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/212131<https://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. - You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmetagenome-atlas%2FTutorial%2Fissues%2F5%23issuecomment-917496618&data=04%7C01%7C%7Cada04884c6be4d15e46a08d97575df28%7Cc7a0410b695b4223af74d14c2e7652e8%7C0%7C0%7C637669971389171789%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3p4XZHZU%2BrDqRA%2BM206xM4xLuUm2poMYgBh9IqsTokA%3D&reserved=0>, or unsubscribe<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAFGBPLD7RT3VJL2A42OPRQ3UBPLY5ANCNFSM5D2ZTY3Q&data=04%7C01%7C%7Cada04884c6be4d15e46a08d97575df28%7Cc7a0410b695b4223af74d14c2e7652e8%7C0%7C0%7C637669971389171789%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=khVRf%2FWeHuqPIMB%2FgI0rcnyXChZN24vYMkBY4G0yB9k%3D&reserved=0>. Triage notifications on the go with GitHub Mobile for iOS<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7C%7Cada04884c6be4d15e46a08d97575df28%7Cc7a0410b695b4223af74d14c2e7652e8%7C0%7C0%7C637669971389181779%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bE0bpiKJXcft%2BGdcNMYk7azHdRLmYNiNnSUSVTgKbh8%3D&reserved=0> or Android<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7C%7Cada04884c6be4d15e46a08d97575df28%7Cc7a0410b695b4223af74d14c2e7652e8%7C0%7C0%7C637669971389191780%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mA3A7SuSomJXLqqE6kXudWpYQmv9Ka5B77jzDljf%2FGo%3D&reserved=0>.

[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