Segmentation fault sambamba

[jfreimer]

Hi,

I am trying to run the pipeline on some files from encode. I keep getting a segmentation fault killing the job when running sambamba to sort the files. However, if I just run the shell command on its own it runs just fine.

[Thu Jul 22 17:58:54 2021]
Job 4: ALIGN: sort bam file for analysis/align/IRF1_K562_input/IRF1_K562_input.bam

/usr/bin/bash: line 1:  2913 Segmentation fault      (core dumped) sambamba sort analysis/align/IRF1_K562_input/IRF1_K562_input.bam -o analysis/align/IRF1_K562_input/IRF1_K562_input.sorted.bam -t 8 -m 4G 2>> analysis/logs/align/IRF1_K562_input.log
[Thu Jul 22 17:59:14 2021]
Error in rule align_sortBams:
    jobid: 4
    output: analysis/align/IRF1_K562_input/IRF1_K562_input.sorted.bam
    log: analysis/logs/align/IRF1_K562_input.log (check log file(s) for error message)
    shell:
        sambamba sort analysis/align/IRF1_K562_input/IRF1_K562_input.bam -o analysis/align/IRF1_K562_input/IRF1_K562_input.sorted.bam -t 8 -m 4G 2>>analysis/logs/align/IRF1_K562_input.log

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

However, if I just run this on a development node it runs fine:
(chips) [jfreimer@dev3 test_chip]$ sambamba sort analysis/align/IRF1_K562_input/IRF1_K562_input.bam -o analysis/align/IRF1_K562_input/IRF1_K562_input.sorted.bam -t 8 -m 8G 2>>analysis/logs/align/IRF1_K562_input.log

[zhangzhiyangcs]

Hi, I get similar error when I run the example from F1000. But I met error at fastp which report Segmentation fault (core dumped). Do you deal with it? Thanks a lot.

[baigal628]

Hi, I guess it might be a memory issue. Allocating larger memory should help.