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I am using oncotator v.220.127.116.11 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 \
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==18.104.22.168', '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.