[ensembl-dev] VEP command line error using dbNSFP on GRCH37

Matteo matteodeg at gmail.com
Fri Feb 26 09:45:09 GMT 2016


Hi all,

I'm using vep tool to annotate variants and this is my command line:

perl variant_effect_predictor.pl -i ~/path/to/my.vcf -o ~/path/to/my.vcf 
--cache --vcf --assembly GRCh37 --offline --force_overwrite -v 
--variant_class --tsl --sift b --poly b --vcf_info_field ANN --hgvs 
--protein --canonical --check_existing --gmaf --pubmed --biotype 
--gene_phenotype --plugin 
dbNSFP,/path/to/ensembl-tools-release-83/dbNSFP.gz,LRT_score,LRT_pred,MutationTaster_score,MutationTaster_pred,FATHMM_score,FATHMM_pred,PROVEAN_score,PROVEAN_pred,MetaSVM_score,MetaSVM_pred,MetaLR_score, 
MetaLR_pred,clinvar_rs,clinvar_clnsig

My vep release is the last one (83) and I'm using GRCH37 but i get the 
following error from dbNSFP:

Use of uninitialized value $2 in concatenation (.) or string at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 3.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 3.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 4.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 5.
Use of uninitialized value $2 in concatenation (.) or string at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 6.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 6.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 7.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 8.
Use of uninitialized value $2 in concatenation (.) or string at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 9.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 9.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 10.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 11.
Use of uninitialized value $2 in concatenation (.) or string at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 12.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 12.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 13.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 14.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 15.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 16.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 17.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 18.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 19.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 20.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 21.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 22.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 23.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 24.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 25.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 26.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 27.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 28.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 29.
Use of uninitialized value $2 in concatenation (.) or string at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 30.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 30.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 31.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 32.
Use of uninitialized value $2 in concatenation (.) or string at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 33.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 189, <RM> line 33.
Use of uninitialized value $col in hash element at 
/home/matteo/.vep/Plugins/dbNSFP.pm line 193, <RM> line 34.
.
.
.
  and so on

In my output file, some variants have been annotated only with clinvar. 
Do you have any idea?
Thank you in advice for your help,

Matteo




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