Stikus
commented
4 years ago Looks like I found the reason of this issue.
According to VEP Cache page all indexed cache is here:
ftp://ftp.ensembl.org/pub/release-98/variation/indexed_vep_cache/
And all non-indexed is here:
ftp://ftp.ensembl.org/pub/release-98/variation/vep/
But default FTP Cache URL for VEP from this line is:
$CACHE_URL ||= "ftp://ftp.ensembl.org/pub/release-$DATA_VERSION/variation/vep";
And it is pointing on not indexed cache.
Am I correct?
Btw - about info files. According to Cache page GRCh37 have dbsnp v152, but according to my info txt above - it have dnsnp v151. And for GRCh38 - my info.txt says:
# CACHE UPDATED 2019-09-30 14:47:57
species homo_sapiens
assembly GRCh38
sift b
polyphen b
source_polyphen 2.2.2
source_sift sift5.2.2
source_genebuild 2014-07
source_gencode GENCODE 32
source_assembly GRCh38.p13
variation_cols chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,clin_sig_allele,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomAD,gnomAD_AFR,gnomAD_AMR,gnomAD_ASJ,gnomAD_EAS,gnomAD_FIN,gnomAD_NFE,gnomAD_OTH,gnomAD_SAS
source_COSMIC 89
source_HGMD-PUBLIC 20184
source_ESP 20141103
source_ClinVar 201907
source_dbSNP 152
source_1000genomes phase3
source_ESP V2-SSA137
source_gnomAD r2.1
regulatory 1
cell_types A549,A673,B,B_(PB),CD14+_monocyte_(PB),CD14+_monocyte_1,CD4+_CD25+_ab_Treg_(PB),CD4+_ab_T,CD4+_ab_T_(PB)_1,CD4+_ab_T_(PB)_2,CD4+_ab_T_(Th),CD4+_ab_T_(VB),CD8+_ab_T_(CB),CD8+_ab_T_(PB),CMP_CD4+_1,CMP_CD4+_2,CMP_CD4+_3,CM_CD4+_ab_T_(VB),DND-41,EB_(CB),EM_CD4+_ab_T_(PB),EM_CD8+_ab_T_(VB),EPC_(VB),GM12878,H1-hESC_2,H1-hESC_3,H9_1,HCT116,HSMM,HUES48,HUES6,HUES64,HUVEC,HUVEC-prol_(CB),HeLa-S3,HepG2,K562,M0_(CB),M0_(VB),M1_(CB),M1_(VB),M2_(CB),M2_(VB),MCF-7,MM.1S,MSC,MSC_(VB),NHLF,NK_(PB),NPC_1,NPC_2,NPC_3,PC-3,PC-9,SK-N.,T_(PB),Th17,UCSF-4,adrenal_gland,aorta,astrocyte,bipolar_neuron,brain_1,cardiac_muscle,dermal_fibroblast,endodermal,eosinophil_(VB),esophagus,foreskin_fibroblast_2,foreskin_keratinocyte_1,foreskin_keratinocyte_2,foreskin_melanocyte_1,foreskin_melanocyte_2,germinal_matrix,heart,hepatocyte,iPS-15b,iPS-20b,iPS_DF_19.11,iPS_DF_6.9,keratinocyte,kidney,large_intestine,left_ventricle,leg_muscle,lung_1,lung_2,mammary_epithelial_1,mammary_epithelial_2,mammary_myoepithelial,monocyte_(CB),monocyte_(VB),mononuclear_(PB),myotube,naive_B_(VB),neuron,neurosphere_(C),neurosphere_(GE),neutro_myelocyte,neutrophil_(CB),neutrophil_(VB),osteoblast,ovary,pancreas,placenta,psoas_muscle,right_atrium,right_ventricle,sigmoid_colon,small_intestine_1,small_intestine_2,spleen,stomach_1,stomach_2,thymus_1,thymus_2,trophoblast,trunk_muscle
source_regbuild 1.0
var_type tabixSo source_gencode GENCODE 32 and source_assembly GRCh38.p13, but Cache page says Genome assembly GRCh38.p12 and GENCODE 31. Looks like something wrong somewhere.
aparton
Hello. If I understand correctly release notes of 97 VEP release - now cache files in tabix indexed already and cache convertion step not needed anymore. Release notes VEP 97
Related issue
But when I updated out VEP installation to 98 version (this problem was at 97 version too btw) conversion still started and too several ours both for 37 and 38 genome.
Context: Our VEP installation command:
perl INSTALL.pl --NO_TEST --NO_UPDATE --NO_HTSLIB --NO_BIOPERL -a ap --PLUGINSDIR "$SOFT/ensembl-vep-${VEP_VERSION}/Plugins" --PLUGINS ProteinSeqs,Downstream,Conservation,GO,G2POur VEP cache install command:
$VEPINSTALL --NO_TEST --NO_UPDATE --NO_HTSLIB --NO_BIOPERL -a cf -s homo_sapiens -y $vepCacheAssembly --CONVERT -c $VEPCACHEDIRIf I understand perl script correctly - this line starts convert_cache.pl and this line is check for need of convertion. So if info.txt contains key:
var_type tabix- variant is skipped.But this is our 98_GRCh37 info's before and after convertion: Before:
After:
Looks like info.txt doesn't contain info about that files are already tabix indexed. Do I missunderstood something on this is wrong?