<div dir="ltr">OK, good to know.<div><br>I wonder if there's some way of checking the integrity of the index...</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 5 February 2014 16:28, David Blaney <span dir="ltr"><<a href="mailto:David.Blaney@ogt.com" target="_blank">David.Blaney@ogt.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-GB" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Will,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Sorted it, I solved the problem by deleting the index to the v73 FASTA file and therefore forcing VEP to recreate the index. This in turn resolved the problem.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks again,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">David<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>] <b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> 05 February 2014 16:09</span></p><div><div class="h5"><br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] VEP version 73 fasta file error<u></u><u></u></div></div><p></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal">I can't recreate the problem; I'm using API v73, VEP 73, the 73 main cache (NOT RefSeq) and the same 73 FASTA file you describe.<u></u><u></u></p><div>
<p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">My output:<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">> perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i duarte.vcf -offline -force -hgvs -fasta /[path]/73/Homo_sapiens.GRCh37.73.dna.primary_assembly.fa<u></u><u></u></p>
</div><div><p class="MsoNormal">> cat variant_effect_output.txt<u></u><u></u></p></div><div><div><p class="MsoNormal">## ENSEMBL VARIANT EFFECT PREDICTOR v73<u></u><u></u></p></div><div><p class="MsoNormal">## Output produced at 2014-02-05 16:07:25<u></u><u></u></p>
</div><div><p class="MsoNormal">## Connected to <u></u><u></u></p></div><div><p class="MsoNormal">## Using cache in /nfs/users/nfs_w/wm2/.vep/homo_sapiens/73<u></u><u></u></p></div><div><p class="MsoNormal">## Using API version 73, DB version ?<u></u><u></u></p>
</div><div><p class="MsoNormal">## Extra column keys:<u></u><u></u></p></div><div><p class="MsoNormal">## DISTANCE : Shortest distance from variant to transcript<u></u><u></u></p></div><div><p class="MsoNormal">## HGVSc : HGVS coding sequence name<u></u><u></u></p>
</div><div><p class="MsoNormal">## HGVSp : HGVS protein sequence name<u></u><u></u></p></div><div><p class="MsoNormal">#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra<u></u><u></u></p>
</div><div><p class="MsoNormal">5_98216957_TT/- 5:98216957-98216958 - ENSG00000153922 ENST00000284049 Transcript intron_variant,feature_truncation - - -<u></u><u></u></p></div><div><p class="MsoNormal">
- - - HGVSc=ENST00000284049.3:c.2964+25_2964+26delAA<u></u><u></u></p></div><div><p class="MsoNormal">5_98216957_TT/- 5:98216957-98216958 - ENSG00000153922 ENST00000511628 Transcript non_coding_exon_variant,nc_transcript_variant,feature_truncation 592-593 - - - - - HGVSc=ENST00000511628.1:n.592_593delAA<u></u><u></u></p>
</div><div><p class="MsoNormal">5_98216957_TT/- 5:98216957-98216958 - ENSG00000153922 ENST00000505982 Transcript downstream_gene_variant - - - - -<u></u><u></u></p></div><div><p class="MsoNormal">
- DISTANCE=1880<u></u><u></u></p></div></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">I get no warning messages, only the usual output.<u></u><u></u></p></div><div><p class="MsoNormal">
<u></u> <u></u></p></div><div><p class="MsoNormal">Are you using any other options besides those described in your config file?<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">
Are you using the RefSeq cache, or the default human one?<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal" style="margin-bottom:12.0pt">Will<u></u><u></u></p><div><p class="MsoNormal">
On 5 February 2014 14:34, Duarte Molha <<a href="mailto:Duarte.Molha@ogt.com" target="_blank">Duarte.Molha@ogt.com</a>> wrote:<u></u><u></u></p><div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dear Will</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">David works with me… Here is an example line where this is happening:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p><p class="MsoNormal">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SS_sample<u></u><u></u></p>
<p class="MsoNormal">5 98216956 . CTT C 16.9698 . AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M2D;DP=7;DPB=22.2692;DPRA=0;EPP=7.35324;EPPR=11.6962;GTI=0;LEN=2;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.88252;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=121;RO=4;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=del;technology.ILLUMINA=1;BVAR GT:DP:RO:QR:AO:QA:GL 0/1:7:4:121:2:63:-5,0,-5<u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best regards</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Duarte</span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>] <b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> 05 February 2014 13:02<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] VEP version 73 fasta file error</span><u></u><u></u></p><div><div><p class="MsoNormal"> <u></u><u></u></p><div>
