exitcode 1 without any error message about nubeamdedup HOT 6 CLOSED

Thank you for the information. This is caused by the inappropriate exit code I specified in the script. There is no problem with the final fastq files. I am sorry about the problem and will fix it and let you know.

from nubeamdedup.

Great, I haven't tested it yet but it should work fine in snakemake.
Thank you very much for your quick fix.

from nubeamdedup.

Thank you for raising the issue Dr. Simon. I have no experience in snakemake, but I find this, perhaps worth a try as a temporary ad hoc measure. Please let me know if it works. Meanwhile, I will check the exitcode issue in nubeam-dedup script and let you know later.

from nubeamdedup.

Thank you, this is indeed what I have been doing so far and it works fine. I am more worried if their is an undetected problem with the final fastq files.

from nubeamdedup.

Just to complete the investigation.
I ran the following script test_nubeam.sh inside a singularity image where nubeam-dedup is installed

#! /usr/bin/env bash

set +e
nubeam-dedup -i1 /opt/nubeamdedup/toydata/1.fq.gz -i2 /opt/nubeamdedup/toydata/2.fq.gz
exitcode=$?
echo "exitcode: ${exitcode}"
wc -l *.fastq

singularity exec assembly_10x/containers/assembly_tools.sif bash test_nubeam.sh

which gives me

Output unique read pairs read 1 to /data/ref_genomes/1.uniq.fastq 
Output unique read pairs read 2 to /data/ref_genomes/2.uniq.fastq 
exitcode: 1    
  276884 1.uniq.fastq 
  276884 2.uniq.fastq 
  553768 total

So even with the test data there is an exicode 1.

from nubeamdedup.

Dear Dr. Simon,

Thank you for raising the issue, which has been fixed as below. Please let me know if it works in snakemake. Thank you.

foo@bar:~/nubeamdedup/Linux$ ./nubeam-dedup -i1 ../toydata/1.fq.gz -i2 ../toydata/2.fq.gz
Output unique read pairs read 1 to ~/nubeamdedup/Linux/1.uniq.fastq
Output unique read pairs read 2 to ~/nubeamdedup/Linux/2.uniq.fastq
foo@bar:~/nubeamdedup/Linux$ echo $?
0

from nubeamdedup.