-output-path '/tmp/tmpmtie51tr/job_working_directory/000/2/outputs/dataset_0fc69b3e-2f48-48de-9482-5eae4fed668c.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-11-12 09:51:51.469891: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-11-12 09:51:52.159425: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-11-12 09:51:57.653830: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-11-12 09:51:57.845159: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-11-12 09:52:00.219492: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-11-12 09:52:02.544653: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-11-12 09:52:04.913329: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpmtie51tr/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpmtie51tr/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpmtie51tr/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpmtie51tr/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpmtie51tr/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpmtie51tr/files/a/5/8/dataset_a5856987-f5d4-4efd-82b1-ff7fa5fb19a7.dat',
 'gff_output_path': '/tmp/tmpmtie51tr/job_working_directory/000/2/outputs/dataset_0fc69b3e-2f48-48de-9482-5eae4fed668c.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpmtie51tr/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpco3xc0g0
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.25 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.40 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.01 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpmtie51tr/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpco3xc0g0/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpco3xc0g0/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpmtie51tr/files/a/5/8/dataset_a5856987-f5d4-4efd-82b1-ff7fa5fb19a7.dat', 'timestamp': '2024-11-12 09:51:54.932057'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpmtie51tr/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpmtie51tr/files/a/5/8/dataset_a5856987-f5d4-4efd-82b1-ff7fa5fb19a7.dat in 0.06 hours. GFF file written to /tmp/tmpmtie51tr/job_working_directory/000/2/outputs/dataset_0fc69b3e-2f48-48de-9482-5eae4fed668c.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5ced9a4ea0db11efa4ecb9e5749f45fe"`
chromInfo	`"/tmp/tmpmtie51tr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpmtie51tr/files/a/5/8/dataset_a5856987-f5d4-4efd-82b1-ff7fa5fb19a7.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-11-12 09:55:02 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-11-12 09:50:49 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 11/12/2024 09:50:49 *****
2024-11-12 09:50:49 INFO:	Configuring BUSCO with local environment
2024-11-12 09:50:49 INFO:	Running genome mode
2024-11-12 09:50:51 INFO:	Input file is /tmp/tmpmtie51tr/files/a/5/8/dataset_a5856987-f5d4-4efd-82b1-ff7fa5fb19a7.dat
2024-11-12 09:50:51 INFO:	No lineage specified. Running lineage auto selector.

2024-11-12 09:50:51 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-11-12 09:50:51 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-11-12 09:50:51 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-11-12 09:50:51 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-11-12 09:50:51 INFO:	Running 1 job(s) on bbtools, starting at 11/12/2024 09:50:51
2024-11-12 09:50:52 INFO:	[bbtools]	1 of 1 task(s) completed
2024-11-12 09:50:52 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-11-12 09:50:52 INFO:	Running Prodigal with genetic code 11 in single mode
2024-11-12 09:50:52 INFO:	Running 1 job(s) on prodigal, starting at 11/12/2024 09:50:52
2024-11-12 09:50:54 INFO:	[prodigal]	1 of 1 task(s) completed
2024-11-12 09:50:54 INFO:	Genetic code 11 selected as optimal
2024-11-12 09:50:54 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:50:55 INFO:	Running 194 job(s) on hmmsearch, starting at 11/12/2024 09:50:55
2024-11-12 09:50:57 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-11-12 09:50:58 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-11-12 09:51:00 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-11-12 09:51:01 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-11-12 09:51:03 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-11-12 09:51:04 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-11-12 09:51:06 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-11-12 09:51:07 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-11-12 09:51:09 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-11-12 09:51:10 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-11-12 09:51:10 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-11-12 09:51:10 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-11-12 09:51:10 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-11-12 09:51:10 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-11-12 09:51:10 INFO:	Skipping BBTools as already run
2024-11-12 09:51:10 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-11-12 09:51:10 INFO:	Running Prodigal with genetic code 4 in single mode
2024-11-12 09:51:10 INFO:	Running 1 job(s) on prodigal, starting at 11/12/2024 09:51:10
2024-11-12 09:51:13 INFO:	[prodigal]	1 of 1 task(s) completed
2024-11-12 09:51:13 INFO:	Genetic code 4 selected as optimal
2024-11-12 09:51:13 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:51:13 INFO:	Running 124 job(s) on hmmsearch, starting at 11/12/2024 09:51:13
2024-11-12 09:51:15 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-11-12 09:51:16 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-11-12 09:51:17 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-11-12 09:51:17 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-11-12 09:51:18 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-11-12 09:51:19 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-11-12 09:51:20 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-11-12 09:51:21 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-11-12 09:51:22 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-11-12 09:51:23 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-11-12 09:51:23 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:51:23 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-11-12 09:51:24 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-11-12 09:51:24 INFO:	Skipping BBTools as already run
2024-11-12 09:51:24 INFO:	Running 1 job(s) on makeblastdb, starting at 11/12/2024 09:51:24
2024-11-12 09:51:24 INFO:	Creating BLAST database with input file
2024-11-12 09:51:24 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-11-12 09:51:24 INFO:	Running a BLAST search for BUSCOs against created database
2024-11-12 09:51:24 INFO:	Running 1 job(s) on tblastn, starting at 11/12/2024 09:51:24
2024-11-12 09:51:26 INFO:	[tblastn]	1 of 1 task(s) completed
2024-11-12 09:51:26 INFO:	Running Augustus gene predictor on BLAST search results.
2024-11-12 09:51:26 INFO:	Running Augustus prediction using fly as species:
2024-11-12 09:51:26 INFO:	Running 6 job(s) on augustus, starting at 11/12/2024 09:51:26
2024-11-12 09:51:29 INFO:	[augustus]	1 of 6 task(s) completed
2024-11-12 09:51:31 INFO:	[augustus]	2 of 6 task(s) completed
2024-11-12 09:51:34 INFO:	[augustus]	3 of 6 task(s) completed
2024-11-12 09:51:36 INFO:	[augustus]	4 of 6 task(s) completed
2024-11-12 09:51:38 INFO:	[augustus]	5 of 6 task(s) completed
2024-11-12 09:51:39 INFO:	[augustus]	6 of 6 task(s) completed
2024-11-12 09:51:39 INFO:	Extracting predicted proteins...
2024-11-12 09:51:39 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:51:40 INFO:	Running 6 job(s) on hmmsearch, starting at 11/12/2024 09:51:40
2024-11-12 09:51:40 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-11-12 09:51:40 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-11-12 09:51:40 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-11-12 09:51:40 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-11-12 09:51:40 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-11-12 09:51:41 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-11-12 09:51:41 INFO:	37 exons in total
2024-11-12 09:51:41 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-11-12 09:51:41 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-11-12 09:51:41 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-11-12 09:51:41 INFO:	Running a BLAST search for BUSCOs against created database
2024-11-12 09:51:41 INFO:	Running 1 job(s) on tblastn, starting at 11/12/2024 09:51:41
2024-11-12 09:51:51 INFO:	[tblastn]	1 of 1 task(s) completed
2024-11-12 09:51:51 INFO:	Converting predicted genes to short genbank files
2024-11-12 09:51:51 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 11/12/2024 09:51:51
2024-11-12 09:51:52 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-11-12 09:51:52 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-11-12 09:51:52 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-11-12 09:51:52 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-11-12 09:51:52 INFO:	Running 1 job(s) on new_species.pl, starting at 11/12/2024 09:51:52
2024-11-12 09:51:52 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-11-12 09:51:52 INFO:	Running 1 job(s) on etraining, starting at 11/12/2024 09:51:52
2024-11-12 09:51:53 INFO:	[etraining]	1 of 1 task(s) completed
2024-11-12 09:51:53 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-11-12 09:51:53 INFO:	Running Augustus gene predictor on BLAST search results.
2024-11-12 09:51:53 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-11-12 09:51:53 INFO:	Running 6 job(s) on augustus, starting at 11/12/2024 09:51:53
2024-11-12 09:51:57 INFO:	[augustus]	1 of 6 task(s) completed
2024-11-12 09:51:59 INFO:	[augustus]	2 of 6 task(s) completed
2024-11-12 09:52:00 INFO:	[augustus]	3 of 6 task(s) completed
2024-11-12 09:52:03 INFO:	[augustus]	4 of 6 task(s) completed
2024-11-12 09:52:05 INFO:	[augustus]	5 of 6 task(s) completed
2024-11-12 09:52:06 INFO:	[augustus]	6 of 6 task(s) completed
2024-11-12 09:52:06 INFO:	Extracting predicted proteins...
2024-11-12 09:52:06 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:52:06 INFO:	Running 6 job(s) on hmmsearch, starting at 11/12/2024 09:52:06
2024-11-12 09:52:07 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-11-12 09:52:07 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-11-12 09:52:07 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-11-12 09:52:07 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-11-12 09:52:07 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-11-12 09:52:07 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-11-12 09:52:07 INFO:	37 exons in total
2024-11-12 09:52:07 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-11-12 09:52:07 INFO:	eukaryota_odb10 selected

2024-11-12 09:52:07 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-11-12 09:52:07 INFO:	Extract markers...
2024-11-12 09:52:08 INFO:	Place the markers on the reference tree...
2024-11-12 09:52:08 INFO:	Running 1 job(s) on sepp, starting at 11/12/2024 09:52:08
2024-11-12 09:54:58 INFO:	[sepp]	1 of 1 task(s) completed
2024-11-12 09:54:58 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-11-12 09:54:58 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-11-12 09:54:58 INFO:	BUSCO analysis done with WARNING(s). Total running time: 247 seconds

