First time trying out HISAT2 and I'm having a problem here, even with the pre-made indices for GRCH38.
$ hisat2 -x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran -1 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R1_001.fastq.gz -2 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R2_001.fastq.gz -S tmp.sam
Could not locate a HISAT2 index corresponding to basename "/share/projects/RNASeq/data/reference/GRCh38/grch38_tran" Error: Encountered internal HISAT2 exception (#1) Command: /home/echang/software/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -S tmp.sam -1 /tmp/31969.inpipe1 -2 /tmp/31969.inpipe2 /share/projects/RNASeq/data/reference/GRCh38/grch38_tran (ERR): hisat2-align exited with value 1
The contents of the
$ ls /share/projects/RNASeq/data/reference/GRCh38/grch38_tran genome_tran.1.ht2 genome_tran.3.ht2 genome_tran.5.ht2 genome_tran.7.ht2 make_grch38_tran.sh genome_tran.2.ht2 genome_tran.4.ht2 genome_tran.6.ht2 genome_tran.8.ht2
I thought perhaps the
genome_tran.*.ht2 needed to change to
grch38_tran.*.ht2, but it still does not work after renaming. I've since untarred the original file again without change. Was there a step I missed? Where can I find
-x <hisat2-idx> The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.ht2 / etc. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2_INDEXES environment variable.