Closed cookersjs closed 7 years ago
Couple of questions:
variant_effect_predictor.pl
? As of release/88 it is simply vep
Thanks for the quick reply:
1) That was just a remnant error message from the prior version, it does execute using the 'vep' command
2) The command is input into the command line like so:
perl "-X" "/Users/jcook/ensembl-vep/vep" "--format" "vcf" "--vcf" "--offline" "--no_progress" "--canonical" "--check_existing" "--check_ref" "--force_overwrite" "--numbers" "--domains" "--cache" "--hgvs" "--pubmed" "--sift" "b" "--polyphen" "b" "--buffer_size" "5000" "--dir_cache" "/Users/jcook/.vep" "--input_file" "common_and_clinical_20170130_UNKNOWN.vcf" "--output_file" "common_and_clinical_20170130_UNKNOWN.vcf.out.vcf" "--fork" "2"
As well, the same error occurs when just using the sample provided in the documentation:
./vep -i examples/homo_sapiens_GRCh38.vcf --cache --force_overwrite --sift b
3) I used option 46: homo_sapiens_vep_88_GRCh38.tar.gz
It may be possible your cache is incomplete or did not unpack correctly, possibly due to lack of disk space.
Can you try:
cat /Users/jcook/.vep/homo_sapiens/88_GRCh38/info.txt
You should get the following:
assembly GRCh38
sift b
polyphen b
source_polyphen 2.2.2
source_sift sift5.2.2
source_genebuild 2014-07
source_gencode GENCODE 26
source_assembly GRCh38.p10
variation_cols variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,ExAC,ExAC_AFR,ExAC_AMR,ExAC_Adj,ExAC_EAS,ExAC_FIN,ExAC_NFE,ExAC_OTH,ExAC_SAS
source_COSMIC 79
source_HGMD-PUBLIC 20164
source_ESP 20141103
source_ClinVar 201701
source_dbSNP 149
source_1000genomes phase3
source_ESP V2-SSA137
source_ExAC 0.3
regulatory 1
source_regbuild 16```
Haha well it seems the cache file never even downloaded now that I looked into that directory -- All that exists currently is the fasta file and its index file. I'll attempt to re-download the cache file and am sure things will cooperate once that is done.
Thanks for the help!
-cookersjs
As an aside, it seems the extraction process is the issue -- Within the tmp folder the file has been unzipped but not 'un-tarred'
This extraction process issue has been fixed in release/88.4
Hello,
I did see the posting relating to this at: https://github.com/Ensembl/ensembl-vep/issues/33 Unfortunately I wasn't able to get a solution to this problem from that issue page.
I'm working on accomodating the new vep methods into my code, but have run into the same error message for both SIFT and Polyphen:
Is there a plugin or anything else needed to rectify this?
I installed using 'perl INSTALL.pl --NO_HTSLIB'
Thanks!
-cookersjs