getopt trap failing

[calizilla]

Hi,

I could only get version 2.6.2 to run by hashing out the trap commands in gridss.sh. I am on a cluster running CentOS 6.10, Linux version 3.10.0-957.21.3.el6.x86_64 GNU/Linux

Command I used was:
./gridss-2.6.2/scripts/gridss.sh
--output test.vcf
--assembly test.assembly.bam
--reference ./Reference/hs38DH.fasta
--threads 2
--jar ./gridss-2.6.2/gridss-2.6.2-gridss-jar-with-dependencies.jar
--blacklist ./exclude_intervals.bed
--jvmheap 4g
--steps All
--workingdir ./out
--labels U16-B
U16-B.final.bam

Regards,
Cali

[d-cameron]

I'll need a bit more details to track this down as I don't get any failures on my CentOS 6.4 test machine.

• What was the error message you received?
• What errors/warning were in the full log file (check the output for a line similar to Mon Sep 30 11:31:54 EST 2019 Running GRIDSS. The full log is in out/gridss.full.20190930_113154.unix305.wehi.edu.au.56718.log)
• What’s the output from running:

env
lsb_release -a
/bin/bash --version
getopt –version
getopt --test
echo $? ${PIPESTATUS[0]}

[calizilla]

Hi Daniel, Thanks for your fast response. The error message received was: getopt --test` failed in this environment. "exit 1" command completed with exit code 1. Log file – I do not have this, I attempted to re-generate the error – deleting the hashes I had placed in the grids.sh script - however it is running smoothly today, confusingly. Command outputs: $env #See output attached $lsb_release -a LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.10 (Final) Release: 6.10 Codename: Final $ /bin/bash --version GNU bash, version 4.1.2(2)-release (x86_64-redhat-linux-gnu) Copyright (C) 2009 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software; you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. $ getopt --version getopt (enhanced) 1.1.4 $ getopt –test #No output $ echo $? ${PIPESTATUS[0]} 4 4 Regards, Cali [env_out.txt](https://github.com/PapenfussLab/gridss/files/3688558/env_out.txt)

[d-cameron]

Should be fixed in next release (2.6.3)