***** Summary of warnings: *****
2024-11-12 09:50:51 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-11-12 09:50:51 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-11-12 09:51:10 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-11-12 09:51:10 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-11-12 09:51:23 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-11-12 09:54:58 INFO:	Results written in /tmp/tmpmtie51tr/job_working_directory/000/3/working/busco_galaxy
2024-11-12 09:54:58 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-11-12 09:54:58 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 127 4096 Nov 12 09:52 augustus_output
drwxr-xr-x 3 1001 127 4096 Nov 12 09:51 blast_output
drwxr-xr-x 5 1001 127 4096 Nov 12 09:51 busco_sequences
-rw-r--r-- 1 1001 127 5831 Nov 12 09:52 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Nov 12 09:51 hmmer_output
-rw-r--r-- 1 1001 127 3548 Nov 12 09:52 missing_busco_list.tsv
drwxr-xr-x 2 1001 127 4096 Nov 12 09:54 placement_files
-rw-r--r-- 1 1001 127 3180 Nov 12 09:52 short_summary.json
-rw-r--r-- 1 1001 127 1078 Nov 12 09:52 short_summary.txt
2024-11-12 09:54:59 INFO:	****************** Start plot generation at 11/12/2024 09:54:59 ******************
2024-11-12 09:54:59 INFO:	Load data ...
2024-11-12 09:54:59 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-11-12 09:54:59 INFO:	Generate the R code ...
2024-11-12 09:54:59 INFO:	Run the R code ...
2024-11-12 09:55:02 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-11-12 09:55:02 INFO:	Plot generation done. Total running time: 2.3373851776123047 seconds
2024-11-12 09:55:02 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5ced9a4ea0db11efa4ecb9e5749f45fe"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpmtie51tr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpmtie51tr/files/a/5/8/dataset_a5856987-f5d4-4efd-82b1-ff7fa5fb19a7.dat' genomeref.fa &&  gffread '/tmp/tmpmtie51tr/files/0/f/c/dataset_0fc69b3e-2f48-48de-9482-5eae4fed668c.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5ced9a4ea0db11efa4ecb9e5749f45fe"`
chr_replace	`None`
chromInfo	`"/tmp/tmpmtie51tr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpmtie51tr/files/0/f/c/dataset_0fc69b3e-2f48-48de-9482-5eae4fed668c.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpmtie51tr/job_working_directory/000/5/outputs/dataset_bca8f3c1-ed2c-4061-81ba-b23e5f546e6f.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpmtie51tr/files/a/5/8/dataset_a5856987-f5d4-4efd-82b1-ff7fa5fb19a7.dat' 2>&1 | tail -n +3 >> '/tmp/tmpmtie51tr/job_working_directory/000/5/outputs/dataset_bca8f3c1-ed2c-4061-81ba-b23e5f546e6f.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpmtie51tr/job_working_directory/000/5/outputs/dataset_bca8f3c1-ed2c-4061-81ba-b23e5f546e6f.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpmtie51tr/job_working_directory/000/5/outputs/dataset_b10d3b24-cb35-4554-ad82-610c31bac858.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m09:56:16 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m09:56:16 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m09:56:16 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m09:56:16 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m09:56:16 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m09:56:16 [stats]�[0m�[0;35m A total of 65 transcripts populated.�[0m
�[0;33m09:56:17 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m09:56:17 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m09:56:17 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m09:56:17 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m09:56:17 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m09:56:17 [__init__]�[0m�[0;35m platform is linux2�[0m
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�[0;33m09:56:17 [font_manager]�[0m�[0;35m font search path ['/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf', '/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm', '/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts']�[0m
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�[0;33m09:56:17 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans-Oblique.ttf�[0m
�[0;33m09:56:17 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizOneSymReg.ttf�[0m
�[0;33m09:56:17 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono.ttf�[0m
�[0;33m09:56:17 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf�[0m
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�[0;33m09:56:17 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSerif-BoldItalic.ttf�[0m
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�[0;33m09:56:17 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBol.ttf�[0m
�[0;33m09:56:17 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUni.ttf�[0m
�[0;33m09:56:17 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono-BoldOblique.ttf�[0m
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�[0;33m09:56:17 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono-Oblique.ttf�[0m
�[0;33m09:56:17 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans-Oblique.ttf�[0m
�[0;33m09:56:17 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizOneSymReg.ttf�[0m
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Warning message:
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Saving 7 x 7 in image
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
�[0;33m09:56:22 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=50 Max=14088 N=205 Mean=547.107317073 SD=1467.30391824 Median=152.0 Sum=112157
�[0;33m09:56:22 [base]�[0m�[0;35m Rscript /tmp/tmpmtie51tr/tmp/tmpIXgpEz�[0m
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
�[0;33m09:56:25 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=111 Max=7371 N=65 Mean=1401.32307692 SD=1130.94596358 Median=1122.0 Sum=91086
�[0;33m09:56:25 [base]�[0m�[0;35m Rscript /tmp/tmpmtie51tr/tmp/tmp9f_Uqa�[0m
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
�[0;33m09:56:29 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=65 Mean=4.15384615385 SD=3.39334538463 Median=3.0 Sum=270
�[0;33m09:56:29 [base]�[0m�[0;35m Rscript /tmp/tmpmtie51tr/tmp/tmpSsMEjG�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5ced9a4ea0db11efa4ecb9e5749f45fe"`
chromInfo	`"/tmp/tmpmtie51tr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmpmtie51tr/job_working_directory/000/6/outputs/dataset_f8eceadb-6dcd-4e6c-b570-d2279528624a_files &&  cp /tmp/tmpmtie51tr/job_working_directory/000/6/configs/tmpqkluwavh /tmp/tmpmtie51tr/job_working_directory/000/6/outputs/dataset_f8eceadb-6dcd-4e6c-b570-d2279528624a_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpmtie51tr/job_working_directory/000/6/outputs/dataset_f8eceadb-6dcd-4e6c-b570-d2279528624a_files /tmp/tmpmtie51tr/job_working_directory/000/6/configs/tmpqkluwavh &&  cp /tmp/tmpmtie51tr/job_working_directory/000/6/outputs/dataset_f8eceadb-6dcd-4e6c-b570-d2279528624a_files/index.html /tmp/tmpmtie51tr/job_working_directory/000/6/outputs/dataset_f8eceadb-6dcd-4e6c-b570-d2279528624a.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"5ced9a4ea0db11efa4ecb9e5749f45fe"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpmtie51tr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpmtie51tr/files/e/f/8/dataset_ef835022-dc79-45bc-a35b-703f9edf1ee0.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-11-12 09:57:37 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-11-12 09:55:53 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 11/12/2024 09:55:53 *****
2024-11-12 09:55:53 INFO:	Configuring BUSCO with local environment
2024-11-12 09:55:53 INFO:	Running proteins mode
2024-11-12 09:55:53 INFO:	Input file is /tmp/tmpmtie51tr/files/e/f/8/dataset_ef835022-dc79-45bc-a35b-703f9edf1ee0.dat
2024-11-12 09:55:53 INFO:	No lineage specified. Running lineage auto selector.

2024-11-12 09:55:53 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-11-12 09:55:53 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:53 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:53 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:53 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-11-12 09:55:53 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:55:53 INFO:	Running 194 job(s) on hmmsearch, starting at 11/12/2024 09:55:53
2024-11-12 09:55:54 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-11-12 09:55:54 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-11-12 09:55:54 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-11-12 09:55:54 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-11-12 09:55:55 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-11-12 09:55:55 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-11-12 09:55:55 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-11-12 09:55:56 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-11-12 09:55:57 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-11-12 09:55:57 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-11-12 09:55:57 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-11-12 09:55:57 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:57 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:57 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:57 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-11-12 09:55:57 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:55:57 INFO:	Running 124 job(s) on hmmsearch, starting at 11/12/2024 09:55:57
2024-11-12 09:55:58 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-11-12 09:55:58 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-11-12 09:55:58 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-11-12 09:55:58 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-11-12 09:55:58 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-11-12 09:55:59 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-11-12 09:55:59 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-11-12 09:55:59 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-11-12 09:55:59 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-11-12 09:55:59 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-11-12 09:55:59 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:55:59 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-11-12 09:55:59 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:59 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:59 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:59 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-11-12 09:55:59 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:55:59 INFO:	Running 255 job(s) on hmmsearch, starting at 11/12/2024 09:55:59
2024-11-12 09:56:02 INFO:	[hmmsearch]	26 of 255 task(s) completed
2024-11-12 09:56:04 INFO:	[hmmsearch]	51 of 255 task(s) completed
2024-11-12 09:56:06 INFO:	[hmmsearch]	77 of 255 task(s) completed
2024-11-12 09:56:08 INFO:	[hmmsearch]	102 of 255 task(s) completed
2024-11-12 09:56:11 INFO:	[hmmsearch]	128 of 255 task(s) completed
2024-11-12 09:56:14 INFO:	[hmmsearch]	153 of 255 task(s) completed
2024-11-12 09:56:16 INFO:	[hmmsearch]	179 of 255 task(s) completed
2024-11-12 09:56:18 INFO:	[hmmsearch]	204 of 255 task(s) completed
2024-11-12 09:56:20 INFO:	[hmmsearch]	230 of 255 task(s) completed
2024-11-12 09:56:22 INFO:	[hmmsearch]	255 of 255 task(s) completed
2024-11-12 09:56:22 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:255	   

2024-11-12 09:56:22 INFO:	Running virus detection pipeline
2024-11-12 09:56:22 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:22 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:22 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:22 INFO:	Running BUSCO using lineage dataset alphabaculovirus_odb10 (viruses, 2020-11-26)
2024-11-12 09:56:22 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:56:22 INFO:	Running 44 job(s) on hmmsearch, starting at 11/12/2024 09:56:22
2024-11-12 09:56:23 INFO:	[hmmsearch]	5 of 44 task(s) completed
2024-11-12 09:56:24 INFO:	[hmmsearch]	9 of 44 task(s) completed
2024-11-12 09:56:24 INFO:	[hmmsearch]	14 of 44 task(s) completed
2024-11-12 09:56:24 INFO:	[hmmsearch]	18 of 44 task(s) completed
2024-11-12 09:56:25 INFO:	[hmmsearch]	23 of 44 task(s) completed
2024-11-12 09:56:25 INFO:	[hmmsearch]	27 of 44 task(s) completed
2024-11-12 09:56:25 INFO:	[hmmsearch]	31 of 44 task(s) completed
2024-11-12 09:56:26 INFO:	[hmmsearch]	36 of 44 task(s) completed
2024-11-12 09:56:26 INFO:	[hmmsearch]	40 of 44 task(s) completed
2024-11-12 09:56:26 INFO:	[hmmsearch]	44 of 44 task(s) completed
2024-11-12 09:56:27 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:27 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:44	   

2024-11-12 09:56:27 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:27 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:27 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:27 INFO:	Running BUSCO using lineage dataset alphaherpesvirinae_odb10 (viruses, 2020-11-26)
2024-11-12 09:56:27 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:56:27 INFO:	Running 21 job(s) on hmmsearch, starting at 11/12/2024 09:56:27
2024-11-12 09:56:28 INFO:	[hmmsearch]	3 of 21 task(s) completed
2024-11-12 09:56:28 INFO:	[hmmsearch]	5 of 21 task(s) completed
2024-11-12 09:56:28 INFO:	[hmmsearch]	7 of 21 task(s) completed
2024-11-12 09:56:28 INFO:	[hmmsearch]	9 of 21 task(s) completed
2024-11-12 09:56:28 INFO:	[hmmsearch]	11 of 21 task(s) completed
2024-11-12 09:56:29 INFO:	[hmmsearch]	13 of 21 task(s) completed
2024-11-12 09:56:29 INFO:	[hmmsearch]	15 of 21 task(s) completed
2024-11-12 09:56:29 INFO:	[hmmsearch]	17 of 21 task(s) completed
2024-11-12 09:56:29 INFO:	[hmmsearch]	19 of 21 task(s) completed
2024-11-12 09:56:29 INFO:	[hmmsearch]	21 of 21 task(s) completed
2024-11-12 09:56:29 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:29 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:21	   

2024-11-12 09:56:29 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:29 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:29 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:29 INFO:	Running BUSCO using lineage dataset aviadenovirus_odb10 (viruses, 2020-11-26)
2024-11-12 09:56:29 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:56:30 INFO:	Running 13 job(s) on hmmsearch, starting at 11/12/2024 09:56:30
2024-11-12 09:56:30 INFO:	[hmmsearch]	2 of 13 task(s) completed
2024-11-12 09:56:30 INFO:	[hmmsearch]	3 of 13 task(s) completed
2024-11-12 09:56:30 INFO:	[hmmsearch]	4 of 13 task(s) completed
2024-11-12 09:56:30 INFO:	[hmmsearch]	6 of 13 task(s) completed
2024-11-12 09:56:31 INFO:	[hmmsearch]	7 of 13 task(s) completed
2024-11-12 09:56:31 INFO:	[hmmsearch]	8 of 13 task(s) completed
2024-11-12 09:56:31 INFO:	[hmmsearch]	10 of 13 task(s) completed
2024-11-12 09:56:31 INFO:	[hmmsearch]	11 of 13 task(s) completed
2024-11-12 09:56:31 INFO:	[hmmsearch]	12 of 13 task(s) completed
2024-11-12 09:56:31 INFO:	[hmmsearch]	13 of 13 task(s) completed
2024-11-12 09:56:31 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:31 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:13	   

2024-11-12 09:56:31 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:31 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:31 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:31 INFO:	Running BUSCO using lineage dataset baculoviridae_odb10 (viruses, 2020-11-26)
2024-11-12 09:56:31 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:56:31 INFO:	Running 12 job(s) on hmmsearch, starting at 11/12/2024 09:56:31
2024-11-12 09:56:32 INFO:	[hmmsearch]	2 of 12 task(s) completed
2024-11-12 09:56:32 INFO:	[hmmsearch]	3 of 12 task(s) completed
2024-11-12 09:56:32 INFO:	[hmmsearch]	4 of 12 task(s) completed
2024-11-12 09:56:32 INFO:	[hmmsearch]	5 of 12 task(s) completed
2024-11-12 09:56:32 INFO:	[hmmsearch]	6 of 12 task(s) completed
2024-11-12 09:56:32 INFO:	[hmmsearch]	8 of 12 task(s) completed
2024-11-12 09:56:33 INFO:	[hmmsearch]	9 of 12 task(s) completed
2024-11-12 09:56:33 INFO:	[hmmsearch]	10 of 12 task(s) completed
2024-11-12 09:56:33 INFO:	[hmmsearch]	11 of 12 task(s) completed
2024-11-12 09:56:33 INFO:	[hmmsearch]	12 of 12 task(s) completed
2024-11-12 09:56:33 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:33 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:12	   

2024-11-12 09:56:33 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:33 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:33 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:33 INFO:	Running BUSCO using lineage dataset bclasvirinae_odb10 (viruses, 2020-11-26)
2024-11-12 09:56:33 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:56:33 INFO:	Running 36 job(s) on hmmsearch, starting at 11/12/2024 09:56:33
2024-11-12 09:56:34 INFO:	[hmmsearch]	4 of 36 task(s) completed
2024-11-12 09:56:34 INFO:	[hmmsearch]	8 of 36 task(s) completed
2024-11-12 09:56:34 INFO:	[hmmsearch]	11 of 36 task(s) completed
2024-11-12 09:56:35 INFO:	[hmmsearch]	15 of 36 task(s) completed
2024-11-12 09:56:35 INFO:	[hmmsearch]	19 of 36 task(s) completed
2024-11-12 09:56:35 INFO:	[hmmsearch]	22 of 36 task(s) completed
2024-11-12 09:56:36 INFO:	[hmmsearch]	26 of 36 task(s) completed
2024-11-12 09:56:36 INFO:	[hmmsearch]	29 of 36 task(s) completed
2024-11-12 09:56:36 INFO:	[hmmsearch]	33 of 36 task(s) completed
2024-11-12 09:56:36 INFO:	[hmmsearch]	36 of 36 task(s) completed
2024-11-12 09:56:36 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:36 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:36	   

