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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Error in test_annotation VEP #328

Closed ChillyMomo709 closed 3 years ago

ChillyMomo709 commented 3 years ago

Hi there,

I tested the annotation part of the pipeline using the test_annotation profile and following command:

nextflow run nf-core/sarek -profile test_annotation,docker --tools vep,snpeff

...
-------------------- EXCEPTION --------------------
MSG: ERROR: Cache assembly version (WBcel235) and database or selected assembly version (GRCh37) do not match

If using human GRCh37 add "--port 3337" to use the GRCh37 database, or --offline to avoid database connection entirely
...

I attached the failed VEP process log files

command.err.txt command.log.txt command.sh.txt

nextflow.log

Best, Momo

maxulysse commented 3 years ago

Hi @ChillyMomo709 This error has been fixed in the PR #288 which has been merged in dev. Adding -r dev to specify the dev branch will solve this problem. Planning for a new release (2.7) soon.