<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";
mso-fareast-language:EN-US;}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";}
span.EmailStyle19
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.EmailStyle20
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.EmailStyle21
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Dear Developers,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></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):<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>####### cache stuff ############# <o:p></o:p></p><p class=MsoNormal>cache 1<o:p></o:p></p><p class=MsoNormal>dir_plugins /NGS_Tools/vep/Plugins<o:p></o:p></p><p class=MsoNormal>dir_cache /ReferenceData/vep_cache<o:p></o:p></p><p class=MsoNormal># cache_region_size 1MB<o:p></o:p></p><p class=MsoNormal>offline 1<o:p></o:p></p><p class=MsoNormal># skip_db_check 1<o:p></o:p></p><p class=MsoNormal>fasta /ReferenceData/vep_cache/homo_sapiens/73/Homo_sapiens.GRCh37.73.dna.primary_assembly.fa<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></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):<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Use of uninitialized value in reverse at /NGS_Tools/v73/ensembl/modules/Bio/EnsEMBL/Utils/Sequence.pm line 81.<o:p></o:p></p><p class=MsoNormal>at /NGS_Tools/v73/ensembl/modules/Bio/EnsEMBL/Utils/Sequence.pm line 81.<o:p></o:p></p><p class=MsoNormal> Bio::EnsEMBL::Utils::Sequence::reverse_comp(SCALAR(0x56bd200)) called at (eval 68)[/NGS_Tools/VEP-latest/variant_effect_predictor.pl:1031] line 22<o:p></o:p></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<o:p></o:p></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<o:p></o:p></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<o:p></o:p></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<o:p></o:p></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<o:p></o:p></p><p class=MsoNormal> Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences(HASH(0x54c0f18), ARRAY(0x53023d0)) called at /NGS_Tools/VEP-latest/variant_effect_predictor.pl line 364<o:p></o:p></p><p class=MsoNormal> main::main(HASH(0x54c0f18)) called at /NGS_Tools/VEP-latest/variant_effect_predictor.pl line 202<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Many thanks,<o:p></o:p></p><p class=MsoNormal>David Blaney<o:p></o:p></p></div></body></html>