8000 build without D causes IgBlast to crash · Issue #31 · Teichlab/bracer · GitHub
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build without D causes IgBlast to crash #31

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scharch opened this issue Jan 7, 2019 · 4 comments
Open

build without D causes IgBlast to crash #31

scharch opened this issue Jan 7, 2019 · 4 comments

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@scharch
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scharch commented Jan 7, 2019

The documentation for build indicates that D_seqs is an optional argument. However, if it is omitted, bracer assemble submits an invalid command to IgBlast that causes a crash:

Traceback (most recent call last):
  File "/nethome/schrammca/bin/bracer", line 11, in <module>
    load_entry_point('bracer==0.1', 'console_scripts', 'bracer')()
  File "/nethome/schrammca/.local/lib/python3.5/site-packages/bracer-0.1-py3.5.egg/bracerlib/launcher.py", line 43, in launch
    Task().run()
  File "/nethome/schrammca/.local/lib/python3.5/site-packages/bracer-0.1-py3.5.egg/bracerlib/tasks.py", line 366, in run
    cell = self.ig_blast()
  File "/nethome/schrammca/.local/lib/python3.5/site-packages/bracer-0.1-py3.5.egg/bracerlib/tasks.py", line 518, in ig_blast
    self.assembled_file)
  File "/nethome/schrammca/.local/lib/python3.5/site-packages/bracer-0.1-py3.5.egg/bracerlib/bracer_func.py", line 1889, in run_IgBlast
    subprocess.check_call(command, stdout=out, stderr=DEVNULL)
  File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/2016-Q3-Python-3.5/lib/python3.5/subprocess.py", line 581, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/nethome/schrammca/bin/igblastn', '-germline_db_V', '/nethome/schrammca/bracer/resources/Hpseud/igblast_dbs/BCR_V.fa', '-germline_db_J', '/nethome/schrammca/bracer/resources/Hpseud/igblast_dbs/BCR_J.fa', '-germline_db_D', '/nethome/schrammca/bracer/resources/Hpseud/igblast_dbs/BCR_D.fa', '-domain_system', 'imgt', '-organism', 'mouse', '-ig_seqtype', 'Ig', '-show_translation', '-num_alignments_V', '20', '-num_alignments_D', '3', '-num_alignments_J', '5', '-outfmt', '7', '-query', '/hpcdata/vrc/vrc1_data/douek_lab/projects/BCRSeq/2019201_pseudogenes/bracer/05/VRC315.05.07_1.F08/Trinity_output/VRC315.05.07_1.F08_BCR_H.Trinity.fasta']' returned non-zero exit status 2

because /nethome/schrammca/bracer/resources/Hpseud/igblast_dbs/BCR_D.fa is empty and there is no associated blastdb.
@scharch
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scharch commented Jan 7, 2019

Related: --V_gapped is also documented as optional, but bracer assemble doesn't test for the absence of the gapped files and so this also causes a crash.

@scharch scharch mentioned this issue Jan 11, 2019
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@idalind
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idalind commented Jan 13, 2019

Hi @scharch ,
Thanks for your feedback. I will look into this issue in the coming days. Did you try creating resources for heavy chain without D sequences, or was it light chain?

@scharch
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scharch commented Jan 14, 2019

I ran bracer build for all 3 loci before attempting bracer assemble.

@idalind
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idalind commented Jan 28, 2019

I see now that the documentation for build was too vague. What I meant was that D sequences were optional in the sense that they are not needed for light chains. However, they are needed for heavy chains. I will update the documentation accordingly. I will also look into the crash caused by absence of V_gapped sequences.

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