TB-Profiler is not working anymore

usegalaxy.org support
, ,
1

Hi there! Did not analyze my WGS data for a while, and now TB-Profiler tool is not working anymore. I have checked everything, and it still shows, that there is an error:
File “/usr/local/lib/python3.9/site-packages/pathogenprofiler/utils.py”, line 404, in run_cmd
raise ValueError(“Command Failed:\n%s\nstderr:\n%s” % (cmd,stderr.decode()))
ValueError: Command Failed:
set -u pipefail; bcftools view -c 1 -a ./05d2bde0-cb67-40ec-a289-8743bf449a96.targets.vcf.gz | bcftools norm -m - | bcftools view -v snps | combine_vcf_variants.py --ref /usr/local/share/tbprofiler//tbdb.fasta --gff /usr/local/share/tbprofiler//tbdb.gff | snpEff ann -dataDir /usr/local/share/snpeff-5.1-2/data -noLog -noStats Mycobacterium_tuberculosis_h37rv - | bcftools sort -Oz -o /corral4/main/jobs/051/330/51330202/working/cf5d8a88-3ebe-4bc4-a0b2-5018d4f00764.vcf.gz && bcftools index /corral4/main/jobs/051/330/51330202/working/cf5d8a88-3ebe-4bc4-a0b2-5018d4f00764.vcf.gz
stderr:
Lines total/split/realigned/skipped: 75/0/0/0
mkdtemp(/tmp/bcftools-sort.EHVcTP) failed: Read-only file system
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/051/330/51330202/_job_tmp -Xmx28g -Xms256m

Cleaning up after failed run
e[91m

I will be extremely grateful for an advice.
Darja

2

Hi @Darja_Sadovska

This part means there is a server issue. Specifically, the container the job is running in is not allowing intermediate files to be written. We’ll need to fix that.

Options:

  1. Try again with a different version of the tool (unlikely to work for this case, but can try)
  2. Try at the EU or AU server for now

I’ll mark this as an open issue, and our team can work on it after the GCC conference is over.

Thanks for reporting the problem and apologies for the troubles!