<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hello,<div class=""><br class=""></div><div class="">You are using the GRCh37 cache. Chromosome 20 on GRCh37 is only <span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class="">63,025,520</span>bp long:</div><div class=""><br class=""></div><div class=""><a href="http://grch37.ensembl.org/Homo_sapiens/Location/Chromosome?r=20" class="">http://grch37.ensembl.org/Homo_sapiens/Location/Chromosome?r=20</a></div><div class=""><br class=""></div><div class="">So it is inevitable there will be no variants reported in that 25kb region at the end, and hence the cache file is not found.</div><div class=""><br class=""></div><div class="">Double check that your data are actually mapped to GRCh37, and not GRCh38, where chromosome 20 is now <span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class="">64,444,167bp long.</span></div><div class=""><span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class="">If you are confident your data are correct and you are using the correct assembly, then you can safely ignore these warnings.</span></div><div class=""><span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class="">Regards</span></div><div class=""><span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class="">Will McLaren</span></div><div class=""><span style="color: rgb(51, 51, 51); white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class="">Ensembl Variation</span></div><div class=""><span style="color: rgb(51, 51, 51); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 12.8000001907349px; white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="color: rgb(51, 51, 51); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 12.8000001907349px; white-space: nowrap; widows: 1; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><div><blockquote type="cite" class=""><div class="">On 14 May 2015, at 09:48, Svein Tore Koksrud Seljebotn <<a href="mailto:s.t.seljebotn@medisin.uio.no" class="">s.t.seljebotn@medisin.uio.no</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Hi,<br class=""><br class="">I'm using VEP release-79 with cache from <a href="ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_merged_vep_79_GRCh37.tar.gz" class="">ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_merged_vep_79_GRCh37.tar.gz</a> .<br class=""><br class="">I tried to annotate some human exome data and I get the following error message in a separate file called {output_name}_warnings.txt:<br class=""><br class="">"WARNING: Could not find variation cache for 20:63000001-64000000"<br class=""><br class="">Looking at the files for this range inside the cache, I can see that those files contain almost not data. There are also other regions that are as small, while most are from 1MB and upwards.<br class=""><br class="">My question, is this something I should worry about? Is my cache corrupted somehow?<br class=""><br class="">Command line:<br class="">vep --cache --dir_cache=/work/genomic/funcAnnot/VEP/cache/ --fasta=/work/genomic/gatkBundle_2.5/human_g1k_v37_decoy.fasta --offline --sift=b --polyphen=b --ccds --hgvs --numbers --domains --regulatory --canonical --protein --biotype --gmaf --maf_1kg --maf_esp --pubmed --allow_non_variant --fork=4 --vcf --allele_number --no_escape --failed=1 --no_stats --merged --symbol -custom /work/genomic/variantDbs/repeatMasker/repeatMasker_hg19.20150508.reformat.sorted.bed.gz,repeatMasker,bed,overlap,0 -i test.na12878.vcf -o vep_processed.vcf<br class=""><br class="">Best regards,<br class="">Svein Tore Koksrud Seljebotn<br class=""><br class="">_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""></div></body></html>