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Expected output log for the test example
Sina Majidian edited this page Nov 8, 2023
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This is the expected stdout log for the test example. There is also mplog.log file that you can check!
$ read2tree --debug --tree --standalone_path marker_genes/ --reads sample_1.fastq sample_2.fastq --output_path output/ --dna_reference dna_ref.fa
--- Load OGs with min 0 species from oma marker_genes - mode = marker_genes ---
Loading files for pre-filter: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 9820.43 OGs/s]
2023-11-08 22:23:38,734 - read2tree.OGSet - INFO - --- Load ogs and find their corresponding DNA seq from dna_ref.fa ---
2023-11-08 22:23:38,735 - read2tree.OGSet - INFO - Loading dna_ref.fa into memory. This might take a while . . .
Loading OGs: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 1144.19 OGs/s]
2023-11-08 22:23:38,755 - read2tree.OGSet - INFO - sample_1: Gathering of DNA seq for 20 OGs took 0.018137693405151367.
--- Generating reference for mapping ---
Loading records: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 195538.65 record/s]
2023-11-08 22:23:38,755 - read2tree.ReferenceSet - INFO - sample_1: Extracted 5 reference species form 20 ogs took 0.0004379749298095703
--- Alignment of 20 OGs ---
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/subprocess.py:961: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
self.stdout = io.open(c2pread, 'rb', bufsize)
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/subprocess.py:966: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
self.stderr = io.open(errread, 'rb', bufsize)
2023-11-08 22:23:43,224 - read2tree.Aligner - INFO - sample_1: Alignment of 20 OGs took 4.467177391052246.
--- Mapping of reads to reference sequences ---
Mapping reads to species: 0%| | 0/5 [00:00<?, ? species/s]2023-11-08 22:23:43,233 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to MNELE reference species ---
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/subprocess.py:961: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
self.stdout = io.open(c2pread, 'rb', bufsize)
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/subprocess.py:966: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
self.stderr = io.open(errread, 'rb', bufsize)
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_y580e8r8/MNELE_OGs.fa.bam'
2023-11-08 22:23:48,970 - read2tree.Mapper - INFO - sample_1: Mapped 27 / 50000 reads to MNELE_OGs.fa
2023-11-08 22:23:49,010 - read2tree.Mapper - INFO - sample_1: Mapping to MNELE_OGs.fa references took 5.77674412727356.
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/site-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/site-packages/numpy/core/_methods.py:269: RuntimeWarning: Degrees of freedom <= 0 for slice
ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/site-packages/numpy/core/_methods.py:226: RuntimeWarning: invalid value encountered in divide
arrmean = um.true_divide(arrmean, div, out=arrmean,
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/site-packages/numpy/core/_methods.py:261: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
Mapping reads to species: 20%|████████████████████████▌ | 1/5 [00:06<00:24, 6.09s/ species]2023-11-08 22:23:49,321 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to HUMAN reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_y580e8r8/HUMAN_OGs.fa.bam'
2023-11-08 22:23:53,776 - read2tree.Mapper - INFO - sample_1: Mapped 93 / 50000 reads to HUMAN_OGs.fa
2023-11-08 22:23:53,801 - read2tree.Mapper - INFO - sample_1: Mapping to HUMAN_OGs.fa references took 4.47956657409668.
Mapping reads to species: 40%|█████████████████████████████████████████████████▏ | 2/5 [00:10<00:15, 5.17s/ species]2023-11-08 22:23:53,842 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to RATNO reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_y580e8r8/RATNO_OGs.fa.bam'
2023-11-08 22:23:57,707 - read2tree.Mapper - INFO - sample_1: Mapped 99 / 50000 reads to RATNO_OGs.fa
2023-11-08 22:23:57,746 - read2tree.Mapper - INFO - sample_1: Mapping to RATNO_OGs.fa references took 3.902667760848999.
