Closed Ist4lri closed 2 months ago
So from what I can see, issue is that null
should have been assigned to genome
.
But in my opinion, sarek should have either failed early.
Or print a huge warning and recompute the basic index from the fasta file:
fai, dict + needed build index.
This is related to #1253 . Can we track there or is there an additional issue you found?
This is related to #1253 . Can we track there or is there an additional issue you found?
Yeah, that sounds similar to me. Let's close this one over the older issue
Description of the bug
I provide a fasta file for running Mutect2 and have this error :
A USER ERROR has occurred: Fasta index file file://GRCh38_latest_genomic.fna.fai for reference file://GRCh38_latest_genomic.fna does not exist. Please see https://gatk.broadinstitute.org/hc/articles/360035531652-FASTA-Reference-genome-format for help creating it.
from Mutect2 of GATK.
But my file is here, and exist.
Command used and terminal output
json :
config :
singularity.cacheDir = '/scratch/plgouttebel/data_Singula/nf-core-sarek_dev/singularity-images'
Output from Log file :
Relevant files
System information
HPC on curta from MCIA (Mésocentre de calcul intensif aquitain) sarek downloaded locally