Cannot use format bigwig without Bio::DB::BigFile module installed

[lqr131115]

Describe the issue

I install vep108 from Ensembl Vep :: Anaconda.org， and install Bio::DB::BigFile successfully, When I do vep , I get an error:

I wonder what are the possible reasons for this phenomenon

Thanks for your help Lqr

System

• VEP version: 108
• VEP Cache version: 108
• Perl version: 5.32.1
• OS: WSL ( Ubuntu )

[likhitha-surapaneni]

Hi @lqr131115 ,

From the error message, it seems like the perl environment used by VEP is different from the one where the module is installed. That being said, we do not support conda installs of VEP as they are not packages created by us. It is recommended to reach out to the creator of the package for any issues related to the conda package.

Alternatively, we provide containerised options to run VEP using docker and singularity.

Kind regards, Likhitha

[likhitha-surapaneni]

Hi @lqr131115 , I want to add that you may also want to check these instructions to install Bio::DB::BigFile.

[lqr131115]

Hi @likhitha-surapaneni ，

Thank for your reply. I tried to do vep by singularity, and another error appear:

I am sure the dir /homo_sapiens_refseq is exist , so what should I do?

And here my vep command:

singularity exec vep.sif vep --input_file positive.sample.ipt.test.vcf --format vcf --output_file positive.sample.opt.test.vcf --vcf --sift s --polyphen s --numbers --symbol --shift_3prime 1 --allele_number --refseq --total_length --no_stats --offline --cache --dir_cache /mnt/g/vep108_dependency/cache_data/GRCh38 --species "homo_sapiens" --assembly GRCh38 --fork 4 --dont_skip --allow_non_variant --use_given_ref --exclude_predicted --flag_pick_allele --plugin Grantham --plugin SpliceAI,snv=/mnt/g/capice_dependency/capice/require_data/spliceai_scores.masked.snv.hg38.vcf.gz,indel=/mnt/g/capice_dependency/capice/require_data/spliceai_scores.masked.indel.hg38.vcf.gz --custom "/mnt/g/capice_dependency/capice/require_data/gnomad.genomes.v3.1.2.sites.stripped.vcf.gz,gnomAD,vcf,exact,0,AF,HN" --custom "/mnt/g/capice_dependency/capice/require_data/hg38.phyloP100way.bw,phyloP,bigwig,exact,0" --dir_plugins /mnt/g/capice_dependency/capice/vep_plugins --force_overwrite 

Update

I add the option --bind ， and resolve the new error . Now I get the correct result. Here my modify:

singularity exec --bind /mnt:/mnt vep.sif vep --input_file positive.sample.ipt.test.vcf  ...

Best wishes, Lqr

[likhitha-surapaneni]

Hi @lqr131115,

Glad that the issue got resolved. I am closing this ticket for now. Please feel free to open a new ticket if you have any further issues.

Kind regards, Likhitha