2024-11-12 09:56:37 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:37 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:37 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:37 INFO:	Running BUSCO using lineage dataset betabaculovirus_odb10 (viruses, 2020-11-26)
2024-11-12 09:56:37 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:56:37 INFO:	Running 58 job(s) on hmmsearch, starting at 11/12/2024 09:56:37
2024-11-12 09:56:38 INFO:	[hmmsearch]	6 of 58 task(s) completed
2024-11-12 09:56:38 INFO:	[hmmsearch]	12 of 58 task(s) completed
2024-11-12 09:56:39 INFO:	[hmmsearch]	18 of 58 task(s) completed
2024-11-12 09:56:39 INFO:	[hmmsearch]	24 of 58 task(s) completed
2024-11-12 09:56:39 INFO:	[hmmsearch]	29 of 58 task(s) completed
2024-11-12 09:56:40 INFO:	[hmmsearch]	35 of 58 task(s) completed
2024-11-12 09:56:40 INFO:	[hmmsearch]	41 of 58 task(s) completed
2024-11-12 09:56:41 INFO:	[hmmsearch]	47 of 58 task(s) completed
2024-11-12 09:56:41 INFO:	[hmmsearch]	53 of 58 task(s) completed
2024-11-12 09:56:42 INFO:	[hmmsearch]	58 of 58 task(s) completed
2024-11-12 09:56:42 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:42 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:58	   

2024-11-12 09:56:42 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:42 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:42 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:42 INFO:	Running BUSCO using lineage dataset betaherpesvirinae_odb10 (viruses, 2020-11-26)
2024-11-12 09:56:42 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:56:42 INFO:	Running 10 job(s) on hmmsearch, starting at 11/12/2024 09:56:42
2024-11-12 09:56:42 INFO:	[hmmsearch]	1 of 10 task(s) completed
2024-11-12 09:56:42 INFO:	[hmmsearch]	2 of 10 task(s) completed
2024-11-12 09:56:42 INFO:	[hmmsearch]	3 of 10 task(s) completed
2024-11-12 09:56:43 INFO:	[hmmsearch]	4 of 10 task(s) completed
2024-11-12 09:56:43 INFO:	[hmmsearch]	5 of 10 task(s) completed
2024-11-12 09:56:43 INFO:	[hmmsearch]	6 of 10 task(s) completed
2024-11-12 09:56:43 INFO:	[hmmsearch]	7 of 10 task(s) completed
2024-11-12 09:56:43 INFO:	[hmmsearch]	8 of 10 task(s) completed
2024-11-12 09:56:43 INFO:	[hmmsearch]	9 of 10 task(s) completed
2024-11-12 09:56:43 INFO:	[hmmsearch]	10 of 10 task(s) completed
2024-11-12 09:56:43 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:43 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:10	   

2024-11-12 09:56:43 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:43 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:43 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:43 INFO:	Running BUSCO using lineage dataset cheoctovirus_odb10 (viruses, 2020-11-26)
2024-11-12 09:56:43 INFO:	***** Run HMMER on gene sequences *****
2024-11-12 09:56:43 INFO:	Running 16 job(s) on hmmsearch, starting at 11/12/2024 09:56:43
2024-11-12 09:56:44 INFO:	[hmmsearch]	2 of 16 task(s) completed
2024-11-12 09:56:44 INFO:	[hmmsearch]	4 of 16 task(s) completed
2024-11-12 09:56:44 INFO:	[hmmsearch]	5 of 16 task(s) completed
2024-11-12 09:56:44 INFO:	[hmmsearch]	7 of 16 task(s) completed
2024-11-12 09:56:44 INF
..
 the selected run mode, proteins
2024-11-12 09:55:57 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:59 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:55:59 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:59 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:55:59 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:22 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:22 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:22 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:27 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:27 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:27 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:27 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:29 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:29 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:29 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:29 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:31 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:31 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:31 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:31 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:33 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:33 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:33 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:33 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:36 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:37 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:37 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:37 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:42 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:42 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:42 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:42 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:43 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:43 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:43 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:43 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:45 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:45 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:45 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:45 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:50 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:50 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:50 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:50 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:52 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:52 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:52 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:52 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:54 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:54 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:54 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:54 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:57 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:57 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:57 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:57 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:59 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:56:59 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:59 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:56:59 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:01 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:01 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:01 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:01 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:02 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:02 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:02 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:02 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:05 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:05 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:05 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:05 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:07 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:07 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:07 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:07 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:10 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:10 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:10 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:10 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:11 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:11 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:11 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:11 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:15 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:15 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:15 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:15 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:18 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:18 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:18 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:18 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:20 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:20 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:20 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:20 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:22 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:23 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:23 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:23 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:24 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:24 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:24 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:24 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:27 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:27 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:27 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:27 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:30 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:30 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:30 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:30 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:34 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-11-12 09:57:34 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:34 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-11-12 09:57:34 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins

2024-11-12 09:57:34 INFO:	Results written in /tmp/tmpmtie51tr/job_working_directory/000/7/working/busco_galaxy
2024-11-12 09:57:34 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-11-12 09:57:34 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 36
drwxr-xr-x 5 1001 127 4096 Nov 12 09:55 busco_sequences
-rw-r--r-- 1 1001 127 5784 Nov 12 09:56 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Nov 12 09:56 hmmer_output
-rw-r--r-- 1 1001 127 3548 Nov 12 09:56 missing_busco_list.tsv
drwxr-xr-x 2 1001 127 4096 Nov 12 09:57 placement_files
drwxr-xr-x 2 1001 127 4096 Nov 12 09:57 sepp_tmp_files
-rw-r--r-- 1 1001 127 2225 Nov 12 09:56 short_summary.json
-rw-r--r-- 1 1001 127  737 Nov 12 09:56 short_summary.txt
2024-11-12 09:57:35 INFO:	****************** Start plot generation at 11/12/2024 09:57:35 ******************
2024-11-12 09:57:35 INFO:	Load data ...
2024-11-12 09:57:35 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-11-12 09:57:35 INFO:	Generate the R code ...
2024-11-12 09:57:35 INFO:	Run the R code ...
2024-11-12 09:57:37 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-11-12 09:57:37 INFO:	Plot generation done. Total running time: 2.1417651176452637 seconds
2024-11-12 09:57:37 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5ced9a4ea0db11efa4ecb9e5749f45fe"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmpmtie51tr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

omamer search --db '/cvmfs/data.galaxyproject.org/byhand/omamer/Primates-v2.0.0.h5' --query '/tmp/tmpmtie51tr/files/e/f/8/dataset_ef835022-dc79-45bc-a35b-703f9edf1ee0.dat' --out 'output_omamer'  &&  omark -f 'output_omamer' -d '/cvmfs/data.galaxyproject.org/byhand/omamer/Primates-v2.0.0.h5'      -o omark_galaxy

Exit Code:

```
0
```

Standard Error:

================================================================================

   _____ _____ _____
  |     |     |  _  |_____ ___ ___
  |  |  | | | |     |     | -_|  _|
  |_____|_|_|_|__|__|_|_|_|___|_|   v2.0.2

  OMAmer is licensed under the GNU Lesser General Public License 3.0 (LGPL-3.0).
    
================================================================================

Loading required libraries  [DONE]

================================================================================

Running OMAmer on 84d6a5b11aef, using:
 - database: /cvmfs/data.galaxyproject.org/byhand/omamer/Primates-v2.0.0.h5
 - query: /tmp/tmpmtie51tr/files/e/f/8/dataset_ef835022-dc79-45bc-a35b-703f9edf1ee0.dat
 - version: 2.0.2

================================================================================

Loading data required for OMAmer search from database...
 - taxonomy information (0.0s) [DONE]
 - family information (0.0s) [DONE]
 - sub-family information (0.2s) [DONE]
 - family hierarchy (0.0s) [DONE]
 - k-mer index (3.5s) [DONE]
 - family probability estimates (0.0s) [DONE]
 - sub-family probability estimates (0.0s) [DONE]

Finished loading required data

================================================================================

�[?25l
Searching -  0 queries in 0s (0.0 queries/s) 
Searching -  0 queries in 5s (0.0 queries/s) 
Searching -  0 queries in 10s (0.0 queries/s) 
Searching -  0 queries in 15s (0.0 queries/s) 
Searching -  0 queries in 20s (0.0 queries/s) 
Searching -  0 queries in 25s (0.0 queries/s) 
Searching -  0 queries in 30s (0.0 queries/s) 
Searching -  0 queries in 35s (0.0 queries/s) 
Searching -  0 queries in 40s (0.0 queries/s) �[?25h�[J
Searching -  65 queries in 45.0s (1.44 queries/s) 

================================================================================

OMAmer search complete:
 - results written to: output_omamer
 - total 50.42 seconds
 - search phase only 1.55 queries/s


Note: family p-values are stated in negative log units.
================================================================================

Thank you for using OMAmer. If you use OMAmer in your research, please cite:

Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz, OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2866-2873, https://doi.org/10.1093/bioinformatics/btab219


OMAmer uses data from the OMA browser. Results can be interpretted further using:
 - OMA browser website (https://omabrowser.org)
 - PyOMADB, the Python OMA API client (https://github.com/DessimozLab/pyomadb)

================================================================================
NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...

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Inserting taxids:       275000 
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Inserting taxids:       2305000 
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Inserting taxids:       2315000 
Inserting taxids:       2320000 
Inserting taxids:       2325000 
Inserting taxids:       2330000 
Inserting taxids:       2335000 
Inserting taxids:       2340000 
Inserting taxids:       2345000 
Inserting taxids:       2350000 
Inserting taxids:       2355000 
Inserting taxids:       2360000 
Inserting taxids:       2365000 
Inserting taxids:       2370000 
Inserting taxids:       2375000 
Inserting taxids:       2380000 
Inserting taxids:       2385000 
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Inserting taxids:       2395000 
Inserting taxids:       2400000 
Inserting taxids:       2405000 
Inserting taxids:       2410000 
Inserting taxids:       2415000 
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Inserting taxids:       2425000 
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Inserting taxids:       2435000 
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Inserting taxids:       2465000 
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Inserting taxids:       2485000 
Inserting taxids:       2490000 
Inserting taxids:       2495000 
Inserting taxids:       2500000 
Inserting taxids:       2505000 
Inserting taxids:       2510000 
Inserting taxids:       2515000 
Inserting taxids:       2520000 
Inserting taxids:       2525000 
Inserting taxids:       2530000 
Inserting taxids:       2535000 
Inserting taxids:       2540000 
Inserting taxids:       2545000 
Inserting taxids:       2550000 
Inserting taxids:       2555000 
Inserting taxids:       2560000 
Inserting taxids:       2565000 
Inserting taxids:       2570000 
Inserting taxids:       2575000 
Inserting taxids:       2580000 
Inserting taxids:       2585000 
Inserting taxids:       2590000 
Inserting taxids:       2595000 
Inserting taxids:       2600000 
Inserting taxids:       2605000 
Inserting taxids:       2610000 
Inserting taxids:       2615000 
Inserting taxids:       2620000 
Inserting taxids:       2625000 WARNING: The selected ancestral lineage is from the phylum rank or higher which means the target species' taxonomic division is not well sampled in our database. The results may lack accuracy.

WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'

Standard Output:

Loading node names...
2628114 names loaded.
372590 synonyms loaded.
Loading nodes...
2628114 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /tmp/tmpmtie51tr/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite ...

