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ohlab / SMEG

Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset
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Halted at draft genome re-order step #4

Closed fannimi2001 closed 4 years ago

fannimi2001 commented 4 years ago

I'm trying to build a database for my interesting species with 90 genomes. The building step halted at re-ordering step for more than a week. I'm wondering is that exceeds the computing limit.

aemiol commented 4 years ago

That is quite weird. SMEG uses the tool Mauve to reorder genomes. Are all your genomes from the same species? I suspect one or some of your genomes are contaminants. Did you successfully run the example test? Is there a way you can share your genomes so I have a quick look?

fannimi2001 commented 4 years ago

B_uni_genomes.tgz https://drive.google.com/file/d/1N44Yh8eGmmeXrW07YP-14yD_VmOfDXOj/view?usp=drive_web Yes, I did successfully run the example test. Please find the genomes attached.

Mi

On Fri, May 29, 2020 at 10:30 PM aemiol notifications@github.com wrote:

That is quite weird. SMEG uses the tool Mauve to reorder genomes. I suspect one or some of your genomes are contaminants. Did you successfully run the example test? Is there a way you can share your genomes so I have a quick look?

  • Tunde

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ohlab/SMEG/issues/4#issuecomment-636263074, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALMM4GDMFTJAPSIDKNLHHXLRUBVUHANCNFSM4NOOY4PA .

aemiol commented 4 years ago

The build ran successfully on my system without a hitch. The command used was "smeg build_species -g . -o B_uni -a -p 30" and it took just over 8 hr on the cluster.

Did you run it on your local machine or on an HPC environment? Anyway, you can download the build results from https://drive.google.com/file/d/1rzKFm-pUBS2P6UGvOJlDdR5-AwVXKQWH/view?usp=sharing

Going through the log file (log.txt), the preferred database will be B_uni/T.0.6/ or B_uni/F.0.6/

Cheers, Tunde

fannimi2001 commented 4 years ago

Thank you so much! The command I ever used was "smeg build_species -g . -o B_uni -a -p 16" on the cluster.

Mi

On Sun, May 31, 2020 at 2:06 AM aemiol notifications@github.com wrote:

The build ran successfully on my system without a hitch. The command used was "smeg build_species -g . -o B_uni -a -p 30" and it took just over 8 hr on the cluster.

Did you run it on your local machine or on the cluster? Anyway, you can download the build results from https://drive.google.com/file/d/1rzKFm-pUBS2P6UGvOJlDdR5-AwVXKQWH/view?usp=sharing

Going through the log file (log.txt), the preferred database will be T.0.6 or F.0.6

Cheers, Tunde

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ohlab/SMEG/issues/4#issuecomment-636427860, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALMM4GCTZUMXTLD6FWEXASLRUHXWRANCNFSM4NOOY4PA .