Question about reproducing a previous metaphlan3 run

Microbial community profiling MetaPhlAn
1

Hi, I needed to reproduce a previous metaphlan3 run to check some results for technical duplicate sequences as well as run some new samples with the exact same database and version as previously.

Thanks, the exact database version and command I originally used is in each output file I saved from the original run. So there cannot be a mistake in that. I have those previous relative abundance files and the read alignment bowtie files.
The database was mpa_v30_CHOCOPhlAn_201901 and metaphlan3 in 2021.

I had to reinstall it and rebuild the environment now since I didn’t have that version any more.
I rebuilt and installed mpa_v30_CHOCOPhlan_201901 from your Google Drive. However, using the same database version and exact same command with the same previous read input files, I get different results (lower) and traced it to having less alignments. No errors.
Does anyone have any thoughts why I might be getting less alignments now with same commands? Is there something I should be checking?
Thanks,
Lisa

2

Hi @Lisa_Crossman
It’s difficult to say, could it be you’re using a different subversion of metaphlan3? e.g. metaphlan3.1 vs metaphlan 3.0?

3

Hi, I have tried both and also metaphlan 3.0.14, that does not seem to be the problem, there are slightly different number of aligns but just a few.
md5 of downloaded database is OK.
Could it be that the version of bowtie causes differences? Or Python?

4

It’s possible there is some difference when using different versions of the tools (e.g. bowtie2) but since we don’t have the exact environment that was used to run the analysis I don’t know how to confirm. How different are the results in terms of relative abundances? In general, if it is a possibility, I would suggest to just use MetaPhlAn4.2.2 on all the samples to have a better resolution and consistency across samples.