oushujun
commented
2 weeks ago 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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wangguiqian
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 (shujun.ou.1@gmail.com) 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