index out range

[bioinfo-dirty-jobs]

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]

Is this a spanning deletion?

On Tue, Mar 20, 2018 at 4:38 AM, bioinfo-dirty-jobs < notifications@github.com> wrote:

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 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

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/oncotator/issues/370, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDXk9ZiO9JuD-WUjRtpJDXA_-cS9ENHks5tgMAfgaJpZM4SxfFC .

-- Lee Lichtenstein Broad Institute 75 Ames Street, Room 8011A Cambridge, MA 02142 617 714 8632

[bioinfo-dirty-jobs]

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]

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]

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']" .