Open androidpifu opened 2 months ago
Hi, thanks for reporting this. Could you please provide me with the logs/vep/R22025_somatic.snvs_annotate.log
file? It should give us more information about what went wrong.
Thanks
Unfortunately, there are no entries in the log file. R22025_somatic.snvs_annotate.log
Ok, thanks.
Could you please verify that the plugins for VEP have been downloaded? And print the content of the folder resources/vep/plugins
. It looks like these have not been downloaded correctly. These should contain: Downstream.pm
, NMD.pm
, and Wildtype.pm
Could you also check if the SNV Vcf file is correct (e.g., bcftools view 'results/R22025/variants/somatic.snvs.vcf.gz') as this is getting piped to VEP. Could be that this causes some issues already. As I understand this happens to multiple samples?
Thank you for your suggestion. The SNV VCF file format is correct, I have tested it. The contents of the resources/vep/plugins folder are complete, and my SNV VCF contains only one sample.
I encounter the following error when executing the command below:
bcftools view 'results/R22031/variants/somatic.snvs.vcf.gz' | vep --everything --fork 4 --format vcf --vcf --offline --cache --dir_cache resources/vep/cache --cache_version 111 --species homo_sapiens --assembly GRCh38 --fasta resources/refs/genome.fasta --dir_plugins resources/vep/plugins --plugin NMD, --plugin Wildtype, --plugin Downstream, --output_file STDOUT --stats_file results/R22031/annotation/somatic.snvs.html | bcftools view -Ov > results/R22031/annotation/somatic.snvs.vcf 2> logs/vep/R22031_somatic.snvs_annotate.log
ERROR:
Can't use an undefined value as an ARRAY reference at /home/zhumc/.conda/envs/scanneo2/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Funcgen/BindingMatrix.pm line 501.
Hello, I can't reproduce this error.. could you maybe provide me the SNV file (or part of it)? Thanks
I tried removing the parameter --everything
and then the exception doesn't appear
Ok thanks for reporting this. It runs through without --everything
? Need to test this. Thanks
Unfortunately,my SNV file is too large and can not be uploaded.
When I was running ScanNeo2, several samples encountered errors during the VEP annotation process, specifically for the main task of SNVs. The following error occurred for all of them. localrule annotate_variants: input: results/R22025/variants/somatic.snvs.vcf.gz, results/R22025/variants/somatic.snvs.vcf.gz.tbi, resources/refs/genome.fasta, resources/vep/cache, resources/vep/plugins
Could you please provide some assistance?