<div dir="ltr">Hi Emma,<div><br></div><div>It looks like the fault is being triggered when the FASTA DB is being prepared.</div><div><br></div><div>Are you running the latest (82) VEP? It's possible that our new FASTA indexer isn't playing nicely with your system. You could try the following:</div><div><br></div>cd /mnt/hds/proj/bioinfo/develop/modules/ensembl-tools-release-82/scripts/variant_effect_predictor/<br>rm -rf FAIDX<br>rm Faidx.*<div><br></div><div>Then re-running your command. This will reset your system to using the old BioPerl FASTA indexer.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 24 November 2015 at 09:32, Emma Sernstad <span dir="ltr"><<a href="mailto:emma.sernstad@scilifelab.se" target="_blank">emma.sernstad@scilifelab.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><span style="font-size:13px">Hi,</span><div style="font-size:13px"><br></div><div style="font-size:13px">we are experiencing problems that are difficult to debug.</div><div style="font-size:13px">Namely we get this output almost right away:</div><div style="font-size:13px"><br></div><div style="font-size:13px"><p style="margin:0px;font-size:16px;line-height:normal;font-family:Consolas;color:rgb(245,245,245);background-color:rgb(0,0,0)">perl /mnt/hds/proj/bioinfo/develop/modules/ensembl-tools-release-82/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl/" target="_blank">variant_effect_predictor.pl</a> --dir_cache /mnt/hds/proj/cust003/develop/modules/ensembl-tools-release-82/cache --cache --force_overwrite --vcf --fork 4 --buffer_size 20000 --offline --chr 21 --hgvs --symbol --numbers --sift p --polyphen p --humdiv --domains --protein --ccds --uniprot --biotype --regulatory --tsl -i /mnt/hds/proj/bioinfo/develop/cust000/337334/analysis/exomes/337334/bwa/gatk/337334_sorted_smd_rreal_brecal_gvcf_vrecal_vt_BOTH_21.vcf -o /mnt/hds/proj/bioinfo/develop/cust000/337334/analysis/exomes/337334/bwa/gatk/337334_sorted_smd_rreal_brecal_gvcf_vrecal_vt_vep_BOTH_21.vcf</p><p style="margin:0px;font-size:16px;line-height:normal;font-family:Consolas;color:rgb(245,245,245);background-color:rgb(0,0,0)">2015-11-24 10:10:10 - Read existing cache info</p><p style="margin:0px;font-size:16px;line-height:normal;font-family:Consolas;color:rgb(245,245,245);background-color:rgb(0,0,0)">2015-11-24 10:10:10 - Auto-detected FASTA file in cache directory</p><p style="margin:0px;font-size:16px;line-height:normal;font-family:Consolas;color:rgb(245,245,245);background-color:rgb(0,0,0)">Segmentation fault</p></div><div style="font-size:13px"><br></div><div style="font-size:13px">Do you think it might be a corrupt cache directory? Can it have anything to do with the perl installation (v5.18.2)?</div><div style="font-size:13px"><br></div><div style="font-size:13px">We are running on CentOS 6.6.</div><span class="HOEnZb"><font color="#888888"><div><br></div>-- <br><div><div dir="ltr"><span style="font-size:x-small">Emma Sernstad</span><div><span style="font-size:x-small">Science for Life Laboratory, KISP</span></div><div><span style="font-family:Helvetica"><span style="font-size:x-small">Tomtebodavägen 23A</span></span></div><div><span style="font-family:Helvetica"><span style="font-size:x-small">SE-171 65 Solna, Sweden</span></span></div><div><font face="Helvetica"><span style="font-size:x-small"><br></span></font></div><div><font face="Helvetica"><span style="font-size:x-small">Email: </span><a href="mailto:emma.sernstad@scilifelab.se" target="_blank"><span style="font-size:x-small">emma.sernstad@scilifelab.se</span></a></font></div><div><font face="Helvetica"><span style="font-size:x-small">Phone: +46 (0)</span></font><span style="font-size:x-small">722503877</span><span style="font-family:Helvetica"><span style="font-size:x-small">(Mobile)</span></span></div></div></div>
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