dgoswamia
commented
9 months ago Hello @nrhorner as you suggested created a new ticket, please review the ticket and help me with the issue. Thanks
Closed dgoswamia closed 7 months ago
dgoswamia
commented
9 months ago Hello @nrhorner as you suggested created a new ticket, please review the ticket and help me with the issue. Thanks
ArchKudo
commented
9 months ago Hi @dgoswamia , exit status 137 might be due to memory constraints could you try this troubleshooting faq: https://labs.epi2me.io/trouble-shooting/#error-command-exit-status-137 and let me know how it goes?
nrhorner
commented
9 months ago Thanks for opening a new ticket @dgoswamia
It looks like I need to assign more memory to the medaka process. A workaround for now is this:
Create a file with the following contents. Lets call it resource.config
process {
withName: medaka_consensus {
memory = 8.GB
}
}And add the following to your command
-r resource.config
You could increase the memory further if that does not work for you
Please let me know if that doesn't work for you.
Thanks
dgoswamia
commented
9 months ago Hello @nrhorner , what is the default memory for medaka_consensus and can you please let me know where it is defined? Thanks
nrhorner
commented
9 months ago @dgoswamia It was set to 2GB (which is too low) https://github.com/epi2me-labs/wf-aav-qc/blob/master/main.nf#L337
I'll get that increased and release it ASAP. In the meantime, the workaround I posted should work for you.
Thanks
nrhorner
commented
9 months ago @dgoswamia The pre-release version has increased the medaka memory allocation to 8GB. You can test that out using -r prerelease
Thanks,
Neil
nrhorner
commented
7 months ago No response so closing this
Operating System
Other Linux (please specify below)
Other Linux
AWS AMI, Linux/UNIX Centos
Workflow Version
v1.0.3
Workflow Execution
Other (please describe)
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-aav-qc \ -r v1.0.3 \ --fastq input_files/fastq_files/ \ --ref_host input_files/ref_host_files/Homo_sapiens.GRCh38.dna.toplevel.fa \ --ref_helper input_files/ref_helper_files/Helper_fiber_removed.fasta \ --ref_rep_cap input_files/ref_rep_cap_files/pTrans_Rep2_AAV9-PHP.eB.fasta \ --ref_transgene_plasmid input_files/ref_transgene_plasmid_files/ HA_MYBPC3.fasta \ --itr1_start 1375 \ --itr1_end 1519 \ --itr2_start 5937 \ --itr2_end 6081 \ -profile standard
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
Error on the workflow
ERROR ~ Error executing process > 'pipeline:medaka_consensus (1)'
Caused by: Process
pipeline:medaka_consensus (1)terminated with an error exit status (137)Command executed:
Extract reads mapping to transgene plasmid
samtools view align.bam -bh " HA_MYBPC3" > transgene_reads.bam samtools index transgene_reads.bam
echo r1041_e82_400bps_sup_variant_g615
echo r1041_e82_400bps_sup_variant_g615
medaka consensus transgene_reads.bam "consensus_probs.hdf" --threads 2 --model r1041_e82_400bps_sup_variant_g615
medaka stitch --threads 2 consensus_probs.hdf transgene_plasmid.fa "fastq_files.transgene_plasmsid_consensus.fasta" bgzip "fastq_files.transgene_plasmsid_consensus.fasta"
medaka variant transgene_plasmid.fa consensus_probs.hdf "transgene_plasmid.vcf"
bcftools sort transgene_plasmid.vcf > "fastq_files.transgene_plasmsid_sorted.vcf.gz"
Command exit status: 137
Command output: r1041_e82_400bps_sup_variant_g615 r1041_e82_400bps_sup_variant_g615
Command error: [18:30:41 - Sampler] Initializing sampler for consensus of region KI270516.1:0-1300. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270389.1:0-1298. [18:30:41 - Sampler] Took 0.05s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270466.1:0-1233. [18:30:41 - Sampler] Took 0.05s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270388.1:0-1216. [18:30:41 - Sampler] Took 0.10s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270544.1:0-1202. [18:30:41 - Sampler] Took 0.04s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270310.1:0-1201. [18:30:41 - Sampler] Took 0.05s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270412.1:0-1179. [18:30:41 - Sampler] Took 0.07s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270395.1:0-1143. [18:30:41 - Sampler] Took 0.06s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270376.1:0-1136. [18:30:41 - Sampler] Took 0.04s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270337.1:0-1121. [18:30:41 - Sampler] Took 0.08s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270335.1:0-1048. [18:30:41 - Sampler] Took 0.06s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270378.1:0-1048. [18:30:41 - Sampler] Took 0.15s to make features. [18:30:41 - Sampler] Initializing sampler for consensus of region KI270379.1:0-1045. [18:30:42 - Sampler] Took 1.26s to make features. [18:30:42 - Sampler] Initializing sampler for consensus of region KI270329.1:0-1040. [18:30:42 - Sampler] Took 1.28s to make features. [18:30:43 - Sampler] Initializing sampler for consensus of region KI270419.1:0-1029. [18:30:43 - Sampler] Took 0.07s to make features. [18:30:43 - Sampler] Initializing sampler for consensus of region KI270336.1:0-1026. [18:30:43 - Sampler] Took 0.06s to make features. [18:30:43 - Sampler] Took 0.07s to make features. [18:30:43 - Sampler] Initializing sampler for consensus of region KI270312.1:0-998. [18:30:43 - Sampler] Initializing sampler for consensus of region KI270539.1:0-993. [18:30:43 - Sampler] Took 0.02s to make features. [18:30:43 - Sampler] Took 0.04s to make features. [18:30:43 - Sampler] Initializing sampler for consensus of region KI270385.1:0-990. [18:30:43 - Sampler] Initializing sampler for consensus of region KI270423.1:0-981. [18:30:43 - Sampler] Took 0.04s to make features. [18:30:43 - Sampler] Initializing sampler for consensus of region KI270392.1:0-971. [18:30:43 - Sampler] Took 0.03s to make features. [18:30:43 - Sampler] Initializing sampler for consensus of region KI270394.1:0-970. [18:30:43 - Sampler] Took 0.07s to make features. [18:30:43 - Sampler] Initializing sampler for consensus of region HA_MYBPC3:0-9850. [18:30:43 - Sampler] Took 0.03s to make features. [18:30:43 - Sampler] Initializing sampler for consensus of region pTrans_Rep2_AAV9-PHP.eB:0-7467. [18:30:43 - Sampler] Took 0.04s to make features. [18:32:22 - Feature] Processed HA_MYBPC3:0.0-9849.0 (median depth 8084.0) [18:32:22 - Sampler] Took 99.15s to make features. .command.sh: line 11: 6619 Killed medaka consensus transgene_reads.bam "consensus_probs.hdf" --threads 2 --model r1041_e82_400bps_sup_variant_g615
Work dir: /mnt/efs/home/dgoswami/running_nextflow/epi2me-labs-wf-aav-qc/work/8c/9805556e17a61d3e50f60af373320b
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.out-- Check '.nextflow.log' file for details
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response