In KisSplice, I already set "ulimit -s unlimited", but I am still getting stack limit error. Is there a work around this?
1
0
Entering edit mode
6 months ago

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 • 1.6k views
ADD COMMENT
0
Entering edit mode

Please do not delete posts that have received feedback. If the feedback was useful, upvote/accept it as appropriate. If it was not helpful, add a comment stating why it did not help.

ADD REPLY
0
Entering edit mode
6 months ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 1660 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6