uninitialized value while using dbNSFP #241
Comments
|
Hi Damian,
Thanks for this report, I’ll look into it. Could you please send me the full input command and a copy of your input data so that I can try to reproduce the issue?
Thanks,
Andrew
… On 16 Jul 2018, at 11:29, Damian ***@***.***> wrote:
Hi, when using all dbNSFP3.5 plugin (VEP92) such messages appears:
2018-07-16 10:10:41 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this
Use of uninitialized value in concatenation (.) or string at /opt/vep/.vep/Plugins/dbNSFP.pm line 227.
Use of uninitialized value in concatenation (.) or string at /opt/vep/.vep/Plugins/dbNSFP.pm line 227.
Use of uninitialized value in concatenation (.) or string at /opt/vep/.vep/Plugins/dbNSFP.pm line 227.
Use of uninitialized value in concatenation (.) or string at /opt/vep/.vep/Plugins/dbNSFP.pm line 227.
Use of uninitialized value in concatenation (.) or string at /opt/vep/.vep/Plugins/dbNSFP.pm line 227.
Probably it's not a big deal. It's hard to localize corresponding, problematic columns.
I run such command:
vep (...) --plugin dbNSFP,/home/vep/DATA/dbNSFPv35a/hg19_dbNSFP3.5a_all_noMT.gz,ref,alt,aaref,aaalt,genename,cds_strand,refcodon,codonpos,codon_degeneracy,Ancestral_allele,AltaiNeandertal,Denisova,Ensembl_geneid,Ensembl_transcriptid,Ensembl_proteinid,aapos,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Uniprot_acc_Polyphen2,Uniprot_id_Polyphen2,Uniprot_aapos_Polyphen2,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,LRT_score,LRT_converted_rankscore,LRT_pred,LRT_Omega,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,MutationTaster_model,MutationTaster_AAE,MutationAssessor_UniprotID,MutationAssessor_variant,MutationAssessor_score,MutationAssessor_score_rankscore,MutationAssessor_pred,FATHMM_score,FATHMM_converted_rankscore,FATHMM_pred,PROVEAN_score,PROVEAN_converted_rankscore,PROVEAN_pred,Transcript_id_VEST3,Transcript_var_VEST3,VEST3_score,VEST3_rankscore,MetaSVM_score,MetaSVM_rankscore,MetaSVM_pred,MetaLR_score,MetaLR_rankscore,MetaLR_pred,Reliability_index,M-CAP_score,M-CAP_rankscore,M-CAP_pred,REVEL_score,REVEL_rankscore,MutPred_score,MutPred_rankscore,MutPred_protID,MutPred_AAchange,MutPred_Top5features,CADD_raw,CADD_raw_rankscore,CADD_phred,DANN_score,DANN_rankscore,fathmm-MKL_coding_score,fathmm-MKL_coding_rankscore,fathmm-MKL_coding_pred,fathmm-MKL_coding_group,Eigen_coding_or_noncoding,Eigen-raw,Eigen-phred,Eigen-PC-raw,Eigen-PC-phred,Eigen-PC-raw_rankscore,GenoCanyon_score,GenoCanyon_score_rankscore,integrated_fitCons_score,integrated_fitCons_score_rankscore,integrated_confidence_value,GM12878_fitCons_score,GM12878_fitCons_score_rankscore,GM12878_confidence_value,H1-hESC_fitCons_score,H1-hESC_fitCons_score_rankscore,H1-hESC_confidence_value,HUVEC_fitCons_score,HUVEC_fitCons_score_rankscore,HUVEC_confidence_value,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phyloP20way_mammalian,phyloP20way_mammalian_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,phastCons20way_mammalian,phastCons20way_mammalian_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,TWINSUK_AC,TWINSUK_AF,ALSPAC_AC,ALSPAC_AF,clinvar_rs,clinvar_clnsig,clinvar_trait,clinvar_golden_stars,Interpro_domain,GTEx_V6p_gene,GTEx_V6p_tissue --no_stats --fork 50
Cheers
DL
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub <#241>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AfvjN8NauW-lS4K5bzTf8mTvBifP4ctJks5uHGsZgaJpZM4VQ5OQ>.
|
|
here it is ;) command: Cheers |
|
Hi Damian,
Thank you for this. The plugin was having issues in finding the correct header description to use and returning those error messages when particular columns were asked for. I’m currently in the process of writing a fix, and I’ll update this issue when finished.
Fortunately, this error message is purely cosmetic and won’t change any of the output data you’re getting, so you can carry on as normal.
