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Oncotator Errno28

mfjonesmfjones ChicagoMember

I am using oncotator v.1.9.2.0 to annotate a VCF with whole-genome variants from 8 samples. This is the command I am using:
oncotator -v -i VCF --skip-no-alt --db-dir $DIR/oncotator_v1_ds_Jan262015 $DIR/VQSR/recalibrated_variants.vcf \
oncotated_variants.tsv hg19
Where $DIR is my project directory.

Oncotator runs happily for about an hour, but then throws this error:

2017-05-26 15:36:32,355 INFO [oncotator.output.TcgaMafOutputRenderer:330] Rendered 4368000 mutations.
2017-05-26 15:36:33,161 INFO [oncotator.output.TcgaMafOutputRenderer:330] Rendered 4369000 mutations.
2017-05-26 15:36:33,959 INFO [oncotator.output.TcgaMafOutputRenderer:330] Rendered 4370000 mutations.
2017-05-26 15:36:34,656 ERROR [oncotator.output.TcgaMafOutputRenderer:333] Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 325, in renderMutations
    self._writeMutationRow(dw, field_map, field_map_keys, m)
  File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 231, in _writeMutationRow
    dw.writerow(row)
  File "/apps/software/gcc-4.9.4/python/2.7.6/lib/python2.7/csv.py", line 148, in writerow
    return self.writer.writerow(self._dict_to_list(rowdict))
IOError: [Errno 28] No space left on device

2017-05-26 15:36:34,656 ERROR [oncotator.output.TcgaMafOutputRenderer:334] Error at mutation 4370819 ['12', '46405050', '46405050', 'C', 'T']:
2017-05-26 15:36:34,656 ERROR [oncotator.output.TcgaMafOutputRenderer:335] Incomplete: rendered 4370819 mutations.
Traceback (most recent call last):
  File "/home/michaeldrazer/godley-lab/CHEK2/CHEK2_WGS/venv/bin/oncotator", line 11, in <module>
    load_entry_point('Oncotator==1.9.1.0', 'console_scripts', 'oncotator')()
  File "build/bdist.linux-x86_64/egg/oncotator/Oncotator.py", line 309, in main
  File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 437, in annotate
  File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 337, in renderMutations
IOError: [Errno 28] No space left on device

I have over 5TB of storage available, so I know it's not a lack of hard drive space. I have tried running with 1TB of memory, so it's probably not a RAM shortage. I think the oncotator python scripts might be writing to a relatively small tmp root partition, but I'm not sure how to check that or change it if that is the case. This is being done on a computing cluster to which I do not have root priveleges. Thanks in advance for any advice you can offer.

Issue · Github
by Sheila

Issue Number
2125
State
closed
Last Updated
Assignee
Array
Closed By
chandrans

Comments

  • SheilaSheila Broad InstituteMember, Broadie admin

    @mfjones
    Hi,

    I have asked one of the developers to respond. He should get back to you soon.

    -Sheila

  • mfjonesmfjones ChicagoMember

    Hello, have you guys made any progress on this?
    Thanks!

  • SheilaSheila Broad InstituteMember, Broadie admin

    @mfjones
    Hi,

    Sorry for the delay. I just pinged the developer. He should get back to you asap, but please post again if you do not get a response within the next few days.

    -Sheila

  • mfjonesmfjones ChicagoMember

    Checking in again. Any word from the developer?
    Thanks

  • SheilaSheila Broad InstituteMember, Broadie admin

    @mfjones
    Hi,

    Sorry for the delay. I just pinged him again. I will ask someone else as well.

    -Sheila

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

    @mfjones Sorry for the late reply... Ideas:

    • If I'm reading your command line properly, your output file is not going to $DIR. Does this matter?
    • Oncotator is writing a fairly large intermediate temp file. Perhaps the temp dir is mounted on a different file system that is smaller? In unix, you can change your temp file location by setting an environment variable (`TMPDIR``) to the desired location. If you set that to a filesystem with more space, this should work.
    • There is a small possibility that Oncotator is writing the big temp file to the local directory. You should see that if it is the case. I would consider that a bug, but in the meantime, it would be easy to work around.
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