<div dir="ltr">My apologies if this is a duplicate. My other email program seems not to have liked the "<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>" address.<div><br></div><div><div tabindex="-1" style="color:rgb(0,0,0);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;font-size:medium"><div tabindex="0"><div class="gmail-_rp_o5" tabindex="-1" style="min-width:350px;clear:both"><div class="gmail-_rp_05 gmail-ms-border-color-neutralLight gmail-ShowConsesusSchedulingLink gmail-ShowReferenceAttachmentsLinks" tabindex="-1" style="border-color:rgb(234,234,234);min-height:70px;border-bottom-width:1px;border-bottom-style:solid;padding-bottom:20px;outline:none"><div class="gmail-_rp_d5 gmail-_rp_c5" style="margin-left:62px;margin-top:12px"><div><div class="gmail-_rp_25" id="gmail-Item.MessagePartBody" style="clear:both;width:auto;word-wrap:break-word;padding-top:4px"><div class="gmail-_rp_35 gmail-ms-font-weight-regular gmail-ms-font-color-neutralDark gmail-rpHighlightAllClass gmail-rpHighlightBodyClass" id="gmail-Item.MessageUniqueBody" style="font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont;color:rgb(33,33,33);font-size:15px"><div><div id="gmail-divtagdefaultwrapper"><font face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android Emoji,EmojiSymbols" size="3" color="black"><span id="gmail-divtagdefaultwrapper" style="font-size:12pt"><div style="margin-top:0px;margin-bottom:0px">I need to run the VEP perl script offline but dairly full-featured.</div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px">I downloaded and installed the current (91) VEP with `perl INSTALL.pl --DESTDIR ${INSTALL_DIR} --CACHEDIR ${INSTALL_DIR} --PLUGINS all;`</div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px">No errors were reported,, and in particular installing Bio::DB::HTS and htslib seemed to go well.</div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px">PERL5LIB includes the DESTDIR for VEP and PATH includes the htslib directory.</div><div style="margin-top:0px;margin-bottom:0px"><br><font face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android Emoji,EmojiSymbols" size="2"><span style="font-size:16px">Bio::DB::HTS::Faidx.pm exists under the Bio directory that the VEP installer created in the </span></font><font face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android Emoji,EmojiSymbols" size="2"><span style="font-size:16px">DESTDIR</span></font><font face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android Emoji,EmojiSymbols" size="2"><span style="font-size:16px">.</span></font></div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px">--fasta is set to .../homo_sapiens/91_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz. The .fai and .gzi files are also present.</div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px">Nonetheless, when I run the VEP, I get the error "<font face="Courier New,monospace" size="1"><span style="font-size:12px">Cannot index bgzipped FASTA file with Bio::DB::Fasta</span></font>".</div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px">It appears that <font face="Courier New,monospace" size="1"><span style="font-size:12px">Bio::EnsEMBL::Variation::Utils::FastaSequence::setup_fasta </span></font>is failing the test `eval { require Bio::DB::HTS::Faidx; 1 }` and therefore not setting $CAN_USE_FAIDX. </div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px"><font size="3"><span style="font-size:12pt">The command and error are below.</span></font><br></div><div style="margin-top:0px;margin-bottom:0px"><font size="3"><span style="font-size:12pt"><br></span></font></div><div style="margin-top:0px;margin-bottom:0px"><font face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android Emoji,EmojiSymbols" size="2"><span style="font-size:16px">Thanks for your help.</span></font><font size="3"><span style="font-size:12pt"><br></span></font></div><div style="margin-top:0px;margin-bottom:0px"><br></div><div style="margin-top:0px;margin-bottom:0px"> </div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> /usr/local/bin/perl \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/vep \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> -i /gpfs/share/cmoco_sys_dev/nfs/storage/cromwell/cromwell-executions/PairedEndSingleSampleWorkflow/ff81a90d-ea94-4f33-9405-98575fd8e0af/call-VariantEffectPredictor/inputs/gpfs/share/cmoco_sys_dev/nfs/storage/cromwell/cromwell-executions/PairedEndSingleSampleWorkflow/ff81a90d-ea94-4f33-9405-98575fd8e0af/call-MakeSitesOnlyVcf/execution/AI-HEP7.lValExome0019.downsampled.recalibrated.filtered.postCGP.GQfiltered.sites.vcf \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --offline \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --cache \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --fasta /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/homo_sapiens/91_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --merged \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --dir /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91 \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --output_file AI-HEP7.lValExome0019.downsampled.json \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --force_overwrite \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --json \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> --everything \</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">> -v</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">2018-02-16 16:03:21 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this</span></font></div><div><br></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">-------------------- EXCEPTION --------------------</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">MSG: ERROR: Cannot index bgzipped FASTA file with Bio::DB::Fasta</span></font></div><div><br></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">STACK Bio::EnsEMBL::Variation::Utils::FastaSequence::setup_fasta /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm:210</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">STACK Bio::EnsEMBL::VEP::BaseVEP::fasta_db /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:477</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">STACK Bio::EnsEMBL::VEP::Runner::init /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:129</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">STACK Bio::EnsEMBL::VEP::Runner::run /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">STACK toplevel /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/vep:222</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">Date (localtime)    = Fri Feb 16 16:03:22 2018</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">Ensembl API version = 91</span></font></div><div><font face="Courier New,monospace" size="2"><span style="font-size:9pt">---------------------------------------------------</span></font></div><div><br></div><br><div style="margin-top:0px;margin-bottom:0px"> </div><div style="margin-top:0px;margin-bottom:0px"> </div><div style="margin:0px"><font face="Calibri,sans-serif" size="2" color="#212121"><span style="font-size:11pt">Michael Yourshaw, JD, PhD</span></font></div><div style="margin:0px"><font face="Calibri,sans-serif" size="2" color="#212121"><span style="font-size:11pt">Bioinformatician</span></font></div><div style="margin:0px"><font face="Calibri,sans-serif" size="2" color="#212121"><span style="font-size:11pt">Colorado Center for Personalized Medicine</span></font></div><div style="margin:0px"><font face="Calibri,sans-serif" size="2" color="#212121"><span style="font-size:11pt">Colorado Molecular Correlates</span></font></div><div style="margin:0px"><font face="Calibri,sans-serif" size="2" color="#212121"><span style="font-size:11pt"><a href="mailto:michael.yourshaw@ucdenver.edu" target="_blank" rel="noopener noreferrer">michael.yourshaw@ucdenver.edu</a></span></font></div></span></font></div></div></div></div><span class="gmail-PersonaPaneLauncher"><div class="gmail-_pe_d gmail-_pe_92" tabindex="-1" style="outline:none;overflow:hidden;width:1058px;display:table;vertical-align:middle;white-space:nowrap"></div></span></div><div class="gmail-_rp_85" style="clear:both"></div></div></div></div></div></div><div class="gmail-_rp_o" tabindex="-1" style="width:1120px;height:1px;color:rgb(0,0,0);font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;font-size:medium"></div></div><div><br clear="all"><div><div class="gmail_signature"><div><div>ॐ<br>Michael Yourshaw<br><a href="mailto:myourshaw@ucla.edu" target="_blank">myourshaw@gmail.com</a><br><br>This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.</div></div></div></div>
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