<div dir="ltr">Hi David,<div><br></div><div>Are you able to provide a line or more of input that recreates the issue?</div><div><br></div><div>This would help greatly with debugging the problem.</div><div><br></div><div>Regards</div>
<div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 5 February 2014 12:00, 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">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><br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>