Inquiry on Analysis Duration with ANIb and ANIm for Streptomyces Genomes about pyani

[widdowquinn]

Hi @ZiliaMR - I think @kiepczi is well-placed to answer this, as she has done exactly this for the complete set of publicly-available Streps.

[widdowquinn]

In general, though - assuming 1s per pairwise comparison, you can calculate an anticipated time for that of $n^2 / 3600$ hours, for $n$ genomes. There are other overheads, though - updating the database, parsing output files, etc. Also, ANIb takes considerably longer than ANIm.

The current GitHub version 0.3+ has a working fastANI implementation, which would speed things up at the cost of providing an ANI estimate, rather than an ANI calculation.

[kiepczi]

Hi @ZiliaMR. I have run aniM (pyANI version 0.3+) on 300 Streptomyces genomes on a computer cluster with 40 cores and 192GB RAM, which took approximately 4 hours.

In comparison, I also ran much smaller analyses of a maximum of 70 Streptomyces genomes on my local computer with 8 cores and 32GB RAM, which took around 3 hours. However, I ran this analysis overnight to limit background processes running on the computer, so there was less competition for the CPU.

Estimating an exact running time for a job is not an easy task, and it can depend on many factors, just as @widdowquinn said. His suggestion of estimating the running job is probably a good point to start. I also hope that my experiences will give a little bit more idea of how long it could take.

[ZiliaMR]

omg! I will then have to request more resources to carry out the analysis. Thank you very much, this is a great help.