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

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

1

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


snp


kissplice


rna-seq


stack


KisSplice

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