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