I was trying to align 2 fastqsanger files that was trimmed using to FASTQ Quality trimmer (window size 4, average score >=20) to the hg19 reference genome using BWA. But I got the following error message from galaxy job runner:
“slurmstepd: error: _prec_extra: Could not find task_memory_cg, this should never happen”
Command line
set -o | grep -q pipefail && set -o pipefail; bwa aln -t "${GALAXY_SLOTS:-1}" '/galaxy/data/hg19/hg19full/bwa_index_v0.7.10-r789/hg19full.fa' '/galaxy-repl/main/files/038/979/dataset_38979636.dat' > first.sai && bwa aln -t "${GALAXY_SLOTS:-1}" '/galaxy/data/hg19/hg19full/bwa_index_v0.7.10-r789/hg19full.fa' '/galaxy-repl/main/files/038/979/dataset_38979657.dat' > second.sai && bwa sampe '/galaxy/data/hg19/hg19full/bwa_index_v0.7.10-r789/hg19full.fa' first.sai second.sai '/galaxy-repl/main/files/038/979/dataset_38979636.dat' '/galaxy-repl/main/files/038/979/dataset_38979657.dat' | samtools sort -@${GALAXY_SLOTS:-2} -O bam -o '/galaxy-repl/main/files/038/988/dataset_38988929.dat'
Tool generated the following standard error:
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate… 106.28 sec
[bwa_aln_core] write to the disk… 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate… 106.06 sec
[bwa_aln_core] write to the disk… 0.05 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate… 100.54 sec
[bwa_aln_core] write to the disk… 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
.
.
.
Galaxy job runner generated the following standard error:
slurmstepd: error: _prec_extra: Could not find task_memory_cg, this should never happen
slurmstepd: error: _prec_extra: Could not find task_memory_cg, this should never happen
slurmstepd: error: _prec_extra: Could not find task_memory_cg, this should never happen
slurmstepd: error: _prec_extra: Could not find task_memory_cg, this should never happen
slurmstepd: error: _prec_extra: Could not find task_memory_cg, this should never happen
.
.
.