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Oncotator error message

asoskinsasoskins Imperial College, Lonfon, UKMember

Hello, I've installed oncotator/1.5.1.0 and try to run it with python/2.7.3 on my vcf files with the following command line:

oncotator -i VCF --db-dir ./oncotator_db -o VCF mutect.vcf annotated.vcf hg19

Here are the first few lines from my input vcf:
1 75960 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:35,1:.:17:0.028:0 0/1:39,4:32:43:0.093:2
1 84492 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:33,0:.:30:0.00:0 0/1:73,4:34:77:0.052:2
1 136787 rs371257153 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:19,0:.:13:0.00:0 0/1:41,6:28:47:0.128:2
1 144527 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:15,0:.:9:0.00:0 0/1:15,5:29:20:0.250:2
1 234575 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:32,0:.:26:0.00:0 0/1:84,5:33:89:0.056:2

I get the following error message:
2015-05-05 17:28:25,452 INFO [oncotator.output.OutputDataManager:146] Creating intermediate tsv file...
2015-05-05 17:28:27,928 INFO [oncotator.output.VcfOutputRenderer:136] Render starting...
2015-05-05 17:28:27,939 ERROR [oncotator.output.VcfOutputRenderer:222] Traceback (most recent call last):
File "/apps/python/2.7.3/lib/python2.7/site-packages/Oncotator-v1.2.7.0-py2.7.egg/oncotator/output/VcfOutputRenderer.py", line 214, in _renderSortedTsv
recordBuilder = self._parseRecordBuilder(m, recordBuilder, dataManager, inferGenotypes)
File "/apps/python/2.7.3/lib/python2.7/site-packages/Oncotator-v1.2.7.0-py2.7.egg/oncotator/output/VcfOutputRenderer.py", line 276, in _parseRecordBuilder
recordBuilder.addInfo(sampleName, ID, num, dataType, val, isSplit)
File "/apps/python/2.7.3/lib/python2.7/site-packages/Oncotator-v1.2.7.0-py2.7.egg/oncotator/output/RecordBuilder.py", line 291, in addInfo
val = self._map(MutUtils.str2bool, self._fixVal(val, isSplit)) # convert the value to boolean
File "/apps/python/2.7.3/lib/python2.7/site-packages/Oncotator-v1.2.7.0-py2.7.egg/oncotator/output/RecordBuilder.py", line 97, in _map
return [func(v) if v not in bad else None for v in iterable]
File "/apps/python/2.7.3/lib/python2.7/site-packages/Oncotator-v1.2.7.0-py2.7.egg/oncotator/utils/MutUtils.py", line 222, in str2bool
return v.lower() in ("yes", "true", "t", "1", "y")
AttributeError: 'NoneType' object has no attribute 'lower'

2015-05-05 17:28:27,939 ERROR [oncotator.output.VcfOutputRenderer:223] Error at mutation 1 ['1', '75960', '75960']:
2015-05-05 17:28:27,939 INFO [oncotator.output.VcfOutputRenderer:225] Rendered all 0 vcf records.
2015-05-05 17:28:27,939 INFO [oncotator.output.VcfOutputRenderer:146] Rendered all mutations.

Can you please help with this issue?
Thanks in advance,
Alona

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Answers

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

    I realize this response is very late. However, the version of Oncotator does not seem to be v1.5.1, but rather v1.2.7. I would upgrade to whatever is most recent and I'll bet this error will be gone. If not, please check the input VCF and post again.

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