FORUMerror with HISAT2:
Victoria asked 1 year ago

Hi all,
I’m trying to extract features from a GTF file using hisat2. This is the code that I am using:

cd $RNA_REFS_DIR $RNA_REF_GTF > $RNA_REFS_DIR/splicesites.tsv $RNA_REF_GTF > $RNA_REFS_DIR/exons.tsv
hisat2-build -p 8 --ss $RNA_REFS_DIR/splicesites.tsv --exon $RNA_REFS_DIR/exons.tsv $RNA_REF_FASTA $RNA_REF_INDEX

but I keep getting errors that none of the commands are found.

-bash :command not found
-bash :command not found
-bash :command not found

I’m not sure if this is an issue with hisat2 or with compute canada.
Any help would be really appreciated!

1 Answers
zhibin Staff answered 1 year ago

Did you load hisat2 module?
module load hisat2/2.1.0

Victoria replied 1 year ago

I loaded module with ‘module load hisat2-2.1.0’ and it didn’t work but it’s running now with ‘module load hisat2/2.1.0’, thanks!