ERROR: Raw TIR results not found in sample_ragtag.fa.mod.EDTA.raw/sample_ragtag.fa.mod.TIR.intact.raw.fa #518
Comments
|
Hello you need to reinstall EDTA. Please check other threads for solutions.
Shujun
…On Sun, Nov 10, 2024 at 10:16 AM kevin Wang ***@***.***> wrote:
Hi Ou shujun,
I come from Huazhong agriculture university in Wuhan city.
When I used the software you developed, EDTA, to annotate the transposons
in fungal genomes, I encountered problems with the results. Please help me
with some guidance. Thank you, Professor Ou.
*The log file :*
Sun Nov 10 19:51:13 CST 2024 Start to find TIR candidates.
Sun Nov 10 19:51:13 CST 2024 Identify TIR candidates from scratch.
Species: others
/usr/local/lib/python3.10/site-packages/dask/dataframe/_pyarrow_compat.py:17:
FutureWarning: Minimal version of pyarrow will soon be increased to 14.0.1
warnings.warn(
find: ./TIR-Learner-+-TIRvish.gff3: No such file or directory
Traceback (most recent call last):
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line
80, in
TIRLearner_instance = TIRLearner(genome_file, genome_name, species,
TIR_length,
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 72, in
*init*
self.execute()
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 110, in
execute
self.execute_M4()
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 634, in
execute_M4
self["base"] = CNN_predict.execute(self)
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line
108, in execute
df = predict(df, TIRLearner_instance.genome_file_path,
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line
59, in predict
model = load_model(path_to_model)
File
"/usr/local/lib/python3.10/site-packages/keras/src/saving/saving_api.py",
line 262, in load_model
return legacy_sm_saving_lib.load_model(
File
"/usr/local/lib/python3.10/site-packages/keras/src/utils/traceback_utils.py",
line 70, in error_handler
raise e.with_traceback(filtered_tb) from None
File
"/usr/local/lib/python3.10/site-packages/tensorflow/python/framework/function_def_to_graph.py",
line 278, in function_def_to_graph_def
input_shape = input_shape.as_proto()
AttributeError: as_proto
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or
directory at /usr/local/share/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list V991_ragtag.fa.mod.TIR.ext30.list is empty.
Error: Error while loading sequence
Filter sequence based on TEsorter classifications. Unclassified sequences
will also be output to the clean file.
Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv
Author: Shujun Ou ***@***.***) 10/11/2019
mv: cannot stat 'V991_ragtag.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln':
No such file or directory
cp: cannot stat
'V991_ragtag.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file
or directory
cp: cannot stat 'V991_ragtag.fa.mod.TIR.intact.raw.fa.anno.list': No such
file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or
directory.
ERROR: No such file or directory at /usr/local/share/EDTA/util/
output_by_list.pl line 39.
Warning: The TIR result file has 0 bp!
Sun Nov 10 20:02:49 CST 2024 Start to find Helitron candidates.
Sun Nov 10 20:02:49 CST 2024 Identify Helitron candidates from scratch.
Sun Nov 10 20:15:43 CST 2024 Finish finding Helitron candidates.
Sun Nov 10 20:15:43 CST 2024 Execution of EDTA_raw.pl is finished!
ERROR: Raw TIR results not found in
V991_ragtag.fa.mod.EDTA.raw/V991_ragtag.fa.mod.TIR.intact.raw.fa
If you believe the program is working properly, this may be caused by the
lack of intact TIRs in your genome. Consider to use the --force 1 parameter
to overwrite this check
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Hello Teacher Ou, I am using Singularity version 2.2.0 of the EDTA container to run it. Is it possible that the software file is incomplete? I used command: |
Please EDTA container request on be online to run ?I use school's LSF system to run it.But i use only be run offlone. |
|
Please try out the v2.2.2 release on singularity or conda. Shujun |
Hi Ou shujun,
I come from Huazhong agriculture university in Wuhan city.
When I used the software you developed, EDTA, to annotate the transposons in fungal genomes, I encountered problems with the results. Please help me with some guidance. Thank you, Professor Ou.
The log file :
Sun Nov 10 19:51:13 CST 2024 Start to find TIR candidates.
Sun Nov 10 19:51:13 CST 2024 Identify TIR candidates from scratch.
Species: others
/usr/local/lib/python3.10/site-packages/dask/dataframe/_pyarrow_compat.py:17: FutureWarning: Minimal version of pyarrow will soon be increased to 14.0.1
warnings.warn(
find: ./TIR-Learner-+-TIRvish.gff3: No such file or directory
Traceback (most recent call last):
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in
TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length,
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 72, in init
self.execute()
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 110, in execute
self.execute_M4()
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 634, in execute_M4
self["base"] = CNN_predict.execute(self)
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 108, in execute
df = predict(df, TIRLearner_instance.genome_file_path,
File "/usr/local/share/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 59, in predict
model = load_model(path_to_model)
File "/usr/local/lib/python3.10/site-packages/keras/src/saving/saving_api.py", line 262, in load_model
return legacy_sm_saving_lib.load_model(
File "/usr/local/lib/python3.10/site-packages/keras/src/utils/traceback_utils.py", line 70, in error_handler
raise e.with_traceback(filtered_tb) from None
File "/usr/local/lib/python3.10/site-packages/tensorflow/python/framework/function_def_to_graph.py", line 278, in function_def_to_graph_def
input_shape = input_shape.as_proto()
AttributeError: as_proto
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /usr/local/share/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list V991_ragtag.fa.mod.TIR.ext30.list is empty.
Error: Error while loading sequence
Filter sequence based on TEsorter classifications. Unclassified sequences will also be output to the clean file.
Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv
Author: Shujun Ou ([email protected]) 10/11/2019
mv: cannot stat 'V991_ragtag.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'V991_ragtag.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'V991_ragtag.fa.mod.TIR.intact.raw.fa.anno.list': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory.
ERROR: No such file or directory at /usr/local/share/EDTA/util/output_by_list.pl line 39.
Warning: The TIR result file has 0 bp!
Sun Nov 10 20:02:49 CST 2024 Start to find Helitron candidates.
Sun Nov 10 20:02:49 CST 2024 Identify Helitron candidates from scratch.
Sun Nov 10 20:15:43 CST 2024 Finish finding Helitron candidates.
Sun Nov 10 20:15:43 CST 2024 Execution of EDTA_raw.pl is finished!
ERROR: Raw TIR results not found in V991_ragtag.fa.mod.EDTA.raw/V991_ragtag.fa.mod.TIR.intact.raw.fa
If you believe the program is working properly, this may be caused by the lack of intact TIRs in your genome. Consider to use the --force 1 parameter to overwrite this check
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