Hi all,
I’m running local Galaxy in a docker container using bgruening/galaxy-stable as a base but running release 22.01 and all other configs are kept standard.
When running a workflow that uses BWA-MEM for processing a collection of 11 pairs, all but 2 jobs error out immediately after starting.
This is the error I get:
/export/galaxy-central/database/job_working_directory/000/330/tool_script.sh: line 43: 3495 Killed bwa mem -t "${GALAXY_SLOTS:-1}" -v 1 -R '@RG\tID:GMM_D9_IgG_S11_L001_001.fastq\tSM:GMM_D9_IgG_S11_L001_001.fastq\tPL:ILLUMINA\tLB:GMM_D9_IgG_S11_L001_001.fastq' '/galaxy-central/tool-data/hg38/bwa_mem_index/BWA_hg38/hg38.fa' '/export/galaxy-central/database/files/000/dataset_7.dat' '/export/galaxy-central/database/files/000/dataset_8.dat'
3500 Done | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/export/galaxy-central/database/files/000/dataset_336.dat'