Open suzyhh opened 3 hours ago
Hi @suzyhh , thank you for reporting the issue. Can you kindly provide us the input file/test input used?
@likhitha-surapaneni
I have attached the input file (bgzipped for compatibility with github) that generates the error - ta! TwEx_ProbandF-TwEx_MotherF-TwEx_FatherF_gnomad_filtered_mt.vcf.gz
Describe the issue
Hello, I'm testing v113 using the v113 docker obtained from docker hub and the v113 cache downloaded using the following command:
docker run --network host -t -i -v /mnt/data1/software/vep/:/opt/vep/.vep ensemblorg/ensembl-vep:release_113.0 INSTALL.pl -a c -s homo_sapiens_merged -y GRCh38
I have successfully tested v113 with a VCF containing structural variants, but I encounter an error when running with a VCF containing SNVs/indels. After the error the process just hangs doing nothing until I kill it. The output files contains the VCF header but no variants.
System
Full VEP command line
Full error message
I have tested my command using v112 and it completes successfully with no errors/warnings so it does seem to be a v113 problem. Running locally I have found that the problem occurs when using the
--hgvsg
flag. If I run using only--hgvs
I do not get the above error, but I do get several warnings, here is a small snippet:I do not receive any errors or warning when I run v113 without both
--hgvs
and--hgvsg
. This unfortunately renders v113 unusable for us as we rely on the hgvs annotations.Many thanks!