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Uploading to /tmp/tmpmtie51tr/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5ced9a4ea0db11efa4ecb9e5749f45fe"`
chromInfo	`"/tmp/tmpmtie51tr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- history_id
  - 0a72b55611d3440a
- history_state
  - ok
- invocation_id
  - 0a72b55611d3440a
- invocation_state
  - scheduled
- workflow_id
  - 0a72b55611d3440a

mvdbeek

Super nice again, thanks so much!

workflows/genome_annotation/annotation_helixer/Galaxy-Workflow-annotation_helixer.ga

workflows/genome_annotation/annotation_helixer/README.md

workflows/genome_annotation/annotation_helixer/plnmotmptestjobu509bkbh.json

workflows/genome_annotation/annotation_helixer/README.md

workflows/genome_annotation/annotation_helixer/Galaxy-Workflow-annotation_helixer-tests.yml

github-actions · 2024-11-25T13:52:06Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '8' (Genome) is not optional and no input provided.","err_code":0}

github-actions · 2024-11-25T13:54:23Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '8' (Genome sequence) is not optional and no input provided.","err_code":0}

mvdbeek

Awesome, it's finally green. Thanks a lot @rlibouba!

github-actions · 2024-12-03T17:01:20Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Problems:

Output with path /tmp/tmpl7uchgnd/Busco on data 1 full table__18bd1de5-19cc-44ce-a0d3-a8f6bdbb5108 different than expected, difference (using sim_size):
( /tmp/planemo_test_file_cntes8tl v. /tmp/tmpatkfzmhuplanemo_test_file_cntes8tl )
Files /tmp/planemo_test_file_cntes8tl=6192b but /tmp/tmpatkfzmhuplanemo_test_file_cntes8tl=47630b - compare by size (delta=30000) failed

Output with path /tmp/tmpubogvx0b/Busco on data 8 full table__2ec54032-c0cf-4a9e-b66f-92bd1c819b71 different than expected, difference (using sim_size):
( /tmp/planemo_test_file_102ap1r7 v. /tmp/tmpdgf5xpw2planemo_test_file_102ap1r7 )
Files /tmp/planemo_test_file_102ap1r7=6143b but /tmp/tmpdgf5xpw2planemo_test_file_102ap1r7=47714b - compare by size (delta=30000) failed

Workflow invocation details

Invocation Messages

Steps

Step 1: Genome sequence:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmp9ni8xuwi/files/8/9/0/dataset_8903fb7c-5bc3-4e6a-a339-abc9e28b95c1.dat' --species '' --gff-output-path '/tmp/tmp9ni8xuwi/job_working_directory/000/2/outputs/dataset_2b0ad43b-61a9-419f-bbba-c3b091560782.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-12-03 16:38:06.225133: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-12-03 16:38:06.949916: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-12-03 16:38:12.579153: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-12-03 16:38:12.851757: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-12-03 16:38:15.096577: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-12-03 16:38:17.350394: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-12-03 16:38:19.682005: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmp9ni8xuwi/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmp9ni8xuwi/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmp9ni8xuwi/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmp9ni8xuwi/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmp9ni8xuwi/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmp9ni8xuwi/files/8/9/0/dataset_8903fb7c-5bc3-4e6a-a339-abc9e28b95c1.dat',
 'gff_output_path': '/tmp/tmp9ni8xuwi/job_working_directory/000/2/outputs/dataset_2b0ad43b-61a9-419f-bbba-c3b091560782.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmp9ni8xuwi/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpzbxx4e59
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.28 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.43 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.02 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmp9ni8xuwi/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpzbxx4e59/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpzbxx4e59/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmp9ni8xuwi/files/8/9/0/dataset_8903fb7c-5bc3-4e6a-a339-abc9e28b95c1.dat', 'timestamp': '2024-12-03 16:38:09.771910'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmp9ni8xuwi/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.06 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmp9ni8xuwi/files/8/9/0/dataset_8903fb7c-5bc3-4e6a-a339-abc9e28b95c1.dat in 0.07 hours. GFF file written to /tmp/tmp9ni8xuwi/job_working_directory/000/2/outputs/dataset_2b0ad43b-61a9-419f-bbba-c3b091560782.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6322244cb19411efa2f1a156edf22684"`
chromInfo	`"/tmp/tmp9ni8xuwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmp9ni8xuwi/files/8/9/0/dataset_8903fb7c-5bc3-4e6a-a339-abc9e28b95c1.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-03 16:47:33 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-12-03 16:35:40 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 12/03/2024 16:35:40 *****
2024-12-03 16:35:40 INFO:	Configuring BUSCO with local environment
2024-12-03 16:35:40 INFO:	Running genome mode
2024-12-03 16:35:42 INFO:	Input file is /tmp/tmp9ni8xuwi/files/8/9/0/dataset_8903fb7c-5bc3-4e6a-a339-abc9e28b95c1.dat
2024-12-03 16:35:43 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2024-12-03 16:35:43 INFO:	Running 1 job(s) on bbtools, starting at 12/03/2024 16:35:43
2024-12-03 16:35:44 INFO:	[bbtools]	1 of 1 task(s) completed
2024-12-03 16:35:44 INFO:	Running 1 job(s) on makeblastdb, starting at 12/03/2024 16:35:44
2024-12-03 16:35:45 INFO:	Creating BLAST database with input file
2024-12-03 16:35:45 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-12-03 16:35:45 INFO:	Running a BLAST search for BUSCOs against created database
2024-12-03 16:35:45 INFO:	Running 1 job(s) on tblastn, starting at 12/03/2024 16:35:45
2024-12-03 16:35:55 INFO:	[tblastn]	1 of 1 task(s) completed
2024-12-03 16:35:55 INFO:	Running Augustus gene predictor on BLAST search results.
2024-12-03 16:35:55 INFO:	Running Augustus prediction using aspergillus_nidulans as species:
2024-12-03 16:35:55 INFO:	Running 76 job(s) on augustus, starting at 12/03/2024 16:35:55
2024-12-03 16:37:40 INFO:	[augustus]	8 of 76 task(s) completed
2024-12-03 16:38:48 INFO:	[augustus]	16 of 76 task(s) completed
2024-12-03 16:39:25 INFO:	[augustus]	23 of 76 task(s) completed
2024-12-03 16:39:46 INFO:	[augustus]	31 of 76 task(s) completed
2024-12-03 16:40:05 INFO:	[augustus]	38 of 76 task(s) completed
2024-12-03 16:40:24 INFO:	[augustus]	46 of 76 task(s) completed
2024-12-03 16:40:43 INFO:	[augustus]	54 of 76 task(s) completed
2024-12-03 16:40:54 INFO:	[augustus]	61 of 76 task(s) completed
2024-12-03 16:41:05 INFO:	[augustus]	69 of 76 task(s) completed
2024-12-03 16:41:19 INFO:	[augustus]	76 of 76 task(s) completed
2024-12-03 16:41:19 INFO:	Extracting predicted proteins...
2024-12-03 16:41:19 INFO:	***** Run HMMER on gene sequences *****
2024-12-03 16:41:19 INFO:	Running 75 job(s) on hmmsearch, starting at 12/03/2024 16:41:19
2024-12-03 16:41:20 INFO:	[hmmsearch]	8 of 75 task(s) completed
2024-12-03 16:41:21 INFO:	[hmmsearch]	15 of 75 task(s) completed
2024-12-03 16:41:22 INFO:	[hmmsearch]	23 of 75 task(s) completed
2024-12-03 16:41:22 INFO:	[hmmsearch]	30 of 75 task(s) completed
2024-12-03 16:41:23 INFO:	[hmmsearch]	38 of 75 task(s) completed
2024-12-03 16:41:24 INFO:	[hmmsearch]	45 of 75 task(s) completed
2024-12-03 16:41:25 INFO:	[hmmsearch]	53 of 75 task(s) completed
2024-12-03 16:41:25 INFO:	[hmmsearch]	60 of 75 task(s) completed
2024-12-03 16:41:26 INFO:	[hmmsearch]	68 of 75 task(s) completed
2024-12-03 16:41:27 INFO:	[hmmsearch]	75 of 75 task(s) completed
2024-12-03 16:41:27 INFO:	0 exons in total
2024-12-03 16:41:27 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-12-03 16:41:27 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-12-03 16:41:31 INFO:	Running a BLAST search for BUSCOs against created database
2024-12-03 16:41:31 INFO:	Running 1 job(s) on tblastn, starting at 12/03/2024 16:41:31
2024-12-03 16:43:15 INFO:	[tblastn]	1 of 1 task(s) completed
2024-12-03 16:43:15 INFO:	Converting predicted genes to short genbank files
2024-12-03 16:43:15 INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 12/03/2024 16:43:15
2024-12-03 16:43:15 INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
2024-12-03 16:43:15 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-12-03 16:43:15 INFO:	Running 1 job(s) on new_species.pl, starting at 12/03/2024 16:43:15
2024-12-03 16:43:16 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-12-03 16:43:16 INFO:	Running 1 job(s) on etraining, starting at 12/03/2024 16:43:16
2024-12-03 16:43:16 INFO:	[etraining]	1 of 1 task(s) completed
2024-12-03 16:43:16 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 2448
2024-12-03 16:43:16 INFO:	Running Augustus gene predictor on BLAST search results.
2024-12-03 16:43:16 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-12-03 16:43:16 INFO:	Running 100 job(s) on augustus, starting at 12/03/2024 16:43:16
2024-12-03 16:44:33 INFO:	[augustus]	10 of 100 task(s) completed
2024-12-03 16:45:36 INFO:	[augustus]	20 of 100 task(s) completed
2024-12-03 16:46:08 INFO:	[augustus]	30 of 100 task(s) completed
2024-12-03 16:46:22 INFO:	[augustus]	40 of 100 task(s) completed
2024-12-03 16:46:35 INFO:	[augustus]	50 of 100 task(s) completed
2024-12-03 16:46:48 INFO:	[augustus]	60 of 100 task(s) completed
2024-12-03 16:46:59 INFO:	[augustus]	70 of 100 task(s) completed
2024-12-03 16:47:09 INFO:	[augustus]	80 of 100 task(s) completed
2024-12-03 16:47:20 INFO:	[augustus]	90 of 100 task(s) completed
2024-12-03 16:47:30 INFO:	[augustus]	100 of 100 task(s) completed
2024-12-03 16:47:30 INFO:	Extracting predicted proteins...
2024-12-03 16:47:30 INFO:	***** Run HMMER on gene sequences *****
2024-12-03 16:47:30 WARNING:	No jobs to run on hmmsearch
2024-12-03 16:47:30 INFO:	0 exons in total
2024-12-03 16:47:30 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449	   

2024-12-03 16:47:30 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449      |
    |1    Complete BUSCOs (C)                          |
    |1    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2448    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2024-12-03 16:47:30 INFO:	BUSCO analysis done with WARNING(s). Total running time: 708 seconds

