Objective: I am trying to use kissplice to obtain SNPs from my RNA-seq (fastq) data.
Problem: Even after setting the stack limit to unlimited, I am still getting stack limit error.
These are my scripts:
ulimit -s unlimited
ulimit -s
hpc biocontainers/kissplice:v2.4.0-p1-4-deb_cv1 \
kissplice \
-r ***/F1-1A_S1_R1_001.fastq.gz \
-r ***F1-1A_S1_R2_001.fastq.gz \
-r ***/F1-1B_S2_R1_001.fastq.gz \
-r ***/F1-1B_S2_R2_001.fastq.gz \
-r ***F1-1C_S3_R1_001.fastq.gz \
-r ***/F1-1C_S3_R2_001.fastq.gz \
-s 1 \
-v \
-o ***/12_kissplice/f1_1/ \
-d ***/f1_1_temps/
These are the size of my inputs:
1A = 18.5 million reads 2x
1B = 55.4 million reads 2x
1C = 17.5 million reads 2x
•
written
by
bioinformaticsstudent •
1 answer
Dear user,
I must say I never run KisSplice on a high performance computer.
I am not sure what the following command does:
hpc biocontainers/kissplice:v2.4.0-p1-4-deb_cv1 \
Does it mean that you are running KisSplice on a different computer?
If so, maybe the command ulimit -s unlimited is actually not run on the same computer on which you are launching KisSplice ?
A way around this is to write a bash script containing all the commands you want to run on the hpc, and then send these commands together.
You may also want to try to download KisSplice from here: http://kissplice.prabi.fr/ to get the latest version
Best,
Vincent
•
written
by
vincent.lacroix
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