VEP error

[androidpifu]

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
```
output: results/R22025/annotation/somatic.snvs.vcf, results/R22025/annotation/somatic.snvs.html
log: logs/vep/R22025_somatic.snvs_annotate.log
jobid: 2
reason: Missing output files: results/R22025/annotation/somatic.snvs.vcf; Input files updated by another job: results/R22025/variants/somatic.snvs.vcf.gz.tbi, results/R22025/variants/somatic.snvs.vcf.gz
wildcards: sample=R22025, vartype=somatic.snvs
threads: 4
resources: tmpdir=/tmp

Traceback (most recent call last):
File "/mnt/work/zhumc/software/ScanNeo2/ScanNeo2/.snakemake/scripts/tmp_6vhvqtx.wrapper.py", line 68, in
shell(
File "/home/zhumc/.conda/envs/scanneo2/lib/python3.12/site-packages/snakemake/shell.py", line 297, in new
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail; (bcftools view 'results/R22025/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/R22025/annotation/somatic.snvs.html | bcftools view -Ov > results/R22025/annotation/somatic.snvs.vcf) 2> logs/vep/R22025_somatic.snvs_annotate.log' returned non-zero exit status 255.
RuleException:
CalledProcessError in file /mnt/work/zhumc/software/ScanNeo2/ScanNeo2/workflow/rules/annotation.smk, line 70:
Command 'set -euo pipefail; /home/zhumc/.conda/envs/scanneo2/bin/python3.12 /mnt/work/zhumc/software/ScanNeo2/ScanNeo2/.snakemake/scripts/tmp_6vhvqtx.wrapper.py' returned non-zero exit status 1.

Could you please provide some assistance?

[riasc]

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

[androidpifu]

Unfortunately, there are no entries in the log file.
R22025_somatic.snvs_annotate.log

[riasc]

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?

[androidpifu]

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.

[androidpifu]

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.

[riasc]

Hello,
I can't reproduce this error.. could you maybe provide me the SNV file (or part of it)? Thanks

[androidpifu]

I tried removing the parameter --everything and then the exception doesn't appear

[riasc]

Ok thanks for reporting this. It runs through without --everything? Need to test this. Thanks

[androidpifu]

Unfortunately，my SNV file is too large and can not be uploaded.