***** Summary of warnings: *****
2024-12-03 16:47:30 WARNING:busco.busco_tools.Toolset	No jobs to run on hmmsearch

2024-12-03 16:47:30 INFO:	Results written in /tmp/tmp9ni8xuwi/job_working_directory/000/3/working/busco_galaxy
2024-12-03 16:47:30 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-03 16:47:30 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 100
drwxr-xr-x 8 1001 127  4096 Dec  3 16:47 augustus_output
drwxr-xr-x 3 1001 127  4096 Dec  3 16:43 blast_output
drwxr-xr-x 5 1001 127  4096 Dec  3 16:35 busco_sequences
-rw-r--r-- 1 1001 127 47630 Dec  3 16:47 full_table.tsv
drwxr-xr-x 4 1001 127  4096 Dec  3 16:41 hmmer_output
-rw-r--r-- 1 1001 127 27820 Dec  3 16:47 missing_busco_list.tsv
-rw-r--r-- 1 1001 127  3175 Dec  3 16:47 short_summary.json
-rw-r--r-- 1 1001 127  1066 Dec  3 16:47 short_summary.txt
2024-12-03 16:47:31 INFO:	****************** Start plot generation at 12/03/2024 16:47:31 ******************
2024-12-03 16:47:31 INFO:	Load data ...
2024-12-03 16:47:31 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2024-12-03 16:47:31 INFO:	Generate the R code ...
2024-12-03 16:47:31 INFO:	Run the R code ...
2024-12-03 16:47:33 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-03 16:47:33 INFO:	Plot generation done. Total running time: 2.3183908462524414 seconds
2024-12-03 16:47:33 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6322244cb19411efa2f1a156edf22684"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmp9ni8xuwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9ni8xuwi/files/8/9/0/dataset_8903fb7c-5bc3-4e6a-a339-abc9e28b95c1.dat' genomeref.fa &&  gffread '/tmp/tmp9ni8xuwi/files/2/b/0/dataset_2b0ad43b-61a9-419f-bbba-c3b091560782.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6322244cb19411efa2f1a156edf22684"`
chr_replace	`None`
chromInfo	`"/tmp/tmp9ni8xuwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9ni8xuwi/files/2/b/0/dataset_2b0ad43b-61a9-419f-bbba-c3b091560782.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp9ni8xuwi/job_working_directory/000/5/outputs/dataset_61c42b24-27de-4919-8b66-4f91f753cb0d.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp9ni8xuwi/files/8/9/0/dataset_8903fb7c-5bc3-4e6a-a339-abc9e28b95c1.dat' 2>&1 | tail -n +3 >> '/tmp/tmp9ni8xuwi/job_working_directory/000/5/outputs/dataset_61c42b24-27de-4919-8b66-4f91f753cb0d.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp9ni8xuwi/job_working_directory/000/5/outputs/dataset_61c42b24-27de-4919-8b66-4f91f753cb0d.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp9ni8xuwi/job_working_directory/000/5/outputs/dataset_4eca36d3-1658-4fdc-a66b-c7833fa4f49a.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m16:42:54 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m16:42:54 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m16:42:54 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m16:42:54 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m16:42:54 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m16:42:54 [stats]�[0m�[0;35m A total of 65 transcripts populated.�[0m
�[0;33m16:42:54 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m16:42:54 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m16:42:54 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m16:42:54 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m16:42:54 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m16:42:54 [__init__]�[0m�[0;35m platform is linux2�[0m
�[0;33m16:42:54 [__init__]�[0m�[0;35m loaded modules: ['numpy.core.info', 'Bio.SeqIO.UniprotIO', 'jcvi.apps.base', 'ctypes.os', 'Bio.os', 'runpy', 'gc', 'distutils.sysconfig', 'matplotlib.cbook._backports', 'Bio._py3k.urllib2', 'logging.weakref', 'base64', 'jcvi.utils', 'jcvi.apps.signal', 'unittest.sys', 'numpy.core.umath', 'string', 'Bio.SeqIO.InsdcIO', 'numpy.lib.arraysetops', '_elementtree', 'xml.etree.warnings', 'xml.etree.sys', 'Bio.SeqUtils.binascii', 'json.encoder', 'Bio.SeqIO.QualityIO', 'numpy.core.machar', 'jcvi.formats.collections', 'unittest.StringIO', 'unittest.types', 'jcvi.apps.threading', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'dis', 'zlib', 'logging.threading', 'jcvi.annotation', 'Bio.SeqIO.Bio', '_json', 'Bio.GenBank.warnings', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'numpy._globals', 'numpy.lib.npyio', 'xml.sax.io', 'Bio._py3k.sys', 'Bio.SeqIO.sys', 'numpy.fft.helper', 'matplotlib.rcsetup', 'optparse', 'unittest.suite', '_ctypes', 'xml.etree', 'json.scanner', 'codecs', 'Bio.collections', 'numpy.os', 'jcvi.annotation.jcvi', 'mkl_fft._numpy_fft', 'StringIO', 'Bio.Alphabet.IUPAC', 'weakref', 'numpy.core._internal', 'distutils.sys', 'numpy.lib.arraypad', 'pprint', 'Bio.SeqIO.math', 'Bio.warnings', 'jcvi.apps.httplib', 'sqlite3.dbapi2', 'select', 'ctypes._ctypes', '_heapq', 'six.moves.urllib', 'numpy.lib.financial', 'Bio.Align.Generic', 'binascii', 'jcvi.formats.sizes', 'unittest.loader', 'unittest.fnmatch', 'numpy.polynomial.chebyshev', '_functools', 'cPickle', 'numpy.polynomial.hermite_e', 'jcvi.apps.urllib', 'jcvi', 'numpy.testing.utils', 'jcvi.graphics.histogram', 'jcvi.utils.UserDict', 'numpy.core.fromnumeric', 'unicodedata', 'numpy.ctypeslib', 'matplotlib._version', '_ast', 'jcvi.utils.range', 'encodings.aliases', 'Bio.SeqIO.SeqXmlIO', 'fnmatch', 'sre_parse', 'pickle', 'Bio.SeqIO.AceIO', 'numpy.random.warnings', 'xml.sax.types', 'jcvi.utils.itertools', 'logging.cStringIO', 'Bio.SeqIO.os', 'numpy.lib.polynomial', 'numpy.compat', 'numbers', 'numpy.core.records', 'strop', 'xml.etree.ElementPath', 'numpy.core.numeric', 'six', 'Bio.array', 'jcvi.apps', 'matplotlib.testing', 'Bio.Alphabet.Bio', 'numpy.lib.utils', 'numpy.lib.arrayterator', 'os.path', 'Bio.GenBank.__future__', '_weakrefset', 'Bio.SeqIO.warnings', 'unittest.traceback', 'unittest.os', 'jcvi.utils.table', 'functools', 'sysconfig', 'sqlite3.collections', 'numpy.polynomial.legendre', 'numpy.matrixlib.defmatrix', 'tempfile', 'imp', 'jcvi.apps.subprocess', 'jcvi.formats.urllib', 'Bio._py3k.commands', 'Bio.SeqIO.Interfaces', 'numpy.linalg.info', 'jcvi.utils.re', 'jcvi.formats.Bio', 'xml.etree._elementtree', 'unittest.util', 'Bio.SeqIO.struct', 'jcvi.apps.time', 'httplib', 'decimal', 'numpy.lib._datasource', 'Bio._py3k.__builtin__', 'jcvi.formats.os', 'jcvi.apps.unicodedata', 'numpy.linalg._umath_linalg', 'cStringIO', 'numpy.polynomial', 'jcvi.annotation.reformat', 'jcvi.graphics.sys', 'numpy.add_newdocs', 'Bio.SeqIO.__future__', 'encodings', 'Bio.sqlite3', 'Bio.Data', 'json.struct', 'numpy.lib.numpy', 'numpy.random.threading', 're', 'jcvi.formats.fasta', 'sqlite3.time', 'math', 'ast', 'numpy.lib.ufunclike', 'ctypes.struct', 'matplotlib.json', '_locale', 'logging', 'thread', 'traceback', 'jcvi.apps.logging', 'jcvi.graphics.os', 'jcvi.utils.logging', 'jcvi.annotation.re', 'Bio.SeqUtils.math', 'jcvi.formats.bed', 'Bio.Sequencing', '_collections', 'Bio._py3k.urlparse', 'numpy.random', 'numpy._mklinit', 'numpy.lib.twodim_base', 'array', 'ctypes.sys', 'Bio.SeqIO.AbiIO', 'posixpath', 'Bio.GenBank.Bio', 'numpy.core.arrayprint', 'types', 'numpy.lib.stride_tricks', 'numpy.lib.scimath', 'matplotlib.cbook.functools', 'json._json', 'xml.sax.os', 'Bio.codecs', '_codecs', 'numpy.__config__', 'Bio._py3k.collections', 'copy', 'hashlib', 'keyword', 'jcvi.annotation.logging', 'numpy.lib.nanfunctions', 'unittest.weakref', 'jcvi.utils.cbook', 'posix', 'matplotlib.fontconfig_pattern', 'Bio.GenBank.utils', 'jcvi.utils.os', 'jcvi.annotation.collections', 'sre_compile', 'Bio.string', '_hashlib', 'numpy.lib.shape_base', 'numpy._import_tools', 'logging.collections', 'backports_abc', 'Bio.SeqIO.PhdIO', 'distutils.errors', '__main__', 'numpy.fft.info', 'numpy.sys', 'jcvi.utils.natsort', 'numpy.random.info', 'xml.etree.cElementTree', 'dateutil._version', 'matplotlib._color_data', 'unittest.result', 'bz2', 'encodings.codecs', 'xml.dom.minicompat', 'unittest.difflib', '_ssl', 'numpy.lib.index_tricks', 'warnings', 'encodings.ascii', 'Bio.SeqUtils.Bio', '_sqlite3', 'json.sys', 'Bio.Bio', 'numpy.testing.nose_tools', 'Bio.SeqIO.SwissIO', 'future_builtins', 'jcvi.formats', 'jcvi.formats.string', '_io', 'linecache', 'numpy.linalg.linalg', 'numpy.lib._iotools', 'random', '_bisect', 'datetime', 'logging.os', 'ctypes._endian', 'encodings.encodings', 'unittest.pprint', 'matplotlib.sys', 'numpy.random.mtrand', 'xml', 'Bio', '_cython_0_28_4', 'six.moves.urllib.request', 'numpy.linalg', 'pyexpat.errors', 'Bio._py3k', 'Bio.File', 'logging.thread', 'xml.etree.ElementTree', '_struct', 'jcvi.formats.base', 'numpy.lib._version', 'jcvi.graphics.logging', 'jcvi.formats.logging', 'ssl', 'numpy.version', 'distutils.re', 'Bio.SeqIO.TabIO', 'Bio.__future__', 'Bio.Sequencing.Bio', 'numpy.lib.type_check', 'jcvi.apps.jcvi', 'jcvi.formats.shutil', 'jcvi.utils.functools', 'bisect', 'unittest.runner', 'unittest.re', 'threading', 'pyexpat.model', 'cycler', 'Bio.SeqRecord', 'locale', 'Bio.SeqIO.re', 'atexit', 'xml.sax.saxutils', 'Bio.GenBank.sys', 'jcvi.utils.collections', 'jcvi.utils.grouper', 'dateutil', 'numpy.testing.decorators', 'urllib', 'numpy.core.numerictypes', 'fcntl', 'unittest.case', 'mkl_fft._version', 'Bio._py3k.urllib', 'mkl_fft._pydfti', 'distutils.os', 'numpy.lib.info', 'ctypes', 'matplotlib', 'Bio.contextlib', 'xml.dom.domreg', 'struct', 'json.re', 'commands', 'jcvi.apps.difflib', 'unittest.signal', 'jcvi.graphics.numpy', 'itertools', 'numpy.ctypes', 'opcode', 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�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvr8an.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagd8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/psyr.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmtt10.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/putri8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pplr8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmsy10.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/putb8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Helvetica.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pplb8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvb8an.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/putr8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvro8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Helvetica-BoldOblique.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Symbol.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pplri8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-Italic.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmb8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmr8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvl8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pzdr.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncri8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmr10.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkl8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Helvetica-Oblique.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-BoldItalic.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvlo8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Courier-Bold.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrbo8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/putbi8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvro8an.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmbi8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrb8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvbo8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncr8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrro8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvb8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/ZapfDingbats.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmmi10.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrr8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncb8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkd8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pzcmi8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagko8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-Roman.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagk8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagdo8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkdi8a.afm�[0m
�[0;33m16:42:55 [font_manager]�[0m�[0;35m generated new fontManager�[0m
�[0;33m16:42:55 [__init__]�[0m�[0;35m backend agg version v2.2�[0m
�[0;33m16:42:55 [stats]�[0m�[0;35m Parsing files in `Exon_Length`..�[0m
Exon_Length/input.txt: Min=1 Max=2026 N=270 Mean=337.355555556 SD=399.160349598 Median=198.0 Sum=91086
�[0;33m16:42:55 [base]�[0m�[0;35m Rscript /tmp/tmp9ni8xuwi/tmp/tmpo8fGXD�[0m
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
�[0;33m16:42:58 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=50 Max=14088 N=205 Mean=547.107317073 SD=1467.30391824 Median=152.0 Sum=112157
�[0;33m16:42:58 [base]�[0m�[0;35m Rscript /tmp/tmp9ni8xuwi/tmp/tmp5EhWx8�[0m
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
�[0;33m16:43:01 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=111 Max=7371 N=65 Mean=1401.32307692 SD=1130.94596358 Median=1122.0 Sum=91086
�[0;33m16:43:01 [base]�[0m�[0;35m Rscript /tmp/tmp9ni8xuwi/tmp/tmpAQLelW�[0m
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
�[0;33m16:43:04 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=65 Mean=4.15384615385 SD=3.39334538463 Median=3.0 Sum=270
�[0;33m16:43:04 [base]�[0m�[0;35m Rscript /tmp/tmp9ni8xuwi/tmp/tmpXNoA_I�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6322244cb19411efa2f1a156edf22684"`
chromInfo	`"/tmp/tmp9ni8xuwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmp9ni8xuwi/job_working_directory/000/6/outputs/dataset_dd422a7d-c343-494c-8b5b-753291c2459b_files &&  cp /tmp/tmp9ni8xuwi/job_working_directory/000/6/configs/tmpgxfd0ad5 /tmp/tmp9ni8xuwi/job_working_directory/000/6/outputs/dataset_dd422a7d-c343-494c-8b5b-753291c2459b_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp9ni8xuwi/job_working_directory/000/6/outputs/dataset_dd422a7d-c343-494c-8b5b-753291c2459b_files /tmp/tmp9ni8xuwi/job_working_directory/000/6/configs/tmpgxfd0ad5 &&  cp /tmp/tmp9ni8xuwi/job_working_directory/000/6/outputs/dataset_dd422a7d-c343-494c-8b5b-753291c2459b_files/index.html /tmp/tmp9ni8xuwi/job_working_directory/000/6/outputs/dataset_dd422a7d-c343-494c-8b5b-753291c2459b.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"6322244cb19411efa2f1a156edf22684"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp9ni8xuwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp9ni8xuwi/files/7/d/b/dataset_7db17a82-32ec-4285-bc92-bd611aeb81a6.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-03 16:46:41 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-12-03 16:42:26 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 12/03/2024 16:42:26 *****
2024-12-03 16:42:26 INFO:	Configuring BUSCO with local environment
2024-12-03 16:42:26 INFO:	Running proteins mode
2024-12-03 16:42:26 INFO:	Input file is /tmp/tmp9ni8xuwi/files/7/d/b/dataset_7db17a82-32ec-4285-bc92-bd611aeb81a6.dat
2024-12-03 16:42:26 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-12-03 16:42:26 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-12-03 16:42:26 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-12-03 16:42:26 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2024-12-03 16:42:26 INFO:	***** Run HMMER on gene sequences *****
2024-12-03 16:42:26 INFO:	Running 2449 job(s) on hmmsearch, starting at 12/03/2024 16:42:26
2024-12-03 16:42:50 INFO:	[hmmsearch]	245 of 2449 task(s) completed
2024-12-03 16:43:10 INFO:	[hmmsearch]	490 of 2449 task(s) completed
2024-12-03 16:43:29 INFO:	[hmmsearch]	735 of 2449 task(s) completed
2024-12-03 16:43:50 INFO:	[hmmsearch]	980 of 2449 task(s) completed
2024-12-03 16:44:10 INFO:	[hmmsearch]	1225 of 2449 task(s) completed
2024-12-03 16:44:30 INFO:	[hmmsearch]	1470 of 2449 task(s) completed
2024-12-03 16:44:50 INFO:	[hmmsearch]	1715 of 2449 task(s) completed
2024-12-03 16:45:10 INFO:	[hmmsearch]	1960 of 2449 task(s) completed
2024-12-03 16:46:16 INFO:	[hmmsearch]	2205 of 2449 task(s) completed
2024-12-03 16:46:36 INFO:	[hmmsearch]	2449 of 2449 task(s) completed
2024-12-03 16:46:37 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:2449       |
    |2    Complete BUSCOs (C)                          |
    |2    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2447    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2024-12-03 16:46:37 INFO:	BUSCO analysis done with WARNING(s). Total running time: 251 seconds

