FORUMerror with HISAT2:
Victoria asked 4 weeks 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
hisat2_extract_splice_sites.py $RNA_REF_GTF > $RNA_REFS_DIR/splicesites.tsv
hisat2_extract_exons.py $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 hisat2_extract_splice_sites.py :command not found
-bash extract_exons.py :command not found
-bash build.py :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 4 weeks ago



Did you load hisat2 module?
module load hisat2/2.1.0

Victoria replied 3 weeks 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!