<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Kurt,<div class=""><br class=""></div><div class="">Unfortunately the error is correct, you cannot use HGVS input format in offline mode.</div><div class=""><br class=""></div><div class="">If there’s something incorrect or unclear in our docs then I would like to update it, could you please point in the direction of the documentation you found?</div><div class=""><br class=""></div><div class="">Kind Regards,</div><div class="">Andrew</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 4 Jan 2021, at 17:54, Kurt Hetrick <<a href="mailto:khetric1@jhmi.edu" class="">khetric1@jhmi.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hello,<br class=""><br class="">From reading the online documentation I was under the impression that one could use hgvs in offline mode provided that they pointed to the fasta file, but the error I received suggests otherwise. Am I missing something or is hgvs not possible in offline mode. Using GRCh37.<br class=""><br class="">I am using a singularity image for ensemble 102 that I pulled from a docker image that I built using the dockerfile from your dockerhub page where I changed the base image from Ubuntu 18.04 to Ubuntu 16.04 and then built the cache locally.<br class=""><br class="">export PERL5LIB=/mnt/resources/vep_data<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">export PATH=$PATH:/mnt/resources/vep_data<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">singularity exec -B /mnt:/mnt /mnt/containers/vep-102.0.simg vep -i file2.txt -o test.vcf --fork 4 --cache --offline --refseq --force_overwrite --dir /mnt/resources/vep_data --fasta /mnt/research/tools/test/human_g1k_v37_decoy.fasta --hgvs --assembly GRCh37 --check_existing --dir_cache /mnt/resources/vep_data<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">2021-01-04 17:43:09 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">-------------------- EXCEPTION --------------------<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">MSG: ERROR: Cannot use HGVS format in offline mode<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">STACK Bio::EnsEMBL::VEP::Parser::HGVS::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm:104<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">STACK Bio::EnsEMBL::VEP::Parser::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:151<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">STACK Bio::EnsEMBL::VEP::Runner::get_Parser /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:805<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:832<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:140<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:203<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">STACK toplevel /opt/vep/src/ensembl-vep/vep:229<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Date (localtime) = Mon Jan 4 17:43:09 2021<o:p class=""></o:p></div><div style="border-style: none none solid; border-bottom-width: 1pt; border-bottom-color: windowtext; padding: 0in 0in 1pt;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; border: none; padding: 0in;" class="">Ensembl API version = 102<o:p class=""></o:p></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">head -n 5 file2.txt<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">NM_000492.4:c.-13_10del23<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">NM_000492.4:c.-9_14del23<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">NM_000492.4:c.-8G>C<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">NM_000492.4:c.[1046C>T;3747delG]<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">NM_000492.4:c.[1093_1094delCT;3705T>G]<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks in advance,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Kurt Hetrick<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; 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