Mapping reads to species: 60%|█████████████████████████████████████████████████████████████████████████▊ | 3/5 [00:14<00:09, 4.61s/ species]2023-11-08 22:23:57,786 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to GORGO reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_y580e8r8/GORGO_OGs.fa.bam'
2023-11-08 22:24:02,321 - read2tree.Mapper - INFO - sample_1: Mapped 90 / 50000 reads to GORGO_OGs.fa
2023-11-08 22:24:02,360 - read2tree.Mapper - INFO - sample_1: Mapping to GORGO_OGs.fa references took 4.573137521743774.
Mapping reads to species: 80%|██████████████████████████████████████████████████████████████████████████████████████████████████▍ | 4/5 [00:19<00:04, 4.61s/ species]2023-11-08 22:24:02,400 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to XENLA reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_y580e8r8/XENLA_OGs.fa.bam'
2023-11-08 22:24:05,825 - read2tree.Mapper - INFO - sample_1: Mapped 43 / 50000 reads to XENLA_OGs.fa
2023-11-08 22:24:05,859 - read2tree.Mapper - INFO - sample_1: Mapping to XENLA_OGs.fa references took 3.4591243267059326.
Mapping reads to species: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5/5 [00:22<00:00, 4.53s/ species]
2023-11-08 22:24:05,889 - read2tree.Mapper - INFO - sample_1: Mapping to all references took 22.65858244895935.
Adding mapped seq to alignments: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 203606.99 alignments/s]
Adding mapped seq to OG: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 330260.16 OGs/s]
--- Add inferred mapped sequence back to OGs ---
Adding mapped seq to OG: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 78766.27 OGs/s]
2023-11-08 22:24:05,915 - read2tree.OGSet - INFO - sample_1: Appending 10 reconstructed sequences to present OG took 0.001190185546875.
--- Add inferred mapped sequence back to alignment ---
Adding mapped seq to alignments: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 2448.80 alignments/s]
2023-11-08 22:24:05,935 - read2tree.Aligner - INFO - sample_1: Appending 3 reconstructed sequences to present Alignments took 0.008440732955932617.
--- Tree inference ---
2023-11-08 22:24:14,996 - read2tree.TreeInference - INFO - sample_1: Tree inference took 9.024619102478027.
(sample_1:0.0511660790,((MNELE:0.9367284506,XENLA:0.1449909363):0.1375879571,(HUMAN:0.0039311940,GORGO:0.0103980330):0.0495969315):0.0632875126,RATNO:0.0169496568);
The following is the old version when the dna_ref.fa is needed to be downloaded.
read2tree --tree --standalone_path marker_genes/ --reads sample_1.fastq sample_2.fastq --output_path output/
--- Load OGs with min 0 species from oma marker gene export! ---
Loading files for pre-filter: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 241.13 OGs/s]
2022-09-14 12:11:37,788 - read2tree.OGSet - INFO - --- Load ogs and find their corresponding DNA seq using the REST api ---
Loading OGs: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:04<00:00, 4.49 OGs/s]
2022-09-14 12:11:42,250 - read2tree.OGSet - INFO - sample_1: Gathering of DNA seq for 20 OGs took 4.461216449737549.
--- Generating reference for mapping ---
Loading records: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 56833.39 record/s]
2022-09-14 12:11:42,251 - read2tree.ReferenceSet - INFO - sample_1: Extracted 5 reference species form 20 ogs took 0.0009484291076660156
--- Alignment of 20 OGs ---
2022-09-14 12:11:45,821 - read2tree.Aligner - INFO - sample_1: Alignment of 20 OGs took 3.566136598587036.
--- Mapping of reads to reference sequences ---
Mapping reads to species: 0%| | 0/5 [00:00<?, ? species/s]2022-09-14 12:11:45,830 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to HUMAN reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_j0p1u43c/HUMAN_OGs.fa.bam'
2022-09-14 12:11:49,884 - read2tree.Mapper - INFO - sample_1: Mapped 29 / 50000 reads to HUMAN_OGs.fa
2022-09-14 12:11:49,913 - read2tree.Mapper - INFO - sample_1: Mapping to HUMAN_OGs.fa references took 4.08157205581665.
