Error from Longitudinal first-differences


Sorry if this has come up before, but after obsessively looking all over the forum, I broke down and made a new post.

I am having a ton of trouble (def user error) running the longitudinal first differences packages. Essentially I am trying to do the same thing this person

This lead me to try to get first-differences. I coded the following based on the longitudinal tutorial.

qiime longitudinal first-differences
--m-metadata-file corn_meta.tsv
--m-metadata-file shannon_vector.qza
--p-state-column period
--p-metric shannon
--p-individual-id-column participant
--p-replicate-handling random
--o-first-differences shannon-first-diff.qza

I get the following error message:

Plugin error from longitudinal:

Debug info has been saved to /var/folders/ps/vxhcfds57kj3sgnrmh8cr58m0000gn/T/qiime2-q2cli-err-132bwe67.log

A few questions along with this "how do I make the above command run?":

  1. the shannon_vector file is directly from my original core-metrics analysis. is this right?
  2. individual ID column- does this require to be in the #q2:types? I am trying to examine them based on participant ID number (rather than participant ID and timepoint as my fastq files are ran as). I have tried it both ways and still get stuck on the error described above.
  3. do I need to merge my metadata? I have tried the following from the tutorial page
    qiime metadata tabulate
    --m-input-file corn_meta.tsv
    --m-input-file shannon_vector.qza
    --o-visualization tabulated-combined-metadata.qzv

however, when I try to use this metadata, I get the following:

'There was an issue with merging QIIME 2 Metadata:
cannot merge metadata with overalapping columns. The following columns overlap: 'shannon_entropy' '

so based on that error, I am assuming the code will automatically merge the results from my original qza files into my metadata to calculate them, but I am just a little lost on how to get my code to run cleanly!

Any help or advice would be much appreciated


Some time ago "shannon" metric column name in the vector was replaced with "shannon_entropy", so I think if you will change it in your command (--p-metric) it should work.


Not sure about this one, just try with your current command (with shannon_entropy).

No need to do it, since plugin will take care of it.

Perfect! That worked! thanks!

Where can I find a list of the current metric names to use? I am trying to do it on my bray curtis distance and 'distance' isn't working as it is stated in the tutorial.

For alpha diversity vectors from core-metrics it should be:

Could you provide a reference to the tutorial you are following, exact command and the error?
I am guessing now but if you are running LME on first-distances output, did you try Distance instead of distance?

Yes, I am sorry. I have been using the longitudinal tutorial page (Performing longitudinal and paired sample comparisons with q2-longitudinal — QIIME 2 2021.11.0 documentation).

I did try both Distance and distance. I was trying however to do a first-difference (the tutorial does it with unweighted-unifrac, so I assumed it would work for all Beta-diversity measures?). Or are there specific ones for each measure like with alpha diversity?

I would also like to create a volatility or some graphical representation of my beta diversity measures. As Beta measures are in a 3D space, I am assuming votaility will not work for that? I remember at a qiime workshop there were moving graphs that did something similar. Where can I find a tutorial on this? I could NOT find one.

Thanks so much for your help

Good news!
@Nicholas_Bokulich answered your questions :star_struck:! I will copy and paste it here .

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.