<p class="MsoNormal">Hi David,<u></u><u></u></p><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">Are you able to provide a line or more of input that recreates the issue?<u></u><u></u></p></div>
<div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">This would help greatly with debugging the problem.<u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">
Regards<u></u><u></u></p></div><div><p class="MsoNormal"> <u></u><u></u></p></div><div><p class="MsoNormal">Will McLaren<u></u><u></u></p></div><div><p class="MsoNormal">Ensembl Variation<u></u><u></u></p></div></div><div>
<p class="MsoNormal" style="margin-bottom:12.0pt"> <u></u><u></u></p><div><p class="MsoNormal">On 5 February 2014 12:00, David Blaney <<a href="mailto:David.Blaney@ogt.com" target="_blank">David.Blaney@ogt.com</a>> wrote:<u></u><u></u></p>
<div><div><p class="MsoNormal">Dear Developers,<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">I am running version 73 of the VEP script and API. I am running the script in offline mode, cache only with the HGVS option selected and a fastq file specified (see snippet from config below):<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">####### cache stuff ############# <u></u><u></u></p><p class="MsoNormal">cache 1<u></u><u></u></p><p class="MsoNormal">
dir_plugins /NGS_Tools/vep/Plugins<u></u><u></u></p><p class="MsoNormal">dir_cache /ReferenceData/vep_cache<u></u><u></u></p><p class="MsoNormal">
# cache_region_size 1MB<u></u><u></u></p><p class="MsoNormal">offline 1<u></u><u></u></p><p class="MsoNormal"># skip_db_check 1<u></u><u></u></p><p class="MsoNormal">
fasta /ReferenceData/vep_cache/homo_sapiens/73/Homo_sapiens.GRCh37.73.dna.primary_assembly.fa<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">
when running the program I get the following warning (with trace, some line numbers may have changed in my vep script due to adding the libs for the modules):<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p><p class="MsoNormal">
Use of uninitialized value in reverse at /NGS_Tools/v73/ensembl/modules/Bio/EnsEMBL/Utils/Sequence.pm line 81.<u></u><u></u></p><p class="MsoNormal">at /NGS_Tools/v73/ensembl/modules/Bio/EnsEMBL/Utils/Sequence.pm line 81.<u></u><u></u></p>
<p class="MsoNormal"> Bio::EnsEMBL::Utils::Sequence::reverse_comp(SCALAR(0x56bd200)) called at (eval 68)[/NGS_Tools/VEP-latest/<a href="http://variant_effect_predictor.pl:1031" target="_blank">variant_effect_predictor.pl:1031</a>] line 22<u></u><u></u></p>
<p class="MsoNormal"> Bio::EnsEMBL::Slice::seq(Bio::EnsEMBL::Slice=HASH(0x97811d0)) called at /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 580<u></u><u></u></p><p class="MsoNormal">
Bio::EnsEMBL::Variation::TranscriptVariationAllele::hgvs_transcript(Bio::EnsEMBL::Variation::TranscriptVariationAllele=HASH(0x971c890)) called at /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/Utils/VEP.pm line 1854<u></u><u></u></p>
<p class="MsoNormal"> Bio::EnsEMBL::Variation::Utils::VEP::tva_to_line(HASH(0x54c0f18), Bio::EnsEMBL::Variation::TranscriptVariationAllele=HASH(0x971c890)) called at /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/Utils/VEP.pm line 1659<u></u><u></u></p>
<p class="MsoNormal"> Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences(HASH(0x54c0f18), Bio::EnsEMBL::Variation::VariationFeature=HASH(0x5c67ba0)) called at /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/Utils/VEP.pm line 1425<u></u><u></u></p>
<p class="MsoNormal"> Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons(HASH(0x54c0f18), ARRAY(0x5006550)) called at /NGS_Tools/v73/ensembl-variation/modules//Bio/EnsEMBL/Variation/Utils/VEP.pm line 985<u></u><u></u></p>
<p class="MsoNormal"> Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences(HASH(0x54c0f18), ARRAY(0x53023d0)) called at /NGS_Tools/VEP-latest/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> line 364<u></u><u></u></p>
<p class="MsoNormal"> main::main(HASH(0x54c0f18)) called at /NGS_Tools/VEP-latest/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> line 202<u></u><u></u></p><p class="MsoNormal">
<u></u><u></u></p><p class="MsoNormal">Could you please shed some light on what is going on? I have not yet figured out if this warning has any effect on the output.<u></u><u></u></p><p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Many thanks,<u></u><u></u></p><p class="MsoNormal">David Blaney<u></u><u></u></p></div></div><p class="MsoNormal" style="margin-bottom:12.0pt"><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
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</div><p class="MsoNormal"> <u></u><u></u></p></div></div></div></div></div><p class="MsoNormal" style="margin-bottom:12.0pt"><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
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<br></blockquote></div><br></div>