Alba Mas Malavila
03/12/2026, 2:16 PMERROR ~ Validation of pipeline parameters failed!
The following invalid input values have been detected:
* --msisensorpro_scan (/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MSIsensorPro/Homo_sapiens_assembly38.msisensor_scan.list): the file or directo
ry 'igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MSIsensorPro/Homo_sapiens_assembly38.msisensor_scan.list' does not exist
* --msisensor2_models (igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MSIsensor2/models_hg38//): the file or directory igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MSIsensor2/models_hg38//' does not exist
I'm running the pipeline with genome GATK.GRCh38 and specifying the path to the downloaded iGenomes references with --igenomes_base. Also, I'm running it without any tools to just perform alignment. Why is it looking for the msisensor references then? Do I need to download all references for the pipeline to work even though I'm not using them?
I've tried running older versions of the pipeline and it happens the same with 3.7.1 but it works properly with 3.5.1. In the log I can see a list of "Reference genome options" with parameters and file paths; in v3.5.1 the msisensor paths are not there, so I guess that's why it's not failing.
Thanks for your help!Alba Mas Malavila
03/12/2026, 3:02 PM