Mapping reads to species: 20%|███████████████████████▌ | 1/5 [00:04<00:17, 4.33s/ species]2022-09-14 12:11:50,159 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to GORGO reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_j0p1u43c/GORGO_OGs.fa.bam'
2022-09-14 12:11:52,815 - read2tree.Mapper - INFO - sample_1: Mapped 27 / 50000 reads to GORGO_OGs.fa
2022-09-14 12:11:52,831 - read2tree.Mapper - INFO - sample_1: Mapping to GORGO_OGs.fa references took 2.6480491161346436.
Mapping reads to species: 40%|███████████████████████████████████████████████▏ | 2/5 [00:07<00:10, 3.38s/ species]2022-09-14 12:11:52,880 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to RATNO reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_j0p1u43c/RATNO_OGs.fa.bam'
2022-09-14 12:11:56,418 - read2tree.Mapper - INFO - sample_1: Mapped 44 / 50000 reads to RATNO_OGs.fa
2022-09-14 12:11:56,447 - read2tree.Mapper - INFO - sample_1: Mapping to RATNO_OGs.fa references took 3.5645296573638916.
Mapping reads to species: 60%|██████████████████████████████████████████████████████████████████████▊ | 3/5 [00:10<00:06, 3.49s/ species]2022-09-14 12:11:56,496 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to XENLA reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_j0p1u43c/XENLA_OGs.fa.bam'
2022-09-14 12:11:59,318 - read2tree.Mapper - INFO - sample_1: Mapped 19 / 50000 reads to XENLA_OGs.fa
2022-09-14 12:11:59,334 - read2tree.Mapper - INFO - sample_1: Mapping to XENLA_OGs.fa references took 2.8225371837615967.
Mapping reads to species: 80%|██████████████████████████████████████████████████████████████████████████████████████████████▍ | 4/5 [00:13<00:03, 3.25s/ species]2022-09-14 12:11:59,371 - read2tree.Mapper - INFO - sample_1: --- Mapping of reads to MNELE reference species ---
[E::idx_find_and_load] Could not retrieve index file for '/tmp/ngm_j0p1u43c/MNELE_OGs.fa.bam'
2022-09-14 12:12:02,773 - read2tree.Mapper - INFO - sample_1: Mapped 3 / 50000 reads to MNELE_OGs.fa
2022-09-14 12:12:02,801 - read2tree.Mapper - INFO - sample_1: Mapping to MNELE_OGs.fa references took 3.4108190536499023.
Mapping reads to species: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5/5 [00:17<00:00, 3.40s/ species]
2022-09-14 12:12:02,834 - read2tree.Mapper - INFO - sample_1: Mapping to all references took 17.006091117858887.
Adding mapped seq to alignments: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 570653.61 alignments/s]
Adding mapped seq to OG: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 590747.04 OGs/s]
--- Add inferred mapped sequence back to OGs ---
Adding mapped seq to OG: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 122640.47 OGs/s]
2022-09-14 12:12:02,845 - read2tree.OGSet - INFO - sample_1: Appending 7 reconstructed sequences to present OG took 0.0011239051818847656.
--- Add inferred mapped sequence back to alignment ---
Adding mapped seq to alignments: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 19840.61 alignments/s]
2022-09-14 12:12:02,860 - read2tree.Aligner - INFO - sample_1: Appending 1 reconstructed sequences to present Alignments took 0.0012431144714355469.
--- Tree inference ---
2022-09-14 12:12:10,413 - read2tree.TreeInference - INFO - sample_1: Tree inference took 7.521272659301758.
(sample_1:0.0057385847,((HUMAN:0.0041201107,GORGO:0.0272788512):0.0432944811,(XENLA:0.1714987394,MNELE:0.9177713687):0.1141522197):0.0628937266,RATNO:0.0107653458);