If there’s anything else we can do to help, please don’t hesitate to ask.
Kind Regards,
Andrew
… On 16 Jul 2018, at 11:39, Damian ***@***.***> wrote:
here it is ;)
##fileformat=VCFv4.2
##FILTER=<ID=medgen,Description="DP>4">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##reference=file:///refs/hs37d5_noHap.fa
##source=HaplotypeCaller
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XXXX
1 3334515 1_3334515_C_A C A . . . GT 0/1
1 3334515 1_3334515_C_G C G . . . GT 0/1
1 3334515 1_3334515_C_T C T . . . GT 0/1
1 3334520 1_3334520_C_T C T . . . GT 0/1
1 3334555 1_3334555_C_T C T . . . GT 0/1
1 3334555 1_3334555_C_A C A . . . GT 0/1
1 3334556 1_3334556_G_A G A . . . GT 0/1
1 3334570 1_3334570_C_G C G . . . GT 0/1
command:
vep -i input.vcf --cache --refseq -o test._out_.tsv --port 3337 --tab --exclude_predicted --ASSEMBLY GRCh37 --shift_hgvs 1 --sift b --polyphen b --humdiv --ccds --uniprot --symbol --numbers --domains --regulatory --canonical --protein --biotype --gene_phenotype --af --af_1kg --af_esp --af_gnomad --max_af --pubmed --variant_class -custom /home/vep/DATA/gnomAD/gnomad.exomes.r2.0.1.sites.noVEP.vcf.gz,gnomADe,vcf,exact,0,AF_NFE,POPMAX,AF -custom /home/vep/DATA/gnomAD/gnomad.genomes.r2.0.1.sites.noVEP.vcf.gz,gnomADg,vcf,exact,0,AF_NFE,POPMAX,AF --use_transcript_ref --hgvs --hgvsg --no_escape --fasta /home/vep/refs/hs37d5.fa --plugin dbscSNV,/home/vep/DATA/dbscSNP/dbscSNV1.1_GRCh37.txt.gz --plugin SpliceRegion --plugin MaxEntScan,/home/vep/DATA/MaxEntScan --plugin GeneSplicer,/home/vep/DATA/GeneSplicer/sources/genesplicer,/home/vep/DATA/GeneSplicer/human --plugin ExACpLI,/home/vep/DATA/ExACpLI/ExACpLI_values.txt --plugin REVEL,/home/vep/DATA/revel/revel_all_chromosomes.csv --plugin LoFtool,/home/vep/DATA/LoFtool/LoFtool_scores.txt --plugin Phenotypes --plugin G2P,file=/home/vep/DATA/G2P/DDG2P.csv.gz --format "vcf" --plugin dbNSFP,/home/vep/DATA/dbNSFPv35a/hg19_dbNSFP3.5a_all_noMT.gz,ref,alt,aaref,aaalt,genename,cds_strand,refcodon,codonpos,codon_degeneracy,Ancestral_allele,AltaiNeandertal,Denisova,Ensembl_geneid,Ensembl_transcriptid,Ensembl_proteinid,aapos,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Uniprot_acc_Polyphen2,Uniprot_id_Polyphen2,Uniprot_aapos_Polyphen2,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,LRT_score,LRT_converted_rankscore,LRT_pred,LRT_Omega,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,MutationTaster_model,MutationTaster_AAE,MutationAssessor_UniprotID,MutationAssessor_variant,MutationAssessor_score,MutationAssessor_score_rankscore,MutationAssessor_pred,FATHMM_score,FATHMM_converted_rankscore,FATHMM_pred,PROVEAN_score,PROVEAN_converted_rankscore,PROVEAN_pred,Transcript_id_VEST3,Transcript_var_VEST3,VEST3_score,VEST3_rankscore,MetaSVM_score,MetaSVM_rankscore,MetaSVM_pred,MetaLR_score,MetaLR_rankscore,MetaLR_pred,Reliability_index,M-CAP_score,M-CAP_rankscore,M-CAP_pred,REVEL_score,REVEL_rankscore,MutPred_score,MutPred_rankscore,MutPred_protID,MutPred_AAchange,MutPred_Top5features,CADD_raw,CADD_raw_rankscore,CADD_phred,DANN_score,DANN_rankscore,fathmm-MKL_coding_score,fathmm-MKL_coding_rankscore,fathmm-MKL_coding_pred,fathmm-MKL_coding_group,Eigen_coding_or_noncoding,Eigen-raw,Eigen-phred,Eigen-PC-raw,Eigen-PC-phred,Eigen-PC-raw_rankscore,GenoCanyon_score,GenoCanyon_score_rankscore,integrated_fitCons_score,integrated_fitCons_score_rankscore,integrated_confidence_value,GM12878_fitCons_score,GM12878_fitCons_score_rankscore,GM12878_confidence_value,H1-hESC_fitCons_score,H1-hESC_fitCons_score_rankscore,H1-hESC_confidence_value,HUVEC_fitCons_score,HUVEC_fitCons_score_rankscore,HUVEC_confidence_value,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phyloP20way_mammalian,phyloP20way_mammalian_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,phastCons20way_mammalian,phastCons20way_mammalian_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,TWINSUK_AC,TWINSUK_AF,ALSPAC_AC,ALSPAC_AF,clinvar_rs,clinvar_clnsig,clinvar_trait,clinvar_golden_stars,Interpro_domain,GTEx_V6p_gene,GTEx_V6p_tissue --no_stats --fork 50
Cheers
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub <#241 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AfvjN5oCkKRHZUJpmIWNhrGzYP8a0P3Fks5uHG1SgaJpZM4VQ5OQ>.
