Comments (6)
Couple of questions:
- why is the script you are running named
variant_effect_predictor.pl
? As of release/88 it is simplyvep
- what is the full command line you are running?
- which cache file (species, version, assembly) did you install?
from ensembl-vep.
Thanks for the quick reply:
-
That was just a remnant error message from the prior version, it does execute using the 'vep' command
-
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
- I used option 46: homo_sapiens_vep_88_GRCh38.tar.gz
from ensembl-vep.
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```
from ensembl-vep.
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
from ensembl-vep.
As an aside, it seems the extraction process is the issue -- Within the tmp folder the file has been unzipped but not 'un-tarred'
from ensembl-vep.
This extraction process issue has been fixed in release/88.4
from ensembl-vep.
Related Issues (20)
- Error with dbNSFP plugin HOT 6
- Inconsistent consequence annotation HOT 2
- Fail to install ensembl-release-111 on MacOS 14.2.1 (23C71) `fatal error: 'lzma.h' file not found` HOT 5
- WARNING: Ignoring non-supported 'five_prime_utr' feature_type from Homo_sapiens.GRCh38.111.gtf.bgzip.gz HOT 3
- Empty fields HGVSc and HGVSp of INFO - CSQ after VCF annotation via GTF and Fasta HOT 2
- Absence MANE and canonical annotation tags in output VCF. HOT 3
- VEP custom anotation not working with gnomad 4.0 file HOT 1
- ERROR: DBI module not found. VEP requires the DBI perl module to function HOT 2
- Annotating with GNOMAD custom vcf makes frequencies become STRING and unable to filter HOT 7
- VEP 111 HGVS C dot annotating dups as Insertions HOT 4
- filter_vep not correctly filtering CADD_PHRED scores HOT 10
- [Question] What is the definition of "coding_sequence_variant"? Why are frameshifts no coding sequence variant? HOT 4
- can not call method "seq" HOT 6
- Normalisation-based allele matching algorithm and custom file HOT 2
- False warning messages with vep 111 when using the range input format HOT 4
- All variants are intergenic with NCBI GFF HOT 6
- filter_vep output file larger than input file HOT 2
- WARNING: Chromosome 22 not found in annotation sources or synonyms on line 1 HOT 8
- VEP in Google Batch fails when more than 5 custom databases are passed HOT 6
- trouble finding cache file "MSG: ERROR: Cache directory /..." HOT 7
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from ensembl-vep.