I used the hisat2 index builder data manager to create a hisat2 reference for a local galaxy server I set up. It ran successfully and now shows up as a built-in genome when running hisat2 and in the "hisat2 indexes" data table entry.
However, every time I try to perform an alignment, it immediately fails and gives me this error. My sense is that somehow hisat2 isn't finding the index I just built, but it definitely exists. Any suggestions?
> Fatal error: Matched on hisat2-align exited with value 1 Warning: Output file 'for' was specified without -S. This will not work in future HISAT 2 versions. Please use -S instead. Extra parameter(s) specified: "hisat", "index/mm10+ERCC", "for", "hisat", "index" Error: Encountered internal HISAT2 exception (#1) Command: /home/chapmanlab/galaxy/database/dependencies/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin/hisat2-align-s --wrapper basic-0 -p 1 -x /home/chapmanlab/galaxy/tool-data/mm10+ERCC/hisat2_index/mm10+ERCC -k 5 -U /media/chapmanlab/3C0B5C6B5F2A43CE/galaxydata/000/dataset_272.dat for hisat index/mm10+ERCC for hisat index (ERR): hisat2-align exited with value 1