***** Summary of warnings: *****
2024-12-03 16:42:26 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-12-03 16:42:26 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-12-03 16:42:26 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins

2024-12-03 16:46:37 INFO:	Results written in /tmp/tmp9ni8xuwi/job_working_directory/000/7/working/busco_galaxy
2024-12-03 16:46:37 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-03 16:46:37 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 92
drwxr-xr-x 5 1001 127  4096 Dec  3 16:42 busco_sequences
-rw-r--r-- 1 1001 127 47714 Dec  3 16:46 full_table.tsv
drwxr-xr-x 4 1001 127  4096 Dec  3 16:46 hmmer_output
-rw-r--r-- 1 1001 127 27808 Dec  3 16:46 missing_busco_list.tsv
-rw-r--r-- 1 1001 127  2230 Dec  3 16:46 short_summary.json
-rw-r--r-- 1 1001 127   741 Dec  3 16:46 short_summary.txt
2024-12-03 16:46:38 INFO:	****************** Start plot generation at 12/03/2024 16:46:38 ******************
2024-12-03 16:46:38 INFO:	Load data ...
2024-12-03 16:46:38 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2024-12-03 16:46:38 INFO:	Generate the R code ...
2024-12-03 16:46:38 INFO:	Run the R code ...
2024-12-03 16:46:41 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-03 16:46:41 INFO:	Plot generation done. Total running time: 2.442732572555542 seconds
2024-12-03 16:46:41 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6322244cb19411efa2f1a156edf22684"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmp9ni8xuwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

omamer search --db '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5' --query '/tmp/tmp9ni8xuwi/files/7/d/b/dataset_7db17a82-32ec-4285-bc92-bd611aeb81a6.dat' --out 'output_omamer'  &&  omark -f 'output_omamer' -d '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5'      -o omark_galaxy

Exit Code:

```
0
```

Standard Error:

================================================================================

   _____ _____ _____
  |     |     |  _  |_____ ___ ___
  |  |  | | | |     |     | -_|  _|
  |_____|_|_|_|__|__|_|_|_|___|_|   v2.0.2

  OMAmer is licensed under the GNU Lesser General Public License 3.0 (LGPL-3.0).
    
================================================================================

Loading required libraries  [DONE]

================================================================================

Running OMAmer on 7be38540fa2e, using:
 - database: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
 - query: /tmp/tmp9ni8xuwi/files/7/d/b/dataset_7db17a82-32ec-4285-bc92-bd611aeb81a6.dat
 - version: 2.0.2

================================================================================

Loading data required for OMAmer search from database...
 - taxonomy information (0.4s) [DONE]
 - family information (0.2s) [DONE]
 - sub-family information (4.8s) [DONE]
 - family hierarchy (0.2s) [DONE]
 - k-mer index (5:37.4) [DONE]
 - family probability estimates (0.2s) [DONE]
 - sub-family probability estimates (0.9s) [DONE]

Finished loading required data

================================================================================

�[?25l
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Searching -  65 queries in 1:05.0 (1.00 queries/s) 

================================================================================

OMAmer search complete:
 - results written to: output_omamer
 - total 411.05 seconds
 - search phase only 1.03 queries/s


Note: family p-values are stated in negative log units.
================================================================================

Thank you for using OMAmer. If you use OMAmer in your research, please cite:

Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz, OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2866-2873, https://doi.org/10.1093/bioinformatics/btab219


OMAmer uses data from the OMA browser. Results can be interpretted further using:
 - OMA browser website (https://omabrowser.org)
 - PyOMADB, the Python OMA API client (https://github.com/DessimozLab/pyomadb)

================================================================================
NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...

Inserting synonyms:          0 
Inserting synonyms:       5000 
Inserting synonyms:      10000 
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Inserting synonyms:      370000 
Inserting synonyms:      375000 
Inserting taxid merges:      0 
Inserting taxid merges:   5000 
Inserting taxid merges:  10000 
Inserting taxid merges:  15000 
Inserting taxid merges:  20000 
Inserting taxid merges:  25000 
Inserting taxid merges:  30000 
Inserting taxid merges:  35000 
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Inserting taxid merges:  45000 
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Inserting taxid merges:  55000 
Inserting taxid merges:  60000 
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Inserting taxid merges:  70000 
Inserting taxid merges:  75000 
Inserting taxid merges:  80000 
Inserting taxids:           0 
Inserting taxids:        5000 
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Inserting taxids:       25000 
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Inserting taxids:       95000 
Inserting taxids:       100000 
Inserting taxids:       105000 
Inserting taxids:       110000 
Inserting taxids:       115000 
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Inserting taxids:       135000 
Inserting taxids:       140000 
Inserting taxids:       145000 
Inserting taxids:       150000 
Inserting taxids:       155000 
Inserting taxids:       160000 
Inserting taxids:       165000 
Inserting taxids:       170000 
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Inserting taxids:       880000 
Inserting taxids:       885000 
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Inserting taxids:       895000 
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Inserting taxids:       910000 
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Inserting taxids:       935000 
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Inserting taxids:       1005000 
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Inserting taxids:       1255000 
Inserting taxids:       1260000 
Inserting taxids:       1265000 
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Inserting taxids:       1275000 
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Inserting taxids:       1285000 
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Inserting taxids:       1455000 
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Inserting taxids:       1785000 
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Inserting taxids:       2615000 
Inserting taxids:       2620000 
Inserting taxids:       2625000 
Inserting taxids:       2630000 WARNING: The selected ancestral lineage is from the species subgroup taxonomic rank. Consider trying a broader rank to validate your results.

WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'

Standard Output:

Loading node names...
2632346 names loaded.
376566 synonyms loaded.
Loading nodes...
2632346 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /tmp/tmp9ni8xuwi/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite ...

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Uploading to /tmp/tmp9ni8xuwi/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6322244cb19411efa2f1a156edf22684"`
chromInfo	`"/tmp/tmp9ni8xuwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"LUCA-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- history_id
  - 371adc4e3d3dc9fe
- history_state
  - ok
- invocation_id
  - 371adc4e3d3dc9fe
- invocation_state
  - scheduled
- workflow_id
  - 371adc4e3d3dc9fe

github-actions · 2024-12-03T17:36:51Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Problems:

Output with path /tmp/tmpj6xps6v4/Busco on data 1 full table__87339cba-52bf-4d11-860a-8b1f4a027b84 different than expected, difference (using sim_size):
( /tmp/planemo_test_file_47h6ssrf v. /tmp/tmp8441orhtplanemo_test_file_47h6ssrf )
Files /tmp/planemo_test_file_47h6ssrf=6192b but /tmp/tmp8441orhtplanemo_test_file_47h6ssrf=47630b - compare by size (delta=30000) failed

Output with path /tmp/tmph45rt9li/Busco on data 8 full table__30f4fa2d-2936-46ae-9e22-10b456f945af different than expected, difference (using sim_size):
( /tmp/planemo_test_file_g29cvxt7 v. /tmp/tmpmk8abjxwplanemo_test_file_g29cvxt7 )
Files /tmp/planemo_test_file_g29cvxt7=6143b but /tmp/tmpmk8abjxwplanemo_test_file_g29cvxt7=47714b - compare by size (delta=30000) failed

