Im trying to run a custom workflow for RNA-seq data structured as follows:
Inputs: reference genome (GRCm38), forward and reverse (paired-end reads)
these feed into HISAT and the outputs of this into Cuffdiff along with GRCm38.85 gtf file.
Unfortunately I keep getting the following error message:
Fatal error: Matched on error [22:18:01] Loading reference annotation and sequence. No fasta index found for /galaxy-repl/main/files/017/273/dataset_17273202.dat. Rebuilding, please wait.. Fasta index rebuilt. Warning: No conditions are replicated, switc
Please does anybody have any ideas about what the problem could be here? Any help would be much appreciated! Many thanks.