Hi,
I have started using GSNAP to align some RNA-Seq reads to a reference genome, and am having some trouble getting the program to run properly. The alignment works fine if I do not use the -s parameter to provide splicing information, but if I do try and use it, the program almost immediately quits for a reason I cannot particularly understand.
Normally I run the command like this:
- gsnap --gunzip -D <directory to="" database=""> -d <database> -t 12 --orientation=FR -A sam > output.sam -N 1 Read1.fastq.gz Read2.fastq.gz
However, when I add splicing (the file is called splicesites.iit and is located in the maps directory of the genome database):
- gsnap --gunzip -D <directory to="" database=""> -d <database> -t 12 --orientation=FR -A sam > output.sam -N 1 -s splicesites Read1.fastq.gz Read2.fastq.gz
the program runs only to the point of allocating memory to everything and then aborts as follows before even starting the alignment:
Allocating memory for ref positions, kmer 8, interval 1...Attached new memory for GSNAP_copy/GSNAP/X.laevis_database/X.laevis_database.ref081locpositions...done (4,891,849,244 bytes, 402.54 sec)
Not expecting version 1
Signal received: SIGABRT
Calling Access_emergency_cleanup
Removed existing memory for shmid 950287
Removed existing memory for shmid 917518
Removed existing memory for shmid 884749
Removed existing memory for shmid 851980
Removed existing memory for shmid 819211
Removed existing memory for shmid 786442
Removed existing memory for shmid 753673
Removed existing memory for shmid 720897
Removed existing memory for shmid 688128
any advice on what might be going on? I am unsure how adding splicing would lead to an abort error like this, but have been unable to find any information in the documentation. I also am fairly amateur when it comes to CS, so its possible I am screwing up something simple with my commands and do not realize. Any help would be appreciated!
Thanks!
