Fails on identification of TIRs about edta HOT 5 CLOSED

On Fri, Jan 24, 2020, 11:27 AM Jeff Maughan ***@***.***> wrote: Shujun, I've installed the Docker version to our HPC. EDTA progesses through the LTR finding, but then crashes when trying to identify the TIR. I'm pasting in the full slurm below. Any help would be greatly appreciated. Thanks, Jeff > ##### Shujun Ou ***@***.***) #### > ######################################################## > > > > Fri Jan 24 02:09:53 UTC 2020 Dependency checking: > All passed! > Fri Jan 24 02:10:03 UTC 2020 Obtain raw TE libraries using various structure-based programs: > Fri Jan 24 02:10:03 UTC 2020 EDTA_raw: Check files and dependencies, prepare working directories. > > Fri Jan 24 02:10:03 UTC 2020 Start to find LTR candidates. > > Fri Jan 24 02:10:03 UTC 2020 Identify LTR retrotransposon candidates from scratch. > > Warning: LOC list ordered_atriplex_hortensis_04Apr2019_hkF1T_namedcorrectly_clean_00.fasta.mod.ltrTE.veryfalse is empty. > Fri Jan 24 02:27:35 UTC 2020 Finish finding LTR candidates. > > Fri Jan 24 02:27:35 UTC 2020 Start to find TIR candidates. > > Fri Jan 24 02:27:35 UTC 2020 Identify TIR candidates from scratch. > > Species: others > 2020-01-24 02:55:41.202424: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr > Aborted (core dumped) > cat: '*-+-DTA.fa': No such file or directory > cat: '*-+-DTC.fa': No such file or directory > cat: '*-+-DTH.fa': No such file or directory > cat: '*-+-DTM.fa': No such file or directory > cat: '*-+-DTT.fa': No such file or directory > cat: '*-+-NonTIR.fa': No such file or directory > cat: '*-+-*-+-*.gff3': No such file or directory > rm: cannot remove '*-+-*-+-*.gff3': No such file or directory > Traceback (most recent call last): > File "/EDTA/bin/TIR-Learner2.4/Module3_New/CombineAll.py", line 75, in <module> > f_m3=removeDupinSingle("%s.gff3"%(genome_Name+spliter+"Module3")) > File "/EDTA/bin/TIR-Learner2.4/Module3_New/CombineAll.py", line 57, in removeDupinSingle > f=pd.read_csv(file,header=None,sep="\t") #shujun > File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 685, in parser_f > return _read(filepath_or_buffer, kwds) > File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 457, in _read > parser = TextFileReader(fp_or_buf, **kwds) > File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 895, in __init__ > self._make_engine(self.engine) > File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 1135, in _make_engine > self._engine = CParserWrapper(self.f, **self.options) > File "/opt/conda/lib/python3.6/site-packages/pandas/io/parsers.py", line 1917, in __init__ > self._reader = parsers.TextReader(src, **kwds) > File "pandas/_libs/parsers.pyx", line 545, in pandas._libs.parsers.TextReader.__cinit__ > pandas.errors.EmptyDataError: No columns to parse from file > multiprocessing.pool.RemoteTraceback: > """ > Traceback (most recent call last): > File "/opt/conda/lib/python3.6/multiprocessing/pool.py", line 119, in worker > result = (True, func(*args, **kwds)) > File "/opt/conda/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar > return list(map(*args)) > File "/EDTA/bin/TIR-Learner2.4/Module3/GetAllSeq.py", line 32, in GetListFromFile > f=open(file,"r+") > FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner_FinalAnn.gff3' > """ > > The above exception was the direct cause of the following exception: > > Traceback (most recent call last): > File "/EDTA/bin/TIR-Learner2.4/Module3/GetAllSeq.py", line 63, in <module> > pool.map(GetListFromFile,fileList) #shujun > File "/opt/conda/lib/python3.6/multiprocessing/pool.py", line 266, in map > return self._map_async(func, iterable, mapstar, chunksize).get() > File "/opt/conda/lib/python3.6/multiprocessing/pool.py", line 644, in get > raise self._value > FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner_FinalAnn.gff3' > mv: cannot stat 'TIR-Learner/*FinalAnn*.gff3': No such file or directory > mv: cannot stat 'TIR-Learner/*FinalAnn*.fa': No such file or directory > Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /EDTA/util/rename_tirlearner.pl line 18. > Warning: LOC list ordered_atriplex_hortensis_04Apr2019_hkF1T_namedcorrectly_clean_00.fasta.TIR.ext30.list is empty. > > Error: Error while loading sequenceCan't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory. > Warning: The TIR result file has 0 bp! > > Fri Jan 24 02:55:51 UTC 2020 Start to find Helitron candidates. > > Fri Jan 24 02:55:51 UTC 2020 Identify Helitron candidates from scratch. > > Fri Jan 24 03:49:16 UTC 2020 Finish finding Helitron candidates. > > Fri Jan 24 03:49:16 UTC 2020 Execution of EDTA_raw.pl is finished! > > ERROR: Raw TIR results not found in ordered_atriplex_hortensis_04Apr2019_hkF1T_namedcorrectly_clean_00.fasta.EDTA.raw/ordered_atriplex_hortensis_04Apr2019_hkF1T_namedcorrectly_clean_00.fasta.TIR.raw.fa at /EDTA/EDTA.pl line 285. > cleaning up image``` — You are receiving this because you are subscribed to this thread. 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On Fri, Jan 24, 2020, 12:11 PM Jeff Maughan ***@***.***> wrote: Thanks for the quick reply. I am just testing to make sure the install was correct - so the data set was a single chromosome, ~113Mb. I've tried the conda version, but had similar issues at the TIR stage, hence the effort to install using the docker. When I reached out to our HPC team, they said that the error was occurring within the container and that perhaps a pip install was missing in the Dockerfile or something. Any ideas? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#49?email_source=notifications&email_token=ABNX4NG7QL54EOYIZHRPRGLQ7MVMTA5CNFSM4KLJQ5D2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJ3T2PA#issuecomment-578239804>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NHQHV3E2DV3NT65AJLQ7MVMTANCNFSM4KLJQ5DQ> .