gsnap error (Unable to retrieve request for thread)

Question

[Mohammad Reza Bakhtiarizadeh]

Hi

I used gsnap (gmap-2014-12-24) to map my RNA-seq data. My PC has 16 Gig RAM and 8 core CPU. my used code was:

gsnap \
  -B 4 \
  -s Oar_v3.1.77.splicesites \
  -n 1 \
  -Q \
  -E 1000 \
  -O \
  --nofails \
  --split-output=outputGsnap \
  -A sam \
  --quality-protocol=illumina \
  -D /home/mrb/Genome/Sheep/Ensemble/gsnap \
  -d Oar_v3.1.77 \
  heart-trim-1.fq heart-trim-2.fq

After running it gave me an error:

366820 splicesites are valid...2 entries with distance > 200000 specified for local splice distance...splicetrie_obs has 479961 entries...splicetrie_max has 49036981 entries...done
GMAP modes: pairsearch, indel_knownsplice, terminal, improvement
Starting alignment
Signal received: Segmentation fault
Unable to retrieve request for thread
Aborted

So I really don't know what the problem is. If possible help me. Thanks a lot in advance.

Best

Answer 1

[emccoy50]

I had the same error. The cause was that the admin did not enable threaded jobs on GSNAP. The original GSNAP is an unthreaded program, but the SAM output option requires multiple threads to run. The admin saw the original documentation and added GSNAP as an unthreaded program.