Dear Qiime2 community,
I got an error while running a diversity core-metrics-phylogenetic analysis:
Plugin error from diversity:
/tmp/q2-LSMatFormat-8m2s9vb9 is not a(n) LSMatFormat file
Debug info has been saved to /tmp/qiime2-q2cli-err-5nhma5vd.log
The command I used is:
qiime diversity core-metrics-phylogenetic
The workflow used to work on all the previous experiment I analyzed before this one. I checked all I could but I still have no idea where come from the problem.
Here you could find the files previously generated to this command:
rep-seq.qza (669.5 KB)
taxonomy.qza (493.8 KB)
rooted-tree.qza (332.9 KB)
table-dada2.qza (435.3 KB)
Manifest.tsv (4.0 KB)
Any help will be appreciated.
Welcome back to the forum!
Thanks for providing these details, and your input data - I was able to reproduce this on my end, and it seems as though the issue is something very subtle (nothing glaringly obvious at this point). I am going to keep digging on this one, but just as a heads up we are heading into a holiday weekend here in the US so I will be back in touch by mid next week. Thanks for your patience with this one, we'll get to the bottom of it!
thank you for helping me. I am pleased to read you that the solution isn't obvious and that I didn't post this topic for not a worthwhile reason.
I finally found the problem: I think that this error occurs because some sample names contain characters (like "," or "="). Indeed, if I replace all the samples names by only numbers all is fine.
Thank you for spending time to help.