Hello

This is my first post on Biostars and my first experience with HISAT2.

I am trying to align paired fastq (gz compressed) files to the mouse genome. I use hisat2-2.0.0-beta on Linux on a remote server.

I dowloaded the pre-made grcm38_tran index:

wget --content-disposition https://cloud.biohpc.swmed.edu/index.php/s/grcm38_tran/download
gunzip grcm38_tran.tar.gz 
tar -xvf grcm38_tran.tar

Then I tried to align a set of paried reads:

hisat2 -p 8 --dta -x /users/katrine/transcriptomics/grcm38_tran/genome_tran -1 /users/katrine/transcriptomics/trimmed_seqs/5677FL_R1_val_1.fq.gz -2 /users/katrine/transcriptomics/trimmed_seqs/5677FL_R2_val_2.fq.gz -S 5677FL.sam

But get the following error message: "hisat2-align died with signal 11 (SEGV)"

I have also tried to remove the options "-p 8" and "--dta" as well as gunzipped the files and running the command with and without specification of the filetype by "-q", but everything returned the same error message.

When I inspect the genome_tran with hisat2-inspect I get the error message "Segmentation fault" for all options exept when I put the option "-names" (that looks ok).

It looks like all index files are there:

ls -l genome_tran*

Output:

-rw-r--r-- 1 katrine mibi 1639574274 Mar 17  2016 genome_tran.1.ht2
-rw-r--r-- 1 katrine mibi  664305504 Mar 17  2016 genome_tran.2.ht2
-rw-r--r-- 1 katrine mibi       6119 Mar 17  2016 genome_tran.3.ht2
-rw-r--r-- 1 katrine mibi  663195875 Mar 17  2016 genome_tran.4.ht2
-rw-r--r-- 1 katrine mibi 1482328835 Mar 17  2016 genome_tran.5.ht2
-rw-r--r-- 1 katrine mibi  675618574 Mar 17  2016 genome_tran.6.ht2
-rw-r--r-- 1 katrine mibi   10349748 Mar 17  2016 genome_tran.7.ht2
-rw-r--r-- 1 katrine mibi    2070619 Mar 17  2016 genome_tran.8.ht2

Any help on how to solve this will be highly appreciated! For example hint on how to obtain some kind of log files for debugging.

Thank you! /Katrine