Closed pditommaso closed 6 years ago
Tried both:
sed -i 's@UR:file:.*genome.fa@UR:file:genome.fa@g' genome.dict
and
sed -i 's@UR:file:.*genome.fa@UR:file:'"$PWD"'/genome.fa@g' genome.dict
But still reporting:
##### ERROR
##### ERROR MESSAGE: Invalid command line: Cannot process the provided BAM/CRAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAM/CRAMs in --unsafe mode, but this feature is unsupported -- use it at your own risk!
When using local scratch folder, the step
5_rnaseq_call_variants
returns an error.This happens because the
genome.dict
input file contains a reference to a file created in temporary folder not accessible to the task, for example: