Question: gsnap error (Unable to retrieve request for thread)
0
gravatar for Mohammad Reza Bakhtiarizadeh
5.3 years ago by
Tehran university

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 know what is the problem. if possible help me. Thanks a lot in advance.

 

Best

snp rna-seq alignment • 1.6k views
ADD COMMENTlink modified 4 months ago by emccoy500 • written 5.3 years ago by Mohammad Reza Bakhtiarizadeh290
0
gravatar for emccoy50
4 months ago by
emccoy500
emccoy500 wrote:

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.

ADD COMMENTlink written 4 months ago by emccoy500
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