Specifying memory and number of jobs #5
Description
Hello,
I trying to figure out my way in to get to know atlas.
And currently I'm running the tutorial data set on a server. and run it generously for 4 data sets
atlas run all --resources mem=500 --jobs 50
But down stream I got this error,
Error in rule error_correction:
jobid: 43
output: sample2/assembly/reads/QC.errorcorr_R1.fastq.gz, sample2/assembly/reads/QC.errorcorr_R2.fastq.gz, sample2/assembly/reads/QC.errorcorr_se.fastq.gz
log: sample2/logs/assembly/pre_process/error_correction_QC.log (check log file(s) for error message)
conda-env: /home/nioo/sewuneta/sorghum_shotgun_metagenome_analysis/atlas.trial/atlas/path/to/fastq/conda_envs/ac12f856310e8bfb503b4ccb5cc5fb23
shell:
tadpole.sh -Xmx51G prealloc=1 in1=sample2/assembly/reads/QC_R1.fastq.gz,sample2/assembly/reads/QC_se.fastq.gz in2=sample2/assembly/reads/QC_R2.fastq.gz out1=sample2/assembly/reads/QC.errorcorr_R1.fastq.gz,sample2/assembly/reads/QC.errorcorr_se.fastq.gz out2=sample2/assembly/reads/QC.errorcorr_R2.fastq.gz mode=correct threads=8 ecc=t ecco=t 2>> sample2/logs/assembly/pre_process/error_correction_QC.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Does this mean the specified figures are not enough or I should have done that in the configuration file?
Thanks and hope to hear from you sooner.