Closed mathavanpu closed 1 year ago
jfy133
commented
1 year ago Hi @mathavanpu
You should not be modifying teh pipeline code!
To adjust resources, you need to use a custom config file - docs are here: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources
If using a custom config still doesn't work, please feel free to re-open (with your config file attached)
mathavanpu
commented
1 year ago Hi, Thank you for the response Again I got an error I am not able to solve it.
I created the custom config files
process { withName: SPADES { cpus = 100 memory = 240.GB time = 16.h } }
process { withName: CONCOCT_CONCOCT { cpus = 2 memory = 12.GB time = 24.h } }
Command executed: nextflow run nf-core/mag -r 2.3.0 -bg -name Project_Meta_859 -profile docker -params-file nf-params.json -c concot.config spades.config
Error message The exit status of the task that caused the workflow execution to fail was: 250. The full error message was:
Error executing process > 'NFCORE_MAG:MAG:SPADES (CookingOil-1_Trimmed_R)'
Caused by:
Process NFCORE_MAG:MAG:SPADES (CookingOil-1_Trimmed_R) terminated with an error exit status (250)
metaspades.py --only-assembler --threads "10" --memory 64 --pe1-1 CookingOil-1_Trimmed_R.phix_removed.unmapped_1.fastq.gz --pe1-2 CookingOil-1_Trimmed_R.phix_removed.unmapped_2.fastq.gz -o spades mv spades/assembly_graph_with_scaffolds.gfa SPAdes-CookingOil-1_Trimmed_R_graph.gfa mv spades/scaffolds.fasta SPAdes-CookingOil-1_Trimmed_R_scaffolds.fasta mv spades/contigs.fasta SPAdes-CookingOil-1_Trimmed_R_contigs.fasta mv spades/spades.log SPAdes-CookingOil-1_Trimmed_R.log gzip "SPAdes-CookingOil-1_Trimmed_R_contigs.fasta" gzip "SPAdes-CookingOil-1_Trimmed_R_graph.gfa" gzip -c "SPAdes-CookingOil-1_Trimmed_R_scaffolds.fasta" > "SPAdes-CookingOil-1_Trimmed_R_scaffolds.fasta.gz"
cat <<-END_VERSIONS > versions.yml "NFCORE_MAG:MAG:SPADES": python: $(python --version 2>&1 | sed 's/Python //g') metaspades: $(metaspades.py --version | sed "s/SPAdes genome assembler v//; s/ [.*//") END_VERSIONS
Command exit status: 250 The config file CPU values is not exhibited in the command metaspades.py --only-assembler --threads "10" --memory 64 --pe1-1 CookingOil-1_Trimmed_R.phix_removed.unmapped_1.fastq.gz --pe1-2 CookingOil-1_Trimmed_R.phix_removed.unmapped_2.fastq.gz -o spades
it took only 10 threads Kindly help
d4straub
commented
1 year ago -c concot.config spades.config doesnt work, every config needs a -c, use -c concot.config -c spades.config
Such questions might be better asked in the nf-core slack channel #mag, see https://nf-co.re/join.
Description of the bug
Hi there, I am trying to run the mag (2.3.0)pipeline, it got failed with the code 250.
I tried to change spdes cpu values 10 to 100 and memory 64 to 164GB in the base.config file but while running mag it throws an error . uncomitted changes nfcore. Kindly help how to change number of cpu in the config file.
Command used and terminal output
Relevant files
No response
System information
mag (2.3.0)pipeline