broadinstitute/oncotator

index out range

Opened this issue · 4 comments

bioinfo-dirty-jobs commented

With oncotator 1.9.8 I have this error:

2018-03-20 09:37:43,124 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config).  Trying configs/ prepend.
2018-03-20 09:37:43,127 INFO [oncotator.output.TcgaMafOutputRenderer:256] TCGA MAF output file: MAF/1003.muetect2.vt.clean.tsv
2018-03-20 09:37:43,127 INFO [oncotator.output.TcgaMafOutputRenderer:257] Render starting...
2018-03-20 09:37:43,127 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config).  Trying configs/ prepend.
2018-03-20 09:37:43,129 WARNING [oncotator.input.VcfInputMutationCreator:294] Tumor-Normal VCF detected.  The Normal will assume GT= 0/0, unless GT field specified otherwise.
2018-03-20 09:37:43,352 ERROR [oncotator.output.TcgaMafOutputRenderer:333] Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 317, in renderMutations
    self._add_output_annotations(m)
  File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 241, in _add_output_annotations
    alt_count = vals[1]
IndexError: list index out of range

2018-03-20 09:37:43,352 ERROR [oncotator.output.TcgaMafOutputRenderer:334] Error at mutation 0 ['1', '985360', '985360', 'G', 'C']: 
2018-03-20 09:37:43,352 ERROR [oncotator.output.TcgaMafOutputRenderer:335] Incomplete: rendered 0 mutations.
Traceback (most recent call last):
  File "/home/maurizio/miniconda3/envs/oncotator/bin/Oncotator", line 11, in <module>
    load_entry_point('Oncotator==1.9.8.0', 'console_scripts', 'Oncotator')()
  File "build/bdist.linux-x86_64/egg/oncotator/Oncotator.py", line 311, 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
IndexError: list index out of range
LeeTL1220 commented
bioinfo-dirty-jobs commented

This s the position of error

zcat /home/maurizio/Desktop/TEST_ONCOT/CALL/1003.varscan.Somatic.vt.vcf.gz|grep 985360
chr1	985360	.	G	C	.	PASS	DP=307;SOMATIC;SS=2;SSC=255;GPV=1;SPV=0	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:197:197:0:0%:109,88,0,0	1/1:.:110:0:109:100%:0,0,63,46
vivekruhela commented

Hi,

I am facing the same issue while using oncotator to generate MAF files. I have found the same error in many patients mutect2 output file. When I googled it first time, then in GATK forum, it was suggested to use ValidateVariants before using oncotator. I also tried this and all the vcf files produced by mutect2 have passed validateVariants test. But still, I am getting the error "list index out of range". Here is the details of error message:

File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 321, in renderMutations
for m in mutations:
File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 448, in _applyManualAnnotations
for m in mutations:
File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 456, in _applyDefaultAnnotations
for m in mutations:
File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 504, in _annotate_mutations_using_datasources
for m in mutations:
File "build/bdist.linux-x86_64/egg/oncotator/input/VcfInputMutationCreator.py", line 282, in createMutations
for record in self.vcf_reader:
File "/usr/local/lib/python2.7/dist-packages/vcf/parser.py", line 572, in next
info = self._parse_info(row[7])
File "/usr/local/lib/python2.7/dist-packages/vcf/parser.py", line 396, in _parse_info
vals = entry[1].split(',')
IndexError: list index out of range

2018-07-11 22:41:41,575 ERROR [oncotator.output.TcgaMafOutputRenderer:334] Error at mutation 6923 ['1', '69872197', '69872197', 'T', 'C']:
2018-07-11 22:41:41,575 ERROR [oncotator.output.TcgaMafOutputRenderer:335] Incomplete: rendered 6923 mutations.
Traceback (most recent call last):
File "/usr/local/bin/oncotator", line 11, in
load_entry_point('Oncotator==1.9.9.0', 'console_scripts', 'oncotator')()
File "build/bdist.linux-x86_64/egg/oncotator/Oncotator.py", line 311, 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
IndexError: list index out of range

When I checked that particular line mentioned in the error [Error at mutation 6923 ['1', '69872197', '69872197', 'T', 'C']: ] , I found nothing wrong, it was transition mutation.

That line is as follows :

zcat -cd /mnt/storage/MM_Data/SM_21_WES/Variant-Calling/SM_21.mutect2.vcf.gz | grep '69872197'
chr1 69872197 rs4650000 T C . t_lod_fstar ABHet=0.00;AS_FS=0.000;AS_MQ=60.00;AS_SOR=0.693;DB;DP=2;ECNT=1;FS=0.000;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60.00;NCC=0;OND=0.00;SOR=2.303;TLOD=5.65 GT:AB:AD:AF:BCS 0/1:0.00:0,2:1.00:0,2,0,0

Can anyone suggest me how to deal with this error....Thanks.

HeXY0515 commented

You should go to check your vcf files around " ['1', '69872197', '69872197', 'T', 'C']"; Usually it's a problem caused by the variants behind the report error location, maybe it is a variant like "['1', '69872197', '69872197', 'T', 'C,G']" .