Question: Problem with HISAT
gravatar for rr14049
17 months ago by
United Kingdom
rr140490 wrote:


Im trying to run a custom workflow for RNA-seq data structured as follows:

  1. Inputs: reference genome (GRCm38), forward and reverse (paired-end reads)

  2. 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.

rna-seq hisat cuffdiff • 520 views
ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson24k • written 17 months ago by rr140490
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson24k wrote:


This is at

It appears that something is wrong with either the inputs or parameters. Double check all inputs to make sure from the same exact reference genome. The library type warning is usually not a fatal error - the default type will assign automatically, but you can also have a look at params set vs the manual.

Best, Jen, Galaxy team

ADD COMMENTlink written 17 months ago by Jennifer Hillman Jackson24k
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