segmentation fault (core dumped)

[sjtu....@gmail.com]

I got the segmentation fault (core dumped) error and a core.file when I used SGE  to qsub trust-job to compute node. While I connected  compute node through ssh and run the trust-job on it directly, it worked well. What is problem?

My trust-job is :

#! /bin/bash 

#$ -S /bin/bash

#$ -V

#$ -N trust

#$ -l vf=10G,p=4,h=compute-1-6

#$ -q default.q

#$ -cwd

#$ -wd /**/USER/yangshuang/data/trust_test/

trust -f /**/USER/yangshuang/data/mapped/**.sorted.bam -g hg38 -c -B -o /**/USER/yangshuang/data/trust_test/ -n 4

core.file :

"Core was generated by `/**/USER/yangshuang/software/anaconda2/bin/python /**/USER/yangshuang/s'.

Program terminated with signal 11, Segmentation fault.

#0  0x00002b4de08de24a in compare_Lgreaterthan64(unsigned long*, int, int, unsigned long*, int, int, int, int*) () at trust/getOverlapInfo.cpp:110

110                 tmp_pre[j] = prefix[j+count_pre];"

result in workdir:

-rw-r--r-- 1 yangshuang **      2767 Jul 29 10:55 **.sorted.bam-BCR-HeavyChain-coverage.txt

-rw-r--r-- 1 yangshuang ** 583771842 Jul 29 10:54 **.sorted.bam-unmapped.bam

-rw-r--r-- 1 yangshuang **   25462985 Jul 29 10:54 **.sorted.bam-Locs.bam

[Bo Li]

Does it work when you run it using login node, or on local computer? If it does, I recommend you to contact the administrator of the computing cluster to figure out. Sometimes such memory segmentation fault happens only in batch submissions.

Best,

Bo

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[sjtu....@gmail.com]

Yes, for some samples, it worked well on both local computer and computing cluster, but for some samples it only worked well on local computer. So I don't know why?

在 2018年7月29日星期日 UTC+8下午10:42:13，Bo Li写道：

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[Bo Li]

Can you try to budget more memory to these tasks, say 50G, instead of 10G?

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[sjtu.syang]

Yes，I have try to budget more than 50G even 100G，but it still did not work.

[Bo Li]

How large is the unmapped.bam file?

Thanks,

Bo