CongLiu37
commented
3 months ago For a third genome, I got an error which looks like insufficient memory:
Thu 21 Mar 01:29:07 JST 2024 EDTA_raw: Check dependencies, prepare working directories.
Thu 21 Mar 01:29:11 JST 2024 Start to find TIR candidates.
Thu 21 Mar 01:29:11 JST 2024 Identify TIR candidates from scratch.
Species: others
Traceback (most recent call last):
File "/bucket/.mabuya/BourguignonU/Cong/Softwares/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in <module>
TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length,
File "/bucket/.mabuya/BourguignonU/Cong/Softwares/EDTA/bin/TIR-Learner3.0/bin/main.py", line 72, in __init__
self.execute()
File "/bucket/.mabuya/BourguignonU/Cong/Softwares/EDTA/bin/TIR-Learner3.0/bin/main.py", line 110, in execute
self.execute_M4()
File "/bucket/.mabuya/BourguignonU/Cong/Softwares/EDTA/bin/TIR-Learner3.0/bin/main.py", line 634, in execute_M4
self["base"] = CNN_predict.execute(self)
File "/bucket/.mabuya/BourguignonU/Cong/Softwares/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 108, in execute
df = predict(df, TIRLearner_instance.genome_file_path,
File "/bucket/.mabuya/BourguignonU/Cong/Softwares/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 75, in predict
pre_feature_tensor = tf.convert_to_tensor(np.stack(pre_feature), np.float32)
File "/bucket/BourguignonU/Cong/Softwares/mamba/lib/python3.10/site-packages/numpy/core/shape_base.py", line 456, in stack
return _nx.concatenate(expanded_arrays, axis=axis, out=out,
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 215. GiB for an array with shape (28869774, 400, 5) and data type float32
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /bucket/.mabuya/BourguignonU/Cong/Softwares/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list Lunk.genome.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 'Lunk.genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'Lunk.genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'Lunk.genome.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.
Warning: The TIR result file has 0 bp!
Fri 22 Mar 12:25:43 JST 2024 Execution of EDTA_raw.pl is finished!However, I have already reached the memory limit of HPC. Do you think reducing some threads is helpful?
Sincerely,
Cong
Hello,
I am running EDTA_raw.pl for TIR identification. The comand looks like this:
I have two genomes of same genus giving error:
The error from another genome:
Does it mean that TIR-learner just failed to find any TIR in the genomes, or there is something wrong in EDTA (say, memory, parameters etc.)?
Sincerely,
Cong