Using CAMISIM v2.0 to generate metagenomes but the storage run out when generating reads using art

[Andyargueasae]

Hi,

I run the metagenomic workflow using your nextflow version of CAMISIM, but found that when running the reads generator art, it pops out an error saying that I am running out of the space. I set my sample size to be 10Gbp.

This is my distribution file. Can someone spot any errors in it?
distribution_0.txt

Cheers
Andy

[AlphaSquad]

Hi Andy,
the distribution file probably is not the problem. I know it sounds like an obvious question, but still: Are you sure that there is enough space available in your out directory? You need more than 2 x #samples x 10 GB available with your sample size.

[Andyargueasae]

Hi Adrian, Thanks for letting me know. I figured out that nextflow is taking the storage of my home directory, that is the reason. Are there any ways to configure it so that it won't take my home directory? Cheers Andy

…

On Tue, Nov 26, 2024 at 8:09 AM Adrian Fritz ***@***.***> wrote: Hi Andy, the distribution file probably is not the problem. I know it sounds like an obvious question, but still: Are you sure that there is enough space available in your out directory? You need more than 2 x #samples x 10 GB available with your sample size. — Reply to this email directly, view it on GitHub <#200 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AU7UKDM3QWINCXRES5WRCR32COGY5AVCNFSM6AAAAABSLUOFEGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJZGAZTSMJXG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[joyceFunk123]

Hi Andy,
You should be able to change the output directory in the CAMISIM/pipelines/metagenomic/config/metagenomic.config file using the outdir directive.
You can find more information about the configuration files in the wiki (https://github.com/CAMI-challenge/CAMISIM/wiki/Configuration-File-Options).
Did this solve the problem?

[Andyargueasae]

Sorry for the late reply. I cleaned up my cache and the problems got solved.

Meanwhile I have another problem. I want to use the merged bam files (single-genome bams merged by samtools) in metagenomic analysis. I tried calculating the mean coverage using coverm, that produces a coverage text profile. But the process failed. So here I wonder whether I picked the wrong mapper or there are something else I should take notes of?