Workflow invocation details

Invocation Messages

Steps

Step 1: Genome sequence:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpl8mqketi/files/5/6/2/dataset_56242ecb-a645-4d60-bb11-79f8863f7b02.dat' --species '' --gff-output-path '/tmp/tmpl8mqketi/job_working_directory/000/2/outputs/dataset_013ca0e5-15c6-412d-8615-4ccbb9ad6844.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-12-03 16:21:04.584687: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-12-03 16:21:05.286586: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-12-03 16:21:10.679116: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-12-03 16:21:10.896205: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-12-03 16:21:13.205087: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-12-03 16:21:15.489690: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-12-03 16:21:17.790948: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpl8mqketi/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpl8mqketi/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpl8mqketi/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpl8mqketi/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpl8mqketi/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpl8mqketi/files/5/6/2/dataset_56242ecb-a645-4d60-bb11-79f8863f7b02.dat',
 'gff_output_path': '/tmp/tmpl8mqketi/job_working_directory/000/2/outputs/dataset_013ca0e5-15c6-412d-8615-4ccbb9ad6844.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpl8mqketi/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpfu6r65c4
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.24 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.39 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.01 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpl8mqketi/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpfu6r65c4/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpfu6r65c4/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpl8mqketi/files/5/6/2/dataset_56242ecb-a645-4d60-bb11-79f8863f7b02.dat', 'timestamp': '2024-12-03 16:21:07.946779'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpl8mqketi/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.06 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpl8mqketi/files/5/6/2/dataset_56242ecb-a645-4d60-bb11-79f8863f7b02.dat in 0.06 hours. GFF file written to /tmp/tmpl8mqketi/job_working_directory/000/2/outputs/dataset_013ca0e5-15c6-412d-8615-4ccbb9ad6844.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2f9001c8b19211efa224232c17b92685"`
chromInfo	`"/tmp/tmpl8mqketi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpl8mqketi/files/5/6/2/dataset_56242ecb-a645-4d60-bb11-79f8863f7b02.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-03 16:32:10 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-12-03 16:20:17 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 12/03/2024 16:20:17 *****
2024-12-03 16:20:17 INFO:	Configuring BUSCO with local environment
2024-12-03 16:20:17 INFO:	Running genome mode
2024-12-03 16:20:27 INFO:	Input file is /tmp/tmpl8mqketi/files/5/6/2/dataset_56242ecb-a645-4d60-bb11-79f8863f7b02.dat
2024-12-03 16:20:28 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2024-12-03 16:20:28 INFO:	Running 1 job(s) on bbtools, starting at 12/03/2024 16:20:28
2024-12-03 16:20:29 INFO:	[bbtools]	1 of 1 task(s) completed
2024-12-03 16:20:29 INFO:	Running 1 job(s) on makeblastdb, starting at 12/03/2024 16:20:29
2024-12-03 16:20:29 INFO:	Creating BLAST database with input file
2024-12-03 16:20:29 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-12-03 16:20:29 INFO:	Running a BLAST search for BUSCOs against created database
2024-12-03 16:20:29 INFO:	Running 1 job(s) on tblastn, starting at 12/03/2024 16:20:29
2024-12-03 16:20:39 INFO:	[tblastn]	1 of 1 task(s) completed
2024-12-03 16:20:39 INFO:	Running Augustus gene predictor on BLAST search results.
2024-12-03 16:20:39 INFO:	Running Augustus prediction using aspergillus_nidulans as species:
2024-12-03 16:20:39 INFO:	Running 76 job(s) on augustus, starting at 12/03/2024 16:20:39
2024-12-03 16:22:37 INFO:	[augustus]	8 of 76 task(s) completed
2024-12-03 16:23:53 INFO:	[augustus]	16 of 76 task(s) completed
2024-12-03 16:24:30 INFO:	[augustus]	23 of 76 task(s) completed
2024-12-03 16:24:49 INFO:	[augustus]	31 of 76 task(s) completed
2024-12-03 16:25:11 INFO:	[augustus]	38 of 76 task(s) completed
2024-12-03 16:25:33 INFO:	[augustus]	46 of 76 task(s) completed
2024-12-03 16:25:54 INFO:	[augustus]	54 of 76 task(s) completed
2024-12-03 16:26:05 INFO:	[augustus]	61 of 76 task(s) completed
2024-12-03 16:26:16 INFO:	[augustus]	69 of 76 task(s) completed
2024-12-03 16:26:28 INFO:	[augustus]	76 of 76 task(s) completed
2024-12-03 16:26:28 INFO:	Extracting predicted proteins...
2024-12-03 16:26:28 INFO:	***** Run HMMER on gene sequences *****
2024-12-03 16:26:28 INFO:	Running 75 job(s) on hmmsearch, starting at 12/03/2024 16:26:28
2024-12-03 16:26:28 INFO:	[hmmsearch]	8 of 75 task(s) completed
2024-12-03 16:26:29 INFO:	[hmmsearch]	15 of 75 task(s) completed
2024-12-03 16:26:29 INFO:	[hmmsearch]	23 of 75 task(s) completed
2024-12-03 16:26:30 INFO:	[hmmsearch]	30 of 75 task(s) completed
2024-12-03 16:26:31 INFO:	[hmmsearch]	38 of 75 task(s) completed
2024-12-03 16:26:32 INFO:	[hmmsearch]	45 of 75 task(s) completed
2024-12-03 16:26:33 INFO:	[hmmsearch]	53 of 75 task(s) completed
2024-12-03 16:26:34 INFO:	[hmmsearch]	60 of 75 task(s) completed
2024-12-03 16:26:38 INFO:	[hmmsearch]	68 of 75 task(s) completed
2024-12-03 16:26:39 INFO:	[hmmsearch]	75 of 75 task(s) completed
2024-12-03 16:26:39 INFO:	0 exons in total
2024-12-03 16:26:39 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-12-03 16:26:39 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-12-03 16:26:46 INFO:	Running a BLAST search for BUSCOs against created database
2024-12-03 16:26:46 INFO:	Running 1 job(s) on tblastn, starting at 12/03/2024 16:26:46
2024-12-03 16:28:14 INFO:	[tblastn]	1 of 1 task(s) completed
2024-12-03 16:28:14 INFO:	Converting predicted genes to short genbank files
2024-12-03 16:28:14 INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 12/03/2024 16:28:14
2024-12-03 16:28:15 INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
2024-12-03 16:28:15 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-12-03 16:28:15 INFO:	Running 1 job(s) on new_species.pl, starting at 12/03/2024 16:28:15
2024-12-03 16:28:15 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-12-03 16:28:15 INFO:	Running 1 job(s) on etraining, starting at 12/03/2024 16:28:15
2024-12-03 16:28:16 INFO:	[etraining]	1 of 1 task(s) completed
2024-12-03 16:28:16 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 2448
2024-12-03 16:28:16 INFO:	Running Augustus gene predictor on BLAST search results.
2024-12-03 16:28:16 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-12-03 16:28:16 INFO:	Running 100 job(s) on augustus, starting at 12/03/2024 16:28:16
2024-12-03 16:29:23 INFO:	[augustus]	10 of 100 task(s) completed
2024-12-03 16:30:21 INFO:	[augustus]	20 of 100 task(s) completed
2024-12-03 16:30:49 INFO:	[augustus]	30 of 100 task(s) completed
2024-12-03 16:31:02 INFO:	[augustus]	40 of 100 task(s) completed
2024-12-03 16:31:15 INFO:	[augustus]	50 of 100 task(s) completed
2024-12-03 16:31:27 INFO:	[augustus]	60 of 100 task(s) completed
2024-12-03 16:31:38 INFO:	[augustus]	70 of 100 task(s) completed
2024-12-03 16:31:48 INFO:	[augustus]	80 of 100 task(s) completed
2024-12-03 16:31:58 INFO:	[augustus]	90 of 100 task(s) completed
2024-12-03 16:32:07 INFO:	[augustus]	100 of 100 task(s) completed
2024-12-03 16:32:07 INFO:	Extracting predicted proteins...
2024-12-03 16:32:07 INFO:	***** Run HMMER on gene sequences *****
2024-12-03 16:32:07 WARNING:	No jobs to run on hmmsearch
2024-12-03 16:32:07 INFO:	0 exons in total
2024-12-03 16:32:07 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449	   

2024-12-03 16:32:07 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449      |
    |1    Complete BUSCOs (C)                          |
    |1    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2448    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2024-12-03 16:32:07 INFO:	BUSCO analysis done with WARNING(s). Total running time: 700 seconds

***** Summary of warnings: *****
2024-12-03 16:32:07 WARNING:busco.busco_tools.Toolset	No jobs to run on hmmsearch

2024-12-03 16:32:07 INFO:	Results written in /tmp/tmpl8mqketi/job_working_directory/000/3/working/busco_galaxy
2024-12-03 16:32:07 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-03 16:32:07 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 100
drwxr-xr-x 8 1001 127  4096 Dec  3 16:32 augustus_output
drwxr-xr-x 3 1001 127  4096 Dec  3 16:28 blast_output
drwxr-xr-x 5 1001 127  4096 Dec  3 16:20 busco_sequences
-rw-r--r-- 1 1001 127 47630 Dec  3 16:32 full_table.tsv
drwxr-xr-x 4 1001 127  4096 Dec  3 16:26 hmmer_output
-rw-r--r-- 1 1001 127 27820 Dec  3 16:32 missing_busco_list.tsv
-rw-r--r-- 1 1001 127  3175 Dec  3 16:32 short_summary.json
-rw-r--r-- 1 1001 127  1066 Dec  3 16:32 short_summary.txt
2024-12-03 16:32:08 INFO:	****************** Start plot generation at 12/03/2024 16:32:08 ******************
2024-12-03 16:32:08 INFO:	Load data ...
2024-12-03 16:32:08 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2024-12-03 16:32:08 INFO:	Generate the R code ...
2024-12-03 16:32:08 INFO:	Run the R code ...
2024-12-03 16:32:10 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-03 16:32:10 INFO:	Plot generation done. Total running time: 1.98996901512146 seconds
2024-12-03 16:32:10 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2f9001c8b19211efa224232c17b92685"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpl8mqketi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpl8mqketi/files/5/6/2/dataset_56242ecb-a645-4d60-bb11-79f8863f7b02.dat' genomeref.fa &&  gffread '/tmp/tmpl8mqketi/files/0/1/3/dataset_013ca0e5-15c6-412d-8615-4ccbb9ad6844.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2f9001c8b19211efa224232c17b92685"`
chr_replace	`None`
chromInfo	`"/tmp/tmpl8mqketi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpl8mqketi/files/0/1/3/dataset_013ca0e5-15c6-412d-8615-4ccbb9ad6844.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpl8mqketi/job_working_directory/000/5/outputs/dataset_dceb1bee-6403-4e94-912a-97e899033506.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpl8mqketi/files/5/6/2/dataset_56242ecb-a645-4d60-bb11-79f8863f7b02.dat' 2>&1 | tail -n +3 >> '/tmp/tmpl8mqketi/job_working_directory/000/5/outputs/dataset_dceb1bee-6403-4e94-912a-97e899033506.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpl8mqketi/job_working_directory/000/5/outputs/dataset_dceb1bee-6403-4e94-912a-97e899033506.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpl8mqketi/job_working_directory/000/5/outputs/dataset_253a46f0-416e-412f-9cf6-ad853fa30be4.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m16:25:24 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m16:25:24 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m16:25:24 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m16:25:24 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m16:25:24 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m16:25:24 [stats]�[0m�[0;35m A total of 65 transcripts populated.�[0m
�[0;33m16:25:25 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m16:25:25 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m16:25:25 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m16:25:25 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m16:25:25 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m16:25:25 [__init__]�[0m�[0;35m platform is linux2�[0m
�[0;33m16:25:25 [__init__]�[0m�[0;35m loaded modules: ['numpy.core.info', 'Bio.SeqIO.UniprotIO', 'jcvi.apps.base', 'ctypes.os', 'Bio.os', 'runpy', 'gc', 'distutils.sysconfig', 'matplotlib.cbook._backports', 'Bio._py3k.urllib2', 'logging.weakref', 'base64', 'jcvi.utils', 'jcvi.apps.signal', 'unittest.sys', 'numpy.core.umath', 'string', 'Bio.SeqIO.InsdcIO', 'numpy.lib.arraysetops', '_elementtree', 'xml.etree.warnings', 'xml.etree.sys', 'Bio.SeqUtils.binascii', 'json.encoder', 'Bio.SeqIO.QualityIO', 'numpy.core.machar', 'jcvi.formats.collections', 'unittest.StringIO', 'unittest.types', 'jcvi.apps.threading', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'dis', 'zlib', 'logging.threading', 'jcvi.annotation', 'Bio.SeqIO.Bio', '_json', 'Bio.GenBank.warnings', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'numpy._globals', 'numpy.lib.npyio', 'xml.sax.io', 'Bio._py3k.sys', 'Bio.SeqIO.sys', 'numpy.fft.helper', 'matplotlib.rcsetup', 'optparse', 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�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans-BoldOblique.ttf�[0m
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�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSerif.ttf�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Helvetica-Bold.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Courier-Oblique.afm�[0m
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�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Courier.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmri8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmex10.afm�[0m
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�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagd8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/psyr.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmtt10.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/putri8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pplr8a.afm�[0m
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�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Helvetica.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pplb8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvb8an.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/putr8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvro8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Helvetica-BoldOblique.afm�[0m
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�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pplri8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-Italic.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmb8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmr8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvl8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pzdr.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncri8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmr10.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkl8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Helvetica-Oblique.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-BoldItalic.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvlo8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Courier-Bold.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrbo8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/putbi8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvro8an.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmbi8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrb8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvbo8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncr8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrro8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvb8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/ZapfDingbats.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmmi10.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrr8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncb8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkd8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pzcmi8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagko8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-Roman.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagk8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagdo8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkdi8a.afm�[0m
�[0;33m16:25:25 [font_manager]�[0m�[0;35m generated new fontManager�[0m
�[0;33m16:25:25 [__init__]�[0m�[0;35m backend agg version v2.2�[0m
�[0;33m16:25:25 [stats]�[0m�[0;35m Parsing files in `Exon_Length`..�[0m
Exon_Length/input.txt: Min=1 Max=2026 N=270 Mean=337.355555556 SD=399.160349598 Median=198.0 Sum=91086
�[0;33m16:25:25 [base]�[0m�[0;35m Rscript /tmp/tmpl8mqketi/tmp/tmpRQBd9e�[0m
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
�[0;33m16:25:29 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=50 Max=14088 N=205 Mean=547.107317073 SD=1467.30391824 Median=152.0 Sum=112157
�[0;33m16:25:29 [base]�[0m�[0;35m Rscript /tmp/tmpl8mqketi/tmp/tmpeYkF7c�[0m
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
�[0;33m16:25:32 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=111 Max=7371 N=65 Mean=1401.32307692 SD=1130.94596358 Median=1122.0 Sum=91086
�[0;33m16:25:32 [base]�[0m�[0;35m Rscript /tmp/tmpl8mqketi/tmp/tmpZHUcd6�[0m
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
�[0;33m16:25:35 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=65 Mean=4.15384615385 SD=3.39334538463 Median=3.0 Sum=270
�[0;33m16:25:35 [base]�[0m�[0;35m Rscript /tmp/tmpl8mqketi/tmp/tmpqSrrfu�[0m
Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2f9001c8b19211efa224232c17b92685"`
chromInfo	`"/tmp/tmpl8mqketi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmpl8mqketi/job_working_directory/000/6/outputs/dataset_f64c0b69-d465-4685-98f7-2dedc22fcbe6_files &&  cp /tmp/tmpl8mqketi/job_working_directory/000/6/configs/tmpbmkp5p9p /tmp/tmpl8mqketi/job_working_directory/000/6/outputs/dataset_f64c0b69-d465-4685-98f7-2dedc22fcbe6_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpl8mqketi/job_working_directory/000/6/outputs/dataset_f64c0b69-d465-4685-98f7-2dedc22fcbe6_files /tmp/tmpl8mqketi/job_working_directory/000/6/configs/tmpbmkp5p9p &&  cp /tmp/tmpl8mqketi/job_working_directory/000/6/outputs/dataset_f64c0b69-d465-4685-98f7-2dedc22fcbe6_files/index.html /tmp/tmpl8mqketi/job_working_directory/000/6/outputs/dataset_f64c0b69-d465-4685-98f7-2dedc22fcbe6.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"2f9001c8b19211efa224232c17b92685"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpl8mqketi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpl8mqketi/files/8/d/2/dataset_8d2d62bb-2f05-40e3-b4a9-29d109deff9e.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-03 16:30:08 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-12-03 16:25:05 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 12/03/2024 16:25:05 *****
2024-12-03 16:25:05 INFO:	Configuring BUSCO with local environment
2024-12-03 16:25:05 INFO:	Running proteins mode
2024-12-03 16:25:05 INFO:	Input file is /tmp/tmpl8mqketi/files/8/d/2/dataset_8d2d62bb-2f05-40e3-b4a9-29d109deff9e.dat
2024-12-03 16:25:05 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2024-12-03 16:25:05 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2024-12-03 16:25:05 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2024-12-03 16:25:05 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2024-12-03 16:25:05 INFO:	***** Run HMMER on gene sequences *****
2024-12-03 16:25:05 INFO:	Running 2449 job(s) on hmmsearch, starting at 12/03/2024 16:25:05
2024-12-03 16:25:22 INFO:	[hmmsearch]	245 of 2449 task(s) completed
2024-12-03 16:25:52 INFO:	[hmmsearch]	490 of 2449 task(s) completed
2024-12-03 16:26:23 INFO:	[hmmsearch]	735 of 2449 task(s) completed
2024-12-03 16:27:03 INFO:	[hmmsearch]	980 of 2449 task(s) completed
2024-12-03 16:27:35 INFO:	[hmmsearch]	1225 of 2449 task(s) completed
2024-12-03 16:28:05 INFO:	[hmmsearch]	1470 of 2449 task(s) completed
2024-12-03 16:28:38 INFO:	[hmmsearch]	1715 of 2449 task(s) completed
2024-12-03 16:29:07 INFO:	[hmmsearch]	1960 of 2449 task(s) completed
2024-12-03 16:29:37 INFO:	[hmmsearch]	2205 of 2449 task(s) completed
2024-12-03 16:30:05 INFO:	[hmmsearch]	2449 of 2449 task(s) completed
2024-12-03 16:30:05 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:2449       |
    |2    Complete BUSCOs (C)                          |
    |2    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2447    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2024-12-03 16:30:05 INFO:	BUSCO analysis done with WARNING(s). Total running time: 300 seconds

