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error on conotator annotation #369

Open bioinfo-dirty-jobs opened 6 years ago

bioinfo-dirty-jobs commented 6 years ago

I try to annotate using contator:


oncotator -v --db-dir  /mnt/mpwork/database_exome_prova/oncotator_v1_ds_April052016  --input_format=VCF -o=TCGAMAF  /home/maurizio/Desktop/TEST_ONCOT/CALL/1003.muetect2.vt.clean.vcf.gz MAF/1003.muetect2.vt.clean.tsv  hg19
 oncotator --version
oncotator v1.10.0.0dev

and I have this error

es v76 | COSMIC_Tissue v76 | HumanDNARepairGenes 20110905 | Familial_Cancer_Genes 20110905 | gencode_xref_refseq metadata_v19 | HGNC Sept172014 | MutSig Published Results 20110905 | UniProt 2014_12 | TCGAScape 110405 | TUMORScape 20100104 
2018-03-15 16:10:52,901 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config).  Trying configs/ prepend.
2018-03-15 16:10:52,903 INFO [oncotator.output.TcgaMafOutputRenderer:256] TCGA MAF output file: MAF/1003.muetect2.vt.clean.tsv
2018-03-15 16:10:52,903 INFO [oncotator.output.TcgaMafOutputRenderer:257] Render starting...
2018-03-15 16:10:52,903 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config).  Trying configs/ prepend.
2018-03-15 16:10:52,906 WARNING [oncotator.input.VcfInputMutationCreator:293] Tumor-Normal VCF detected.  The Normal will assume GT= 0/0, unless GT field specified otherwise.
2018-03-15 16:10:53,118 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

2018-03-15 16:10:53,118 ERROR [oncotator.output.TcgaMafOutputRenderer:334] Error at mutation 0 ['1', '985360', '985360', 'G', 'C']: 
2018-03-15 16:10:53,118 ERROR [oncotator.output.TcgaMafOutputRenderer:335] Incomplete: rendered 0 mutations.
(oncotator) [maurizio@localhost TEST_ONCOT]$
LeeTL1220 commented 6 years ago

Can you use a released version? It seems like you are running on what is in the develop branch.

On Mon, Mar 19, 2018 at 10:49 AM, bioinfo-dirty-jobs < notifications@github.com> wrote:

I try to annotate using contator:

oncotator -v --db-dir /mnt/mpwork/database_exome_prova/oncotator_v1_ds_April052016 --input_format=VCF -o=TCGAMAF /home/maurizio/Desktop/TEST_ONCOT/CALL/1003.muetect2.vt.clean.vcf.gz MAF/1003.muetect2.vt.clean.tsv hg19 oncotator --version oncotator v1.10.0.0dev

and I have this error

es v76 | COSMIC_Tissue v76 | HumanDNARepairGenes 20110905 | Familial_Cancer_Genes 20110905 | gencode_xref_refseq metadata_v19 | HGNC Sept172014 | MutSig Published Results 20110905 | UniProt 2014_12 | TCGAScape 110405 | TUMORScape 20100104 2018-03-15 16:10:52,901 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config). Trying configs/ prepend. 2018-03-15 16:10:52,903 INFO [oncotator.output.TcgaMafOutputRenderer:256] TCGA MAF output file: MAF/1003.muetect2.vt.clean.tsv 2018-03-15 16:10:52,903 INFO [oncotator.output.TcgaMafOutputRenderer:257] Render starting... 2018-03-15 16:10:52,903 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config). Trying configs/ prepend. 2018-03-15 16:10:52,906 WARNING [oncotator.input.VcfInputMutationCreator:293] Tumor-Normal VCF detected. The Normal will assume GT= 0/0, unless GT field specified otherwise. 2018-03-15 16:10:53,118 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

2018-03-15 16:10:53,118 ERROR [oncotator.output.TcgaMafOutputRenderer:334] Error at mutation 0 ['1', '985360', '985360', 'G', 'C']: 2018-03-15 16:10:53,118 ERROR [oncotator.output.TcgaMafOutputRenderer:335] Incomplete: rendered 0 mutations. (oncotator) [maurizio@localhost TEST_ONCOT]$

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

bioinfo-dirty-jobs commented 6 years ago

Thanks so much.. I tried to use now the 1.98 But however I have this error:

2018-03-19 17:14:55,094 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config).  Trying configs/ prepend.
2018-03-19 17:14:55,097 INFO [oncotator.output.TcgaMafOutputRenderer:256] TCGA MAF output file: MAF/452.muetect2.vt.clean.tsv
2018-03-19 17:14:55,097 INFO [oncotator.output.TcgaMafOutputRenderer:257] Render starting...
2018-03-19 17:14:55,097 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config).  Trying configs/ prepend.
2018-03-19 17:14:58,227 WARNING [oncotator.output.TcgaMafOutputRenderer:219] Entrez Gene ID was zero, but Hugo Symbol was not Unknown.  Is the HGNC and/or Transcript datasource complete?
LeeTL1220 commented 6 years ago

Unfortunately, this cannot be fixed without creating a new datasource. Is Entrez Gene ID important for your work?

On Mon, Mar 19, 2018 at 12:15 PM, bioinfo-dirty-jobs < notifications@github.com> wrote:

Thanks so much.. I tried to use now the 1.98 But however I have this error:

2018-03-19 17:14:55,094 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config). Trying configs/ prepend. 2018-03-19 17:14:55,097 INFO [oncotator.output.TcgaMafOutputRenderer:256] TCGA MAF output file: MAF/452.muetect2.vt.clean.tsv 2018-03-19 17:14:55,097 INFO [oncotator.output.TcgaMafOutputRenderer:257] Render starting... 2018-03-19 17:14:55,097 INFO [oncotator.utils.ConfigUtils:197] Could not find config file (vcf.in.config). Trying configs/ prepend. 2018-03-19 17:14:58,227 WARNING [oncotator.output.TcgaMafOutputRenderer:219] Entrez Gene ID was zero, but Hugo Symbol was not Unknown. Is the HGNC and/or Transcript datasource complete?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/oncotator/issues/369#issuecomment-374270539, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDXkzfvnyZ55Y1fQVnx24YA8NJI10H1ks5tf9m_gaJpZM4SwTQ5 .

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

bioinfo-dirty-jobs commented 6 years ago

At the moment I only want to prepare maf file like TCGA.. for comparison reason.. What do you suggest? Thanks for your help

LeeTL1220 commented 6 years ago

I suggest ignoring the warning.

On Mon, Mar 19, 2018 at 12:22 PM, bioinfo-dirty-jobs < notifications@github.com> wrote:

At the moment I only want to prepare maf file like TCGA.. for comparison reason.. What do you suggest? Thanks for your help

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/oncotator/issues/369#issuecomment-374272987, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDXkyX7KKbD_DBen1Z2K3PhQlq33LROks5tf9tbgaJpZM4SwTQ5 .

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

adammaikai commented 6 years ago

Is there a way to ignore errors and force skipoing of mutations that cause errors?

LeeTL1220 commented 6 years ago

Unfortunately, not....

On Fri, Jun 22, 2018 at 1:35 PM, adammaikai notifications@github.com wrote:

Is there a way to ignore errors and force skipoing of mutations that cause errors?

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