# problem with using BWA on usegalaxy.org

**URL:** <https://help.galaxyproject.org/t/problem-with-using-bwa-on-usegalaxy-org/3319>\
**Category:** usegalaxy.org support\
**Tags:** bwa, exceeds-memory-error\
**Created:** [April 4, 2020, 7:11pm UTC](https://help.galaxyproject.org/t/problem-with-using-bwa-on-usegalaxy-org/3319 "2020-04-04T19:11:11Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![kct913](https://avatars.discourse-cdn.com/v4/letter/k/ecd19e/32.png) [@kct913](https://help.galaxyproject.org/u/kct913)\
**Post date:** [April 4, 2020, 7:11pm UTC](https://help.galaxyproject.org/t/problem-with-using-bwa-on-usegalaxy-org/3319/1 "2020-04-04T19:11:11Z")

</div>

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  
.  
.  
.

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<div class="post-metadata">

**Author:** ![GraemeT](https://avatars.discourse-cdn.com/v4/letter/g/e495f1/32.png) [@GraemeT](https://help.galaxyproject.org/u/GraemeT)\
**Post date:** [April 5, 2020, 6:32am UTC](https://help.galaxyproject.org/t/problem-with-using-bwa-on-usegalaxy-org/3319/2 "2020-04-05T06:32:26Z")

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Hello  
I was about to file a similar problem/topic so no help here just confirming your report.

I too have been getting “_slurmstepd: error: \_prec\_extra: Could not find task\_memory\_cg, this should never happen_” working on [usegalaxy.org](http://usegalaxy.org).

I succesfully mapped a set of Illumina PE reads against a refenence genome in fasta format using BWA-MEM. As from yesterday (04 April 2020) I have failed consistently to filter the resulting bam file using Filter BAM. Initially I was chaining three filters and thought that may contribute.

However subsequent attempt to run a single filter (is mapped or quality \> 20) keep failing with the same error:  
_slurmstepd: error: \_prec\_extra: Could not find task\_memory\_cg, this should never happen_

The job does partially run as I can see partial results in the centre pane.

p.s. same error if filtering using samtools view