I’m running Maaslin2 on two separate groups of samples. For one set, the output appears to be correct. For the other, Maaslin runs successfully without errors but there is not data in the ‘all_results.tsv’ file. The column names are present but no other data. Shouldn’t there be results here if Maaslin ran successfully?
Hi Dana,
Could you post your maaslin2.log file from that run.
Did it produce any other results? (i.e. heatmaps/boxplots for the covariates of interest).
Also can you run sessioninfo::session_info() and post the resulting text.
Thanks,
Jacob Nearing
Nope, it didn’t produce any figures. Session info:
setting value
version R version 4.2.2 (2022-10-31)
os macOS Ventura 13.1
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Chicago
date 2023-05-16
rstudio 2022.02.3+492 Prairie Trillium (desktop)
pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
And the massli2.log is attached as a txt document. Thanks so much for your help!
maaslin2.log.txt (37.6 KB)
On first look it seems that you have a very complicated model (22 fixed effects) on 18 samples.
I would guess based on the log file that it is likely that you are running into issues during model construction. I would try re-running this with fewer fixed effects to confirm this.
Cheers,
Jacob
Hi Jacob,
Thanks! I did find this morning that it would produce output with fewer than 22 fixed effects and suspected that was the case. Will try fewer! Thanks so much!
Dana