Specifying memory and number of jobs

[Sewunet-Abera]

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.

[SilasK]

By the way, I'm giving a course on metagenome atlas https://oulu.fi/uniogs/node/212131 If you want and can attend. try to register.

For the error check what's in sample2/logs/assembly/pre_process/error_correction_QC.log If it's the memory, yes increase 'mem' in the econfig.

[Sewunet-Abera]

Thank you so much, I would love to attend that. But is it a free training or do you have exemptions for sandwich students?

Greetings

From: Silas Kieser @.> Sent: Sunday, September 12, 2021 12:46 AM To: metagenome-atlas/Tutorial @.> Cc: AberaDinke, Sewunet @.>; Author @.> Subject: Re: [metagenome-atlas/Tutorial] Specifying memory and number of jobs (#5)

By the way, I'm giving a course on metagenome atlas https://oulu.fi/uniogs/node/212131https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Foulu.fi%2Funiogs%2Fnode%2F212131&data=04%7C01%7C%7Cada04884c6be4d15e46a08d97575df28%7Cc7a0410b695b4223af74d14c2e7652e8%7C0%7C0%7C637669971389161794%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=GjBpAlewQQRiCcnDd8%2F%2BJ22OlbL9XO%2BmNzvavsc5PfY%3D&reserved=0 If you want and can attend. try to register.

For the error check what's in sample2/logs/assembly/pre_process/error_correction_QC.log If it's the memory, yes increase 'mem' in the econfig.

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[SilasK]

Check the log: sample2/logs/assembly/pre_process/error_correction_QC.log

If it's due to the memory increase mem in the config file to 100