***** Summary of warnings: *****
2024-12-03 16:25:05 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2024-12-03 16:25:05 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2024-12-03 16:25:05 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins

2024-12-03 16:30:05 INFO:	Results written in /tmp/tmpl8mqketi/job_working_directory/000/7/working/busco_galaxy
2024-12-03 16:30:05 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-03 16:30:05 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 92
drwxr-xr-x 5 1001 127  4096 Dec  3 16:25 busco_sequences
-rw-r--r-- 1 1001 127 47714 Dec  3 16:30 full_table.tsv
drwxr-xr-x 4 1001 127  4096 Dec  3 16:30 hmmer_output
-rw-r--r-- 1 1001 127 27808 Dec  3 16:30 missing_busco_list.tsv
-rw-r--r-- 1 1001 127  2230 Dec  3 16:30 short_summary.json
-rw-r--r-- 1 1001 127   741 Dec  3 16:30 short_summary.txt
2024-12-03 16:30:06 INFO:	****************** Start plot generation at 12/03/2024 16:30:06 ******************
2024-12-03 16:30:06 INFO:	Load data ...
2024-12-03 16:30:06 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2024-12-03 16:30:06 INFO:	Generate the R code ...
2024-12-03 16:30:06 INFO:	Run the R code ...
2024-12-03 16:30:08 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-03 16:30:08 INFO:	Plot generation done. Total running time: 2.3843977451324463 seconds
2024-12-03 16:30:08 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2f9001c8b19211efa224232c17b92685"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmpl8mqketi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

omamer search --db '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5' --query '/tmp/tmpl8mqketi/files/8/d/2/dataset_8d2d62bb-2f05-40e3-b4a9-29d109deff9e.dat' --out 'output_omamer'  &&  omark -f 'output_omamer' -d '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5'      -o omark_galaxy

Exit Code:

```
0
```

Standard Error:

================================================================================

   _____ _____ _____
  |     |     |  _  |_____ ___ ___
  |  |  | | | |     |     | -_|  _|
  |_____|_|_|_|__|__|_|_|_|___|_|   v2.0.2

  OMAmer is licensed under the GNU Lesser General Public License 3.0 (LGPL-3.0).
    
================================================================================

Loading required libraries  [DONE]

================================================================================

Running OMAmer on 0941b5785e07, using:
 - database: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
 - query: /tmp/tmpl8mqketi/files/8/d/2/dataset_8d2d62bb-2f05-40e3-b4a9-29d109deff9e.dat
 - version: 2.0.2

================================================================================

Loading data required for OMAmer search from database...
 - taxonomy information (2.3s) [DONE]
 - family information (2.3s) [DONE]
 - sub-family information (46.1s) [DONE]
 - family hierarchy (0.6s) [DONE]
 - k-mer index (58:31.6) [DONE]
 - family probability estimates (2.3s) [DONE]
 - sub-family probability estimates (12.9s) [DONE]

Finished loading required data

================================================================================

�[?25l
Searching -  0 queries in 0s (0.0 queries/s) 
Searching -  0 queries in 5s (0.0 queries/s) 
Searching -  0 queries in 10s (0.0 queries/s) 
Searching -  0 queries in 15s (0.0 queries/s) 
Searching -  0 queries in 20s (0.0 queries/s) 
Searching -  0 queries in 25s (0.0 queries/s) 
Searching -  0 queries in 30s (0.0 queries/s) 
Searching -  0 queries in 35s (0.0 queries/s) 
Searching -  0 queries in 40s (0.0 queries/s) 
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Searching -  0 queries in 50s (0.0 queries/s) 
Searching -  0 queries in 55s (0.0 queries/s) 
Searching -  0 queries in 1:00 (0.0 queries/s) �[?25h�[J
Searching -  65 queries in 1:05.0 (1.00 queries/s) 

================================================================================

OMAmer search complete:
 - results written to: output_omamer
 - total 3656.19 seconds
 - search phase only 1.01 queries/s


Note: family p-values are stated in negative log units.
================================================================================

Thank you for using OMAmer. If you use OMAmer in your research, please cite:

Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz, OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2866-2873, https://doi.org/10.1093/bioinformatics/btab219


OMAmer uses data from the OMA browser. Results can be interpretted further using:
 - OMA browser website (https://omabrowser.org)
 - PyOMADB, the Python OMA API client (https://github.com/DessimozLab/pyomadb)

================================================================================
NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...

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Inserting taxids:       2065000 
Inserting taxids:       2070000 
Inserting taxids:       2075000 
Inserting taxids:       2080000 
Inserting taxids:       2085000 
Inserting taxids:       2090000 
Inserting taxids:       2095000 
Inserting taxids:       2100000 
Inserting taxids:       2105000 
Inserting taxids:       2110000 
Inserting taxids:       2115000 
Inserting taxids:       2120000 
Inserting taxids:       2125000 
Inserting taxids:       2130000 
Inserting taxids:       2135000 
Inserting taxids:       2140000 
Inserting taxids:       2145000 
Inserting taxids:       2150000 
Inserting taxids:       2155000 
Inserting taxids:       2160000 
Inserting taxids:       2165000 
Inserting taxids:       2170000 
Inserting taxids:       2175000 
Inserting taxids:       2180000 
Inserting taxids:       2185000 
Inserting taxids:       2190000 
Inserting taxids:       2195000 
Inserting taxids:       2200000 
Inserting taxids:       2205000 
Inserting taxids:       2210000 
Inserting taxids:       2215000 
Inserting taxids:       2220000 
Inserting taxids:       2225000 
Inserting taxids:       2230000 
Inserting taxids:       2235000 
Inserting taxids:       2240000 
Inserting taxids:       2245000 
Inserting taxids:       2250000 
Inserting taxids:       2255000 
Inserting taxids:       2260000 
Inserting taxids:       2265000 
Inserting taxids:       2270000 
Inserting taxids:       2275000 
Inserting taxids:       2280000 
Inserting taxids:       2285000 
Inserting taxids:       2290000 
Inserting taxids:       2295000 
Inserting taxids:       2300000 
Inserting taxids:       2305000 
Inserting taxids:       2310000 
Inserting taxids:       2315000 
Inserting taxids:       2320000 
Inserting taxids:       2325000 
Inserting taxids:       2330000 
Inserting taxids:       2335000 
Inserting taxids:       2340000 
Inserting taxids:       2345000 
Inserting taxids:       2350000 
Inserting taxids:       2355000 
Inserting taxids:       2360000 
Inserting taxids:       2365000 
Inserting taxids:       2370000 
Inserting taxids:       2375000 
Inserting taxids:       2380000 
Inserting taxids:       2385000 
Inserting taxids:       2390000 
Inserting taxids:       2395000 
Inserting taxids:       2400000 
Inserting taxids:       2405000 
Inserting taxids:       2410000 
Inserting taxids:       2415000 
Inserting taxids:       2420000 
Inserting taxids:       2425000 
Inserting taxids:       2430000 
Inserting taxids:       2435000 
Inserting taxids:       2440000 
Inserting taxids:       2445000 
Inserting taxids:       2450000 
Inserting taxids:       2455000 
Inserting taxids:       2460000 
Inserting taxids:       2465000 
Inserting taxids:       2470000 
Inserting taxids:       2475000 
Inserting taxids:       2480000 
Inserting taxids:       2485000 
Inserting taxids:       2490000 
Inserting taxids:       2495000 
Inserting taxids:       2500000 
Inserting taxids:       2505000 
Inserting taxids:       2510000 
Inserting taxids:       2515000 
Inserting taxids:       2520000 
Inserting taxids:       2525000 
Inserting taxids:       2530000 
Inserting taxids:       2535000 
Inserting taxids:       2540000 
Inserting taxids:       2545000 
Inserting taxids:       2550000 
Inserting taxids:       2555000 
Inserting taxids:       2560000 
Inserting taxids:       2565000 
Inserting taxids:       2570000 
Inserting taxids:       2575000 
Inserting taxids:       2580000 
Inserting taxids:       2585000 
Inserting taxids:       2590000 
Inserting taxids:       2595000 
Inserting taxids:       2600000 
Inserting taxids:       2605000 
Inserting taxids:       2610000 
Inserting taxids:       2615000 
Inserting taxids:       2620000 
Inserting taxids:       2625000 
Inserting taxids:       2630000 WARNING: The selected ancestral lineage is from the species subgroup taxonomic rank. Consider trying a broader rank to validate your results.

WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'

Standard Output:

Loading node names...
2632346 names loaded.
376566 synonyms loaded.
Loading nodes...
2632346 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /tmp/tmpl8mqketi/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite ...

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..
. 
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Uploading to /tmp/tmpl8mqketi/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2f9001c8b19211efa224232c17b92685"`
chromInfo	`"/tmp/tmpl8mqketi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"LUCA-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- history_id
  - 14d9bd2b0765a4a1
- history_state
  - ok
- invocation_id
  - 14d9bd2b0765a4a1
- invocation_state
  - scheduled
- workflow_id
  - 14d9bd2b0765a4a1

add_helixer_workflow

aafd1a4

rlibouba marked this pull request as draft October 8, 2024 13:55

rlibouba added 2 commits October 8, 2024 16:22

fix dockstore error

78f38cf

fix dockstore error

261b7f3

rlibouba added 4 commits October 8, 2024 17:42

modify Galaxy-Workflow-annotation_helixer.ga

081f2c5

fix lint

9abf6e1

typo error

450bfcf

error

351aebd

modify omark

eaa461e

retry

a9c5bf0

rename

77546e6

rlibouba marked this pull request as ready for review October 21, 2024 08:49

rlibouba added 2 commits November 12, 2024 10:36

addition of coloured borders and titles

1244008

fix lint

12c4537

mvdbeek previously approved these changes Nov 22, 2024

View reviewed changes

rlibouba dismissed mvdbeek’s stale review via fa5a9ba November 25, 2024 13:45

rlibouba added 3 commits November 25, 2024 14:45

update helixer workflow

fa5a9ba

error typo

f021c32

fix lint

4409347

rlibouba added 2 commits November 25, 2024 15:12

fix lint

3afd41e

change database for OMArk

d52f561

rlibouba and others added 2 commits December 3, 2024 17:09

small modification

2b04d77

Rename workflow directory and add orcid to .dockstore.yml

58acaec

mvdbeek approved these changes Dec 3, 2024

View reviewed changes

mvdbeek enabled auto-merge December 3, 2024 16:28

fix tests

10a453a

auto-merge was automatically disabled December 12, 2024 09:30
Head branch was pushed to by a user without write access

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add_helixer_workflow #555

add_helixer_workflow #555

rlibouba commented Oct 8, 2024

github-actions bot commented Oct 8, 2024

Workflow invocation details

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

add_helixer_workflow #555

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add_helixer_workflow #555

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