|
|
Hi, still it doesn't work. Additionally again there's G2P error. Cheers |
|
Hiya, A fix has now gone in for this issue, if you update the dbNSFP.pm file now then it should resolve this issue. Kind Regards, |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hi, VEP92, when using dbNSFP3.5a plugin with all columns such messages appears:
Probably it's not a big deal, but it's hard to localize corresponding, problematic columns, to really see if this warning affects the output.
I run such command:
vep (...) --plugin dbNSFP,/home/vep/DATA/dbNSFPv35a/hg19_dbNSFP3.5a_all_noMT.gz,ref,alt,aaref,aaalt,genename,cds_strand,refcodon,codonpos,codon_degeneracy,Ancestral_allele,AltaiNeandertal,Denisova,Ensembl_geneid,Ensembl_transcriptid,Ensembl_proteinid,aapos,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Uniprot_acc_Polyphen2,Uniprot_id_Polyphen2,Uniprot_aapos_Polyphen2,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,LRT_score,LRT_converted_rankscore,LRT_pred,LRT_Omega,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,MutationTaster_model,MutationTaster_AAE,MutationAssessor_UniprotID,MutationAssessor_variant,MutationAssessor_score,MutationAssessor_score_rankscore,MutationAssessor_pred,FATHMM_score,FATHMM_converted_rankscore,FATHMM_pred,PROVEAN_score,PROVEAN_converted_rankscore,PROVEAN_pred,Transcript_id_VEST3,Transcript_var_VEST3,VEST3_score,VEST3_rankscore,MetaSVM_score,MetaSVM_rankscore,MetaSVM_pred,MetaLR_score,MetaLR_rankscore,MetaLR_pred,Reliability_index,M-CAP_score,M-CAP_rankscore,M-CAP_pred,REVEL_score,REVEL_rankscore,MutPred_score,MutPred_rankscore,MutPred_protID,MutPred_AAchange,MutPred_Top5features,CADD_raw,CADD_raw_rankscore,CADD_phred,DANN_score,DANN_rankscore,fathmm-MKL_coding_score,fathmm-MKL_coding_rankscore,fathmm-MKL_coding_pred,fathmm-MKL_coding_group,Eigen_coding_or_noncoding,Eigen-raw,Eigen-phred,Eigen-PC-raw,Eigen-PC-phred,Eigen-PC-raw_rankscore,GenoCanyon_score,GenoCanyon_score_rankscore,integrated_fitCons_score,integrated_fitCons_score_rankscore,integrated_confidence_value,GM12878_fitCons_score,GM12878_fitCons_score_rankscore,GM12878_confidence_value,H1-hESC_fitCons_score,H1-hESC_fitCons_score_rankscore,H1-hESC_confidence_value,HUVEC_fitCons_score,HUVEC_fitCons_score_rankscore,HUVEC_confidence_value,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phyloP20way_mammalian,phyloP20way_mammalian_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,phastCons20way_mammalian,phastCons20way_mammalian_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,TWINSUK_AC,TWINSUK_AF,ALSPAC_AC,ALSPAC_AF,clinvar_rs,clinvar_clnsig,clinvar_trait,clinvar_golden_stars,Interpro_domain,GTEx_V6p_gene,GTEx_V6p_tissue --no_stats --fork 50Cheers
DL
The text was updated successfully, but these errors were encountered: