In KisSplice, I already set "ulimit -s unlimited", but I am still getting stack limit error. Is there a work around this?

Question

[bioinformaticsstudent]

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

[Ram]

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Answer 1

[vincent.lacroix]

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