deepbgc pipeline does not seem to use more than 2 cores?

[bkm23644]

Hello,

Thank you for taking the time to develop this tool, it does exactly what I need it to do for my odd gene clusters. However, the only issue is that it takes more than 20 minutes per fasta file for some bacterial genomes. Is this normal?

I have made a simple model both locally on my macbook and on my university's computational cluster and ran deepbgc pipeline on a single bacterial genome fasta file and in both cases there is no improvement in processing speed past 2 cores. When reading the HMMER user manual, it suggests that it should be capable of utilizing all of the cores available. However, deepbgc pipeline --help does not suggest there is a command to specify how many cpu's it can utilize.

Am I missing something obvious here? Should it take 20 minutes for one fasta file? It seems like it would take decades to get through a metagenome at that rate. My apologies for the ignorance, but how does deepbgc call hmmscan/search?

I looked through some of the other issue reports, but we do not seem to be having the same problems. Any advice you can offer is greatly appreciated, I really would like to use this tool for my work.

Thanks

[LuisFF]

You could try setting up HMMER_NCPU environment variable. Check --cpu flag in HMMER documentation.

[bkm23644]

Heya, Thank you for the response! We tried that and it did not seem to work on our computing cluster. I can try it again in case we messed it up, but is there another variable we can mess with? Or perhaps I am misunderstanding how to utilize the HMMER options in a bash script as it is part of the Deepbgc pipeline. It certainly did not seem to alter the variable when set like that. Is it possible to get an example bash script? Sorry for all of the silly questions. I am a baby at bioinformatics, and I love this program for what I need, but the one-CPU/core requirement is suffocating our computing cluster. BKM

…

________________________________ From: Luis F. de Figueiredo ***@***.***> Sent: Thursday, March 17, 2022 1:04 PM To: Merck/deepbgc ***@***.***> Cc: Brendon Myers ***@***.***>; Author ***@***.***> Subject: Re: [Merck/deepbgc] deepbgc pipeline does not seem to use more than 2 cores? (Issue #65) [EXTERNAL SENDER - PROCEED CAUTIOUSLY] You could try setting up HMMER_NCPU environment variable. Check --cpu flag in HMMER documentation. — Reply to this email directly, view it on GitHub<#65 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ANASOOGXZKFYESLQGTFX33DVANQY5ANCNFSM5MK3DKZQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>