Question: pVAC-Seq (personalized Variant Antigens by Cancer Sequencing) with qsub
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gravatar for soribaby88
9 days ago by
soribaby880
soribaby880 wrote:

Hi. I'm trying to do a job with pVAC-seq. But, a error occured and I don't understand the error message.

My command

/opt/sge/bin/lx-amd64/qsub  /src/qsub.8 
/data/D161740/Research/DongJin/01.programs/Python-3.5.6/python \
/data/D161740/.local/lib/python3.5/site-packages/pvacseq/pvacseq.py run \
--iedb-install-directory /data/D161740/Research/DongJin/01.programs/pVACseq \
/data/D161740/Research/DongJin/02.CCA/pVACseq_01.input_vcf/somatic/10T.somatic.vcf \
temp_10T \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
NetMHC NetMHCIIpan \
/data/D161740/Research/DongJin/02.CCA/pVACseq_04.results/temp_10T \
-e 9

And the error message like

Executing MHC Class I predictions
Converting VCF to TSV
Completed
Splitting TSV into smaller chunks
Splitting TSV into smaller chunks - Entries 1-100
Splitting TSV into smaller chunks - Entries 101-200
Splitting TSV into smaller chunks - Entries 201-300
Splitting TSV into smaller chunks - Entries 301-354
Completed
Generating Variant Peptide FASTA and Key Files
Generating Variant Peptide FASTA and Key Files - Entries 1-200
Generating Variant Peptide FASTA and Key Files - Entries 201-400
Generating Variant Peptide FASTA and Key Files - Entries 401-600
Generating Variant Peptide FASTA and Key Files - Entries 601-708
Completed
Processing entries for Allele HLA-A*02:01 and Epitope Length 9 - Entries 1-200
Running IEDB on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - Entries 1-200
Traceback (most recent call last):
  File "/data/D161740/Research/DongJin/01.programs/pVACseq/mhc_i/src/predict_binding.py", line 12, in <module>
    from seqpredictor import MHCBindingPredictions
  File "/data/D161740/Research/DongJin/01.programs/pVACseq/mhc_i/src/seqpredictor.py", line 10, in <module>
    from netmhcpan_4_0_executable import predict_many as predict_netmhcpan
  File "/data/D161740/Research/DongJin/01.programs/pVACseq/mhc_i/src/../method/netmhcpan-4.0-executable/netmhcpan_4_0_executable/__init__.py", line 7, in <module>
    import pkg_resources
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 2897, in <module>
    add_activation_listener(lambda dist: dist.activate())
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 712, in subscribe
    callback(dist)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 2897, in <lambda>
    add_activation_listener(lambda dist: dist.activate())
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 2329, in activate
    self.insert_on(path)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 2436, in insert_on
    self.check_version_conflict()
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 2475, in check_version_conflict
    for modname in self._get_metadata('top_level.txt'):
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 2323, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 1246, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 1238, in get_metadata
    return self._get(self._fn(self.egg_info,name))
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py", line 1353, in _get
    stream = open(path, 'rb')
IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/RSeQC-2.4-py2.7-linux-x86_64.egg/EGG-INFO/top_level.txt'
Traceback (most recent call last):
  File "/data/D161740/.local/lib/python3.5/site-packages/pvacseq/pvacseq.py", line 92, in <module>
    main()
  File "/data/D161740/.local/lib/python3.5/site-packages/pvacseq/pvacseq.py", line 84, in main
    args[0].func.main(args[1])
  File "/data/D161740/.local/lib/python3.5/site-packages/pvacseq/lib/main.py", line 291, in main
    pipeline.execute()
  File "/data/D161740/.local/lib/python3.5/site-packages/pvacseq/lib/pipeline.py", line 300, in execute
    split_parsed_output_files = self.call_iedb_and_parse_outputs(chunks)
  File "/data/D161740/.local/lib/python3.5/site-packages/pvacseq/lib/pipeline.py", line 422, in call_iedb_and_parse_outputs
    '-e', self.iedb_executable,
  File "/data/D161740/.local/lib/python3.5/site-packages/pvacseq/lib/call_iedb.py", line 60, in main
    response = run(prediction_class_object.iedb_executable_params(args), stdout=PIPE, check=True)
  File "/data/D161740/Research/DongJin/01.programs/Python-3.5.6/Lib/subprocess.py", line 398, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['python2.7', '/data/D161740/Research/DongJin/01.programs/pVACseq/mhc_i/src/predict_binding.py', 'ann', 'HLA-A*02:01', '9', '/data/D161740/Research/DongJin/02.CCA/pVACseq_04.results/temp_10T/MHC_Class_I/tmp/temp_10T_21.fa.split_1-200']' returned non-zero exit status 1

However, when I don't use qsub I get a correct results.

/data/D161740/Research/DongJin/01.programs/Python-3.5.6/python \
/data/D161740/.local/lib/python3.5/site-packages/pvacseq/pvacseq.py run \
--iedb-install-directory /data/D161740/Research/DongJin/01.programs/pVACseq \
/data/D161740/Research/DongJin/02.CCA/pVACseq_01.input_vcf/somatic/10T.somatic.vcf \
temp_10T \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
NetMHC NetMHCIIpan \
/data/D161740/Research/DongJin/02.CCA/pVACseq_04.results/temp_10T \
-e 9

Also, the server I used don't have "distribute-0.6.49-py2.7.egg" directory in "/usr/local/lib/python2.7/site-packages/". Is there someone have a clue about this error?

software error • 74 views
ADD COMMENTlink written 9 days ago by soribaby880
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