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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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Output for Test Dataset #10

Closed raufs closed 1 year ago

raufs commented 3 years ago

Hi,

Thank you for developing such a really great method and very cool study too!

I am wondering if it is possible to share the expected results of the test dataset provided to help check if we have SMEG set up correctly?

Kind regards, Rauf

aemiol commented 3 years ago

Hi, Sorry for the slow response. Below is the expected result for the test set

Cluster SMEG Coverage No of SNPs SMEG range cluster1 1.75370127210152 4.08426832179518 10971 1.683 - 1.808 cluster2 1.12409093832417 2.08503190107843 9164 1.114 - 1.169

Thanks. Tunde

raufs commented 3 years ago

Thank you Tunde!

It appears I see similar trends in the results but differences in the values beyond simple rounding error. For instance, I also get that cluster1 has a higher SMEG value than cluster2. I ended up installing through conda and manual tinkering of certain steps in the pipeline, so perhaps I broke something in the process.

Also, I saw it was recommended that we use the Singularity instance, however, it seems that the instance provided might not be compatible with the new Singularity version (at least that's what I interpreted the issue as). Would it be possible to update the Singularity instance/container to work with the latest version?

My exact results are the following:

Cluster SMEG Coverage No of SNPs SMEG range cluster1 1.49942916402499 1.21812828266752 5090 1.416 - 1.517 cluster2 1.17742009741453 2.70058155948281 11114 1.139 - 1.199

Kind regards, Rauf