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`Align` step fails with `could not open input file /geneInfo.tab`

Open benostendorf opened this issue 1 year ago • 5 comments

I have deployed the latest version of this workflow (v2.1.2) and only adjusted the config files. I use the ENSEMBL GRCm38 mouse reference genome (release 102).
Unfortunately, the mapping step fails with the following error:

Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab
Solution: check that the file exists and you have read permission for this file
          SOLUTION: utilize --sjdbGTFfile /path/to/annotations.gtf option at the genome generation step or mapping step

Jun 06 19:42:37 ...... FATAL ERROR, exiting

This seems to be the same error as reported here. Thank you for looking into this!

benostendorf avatar Jun 06 '24 17:06 benostendorf