Longitudinal error - index out of bounds

[tbranck1]

Hello,

I am getting a similar error as the one above when trying to run the linear-mixed-effects command using the q2-longitudinal plugin.

The error is:
Plugin error from longitudinal:

index 78 is out of bounds for axis 1 with size 72

and the command I used is:
qiime longitudinal linear-mixed-effects --m-metadata-file PAC_domain_sample_metadata_repeatedmeasurestest.txt --m-metadata-file core-metrics-results/shannon_vector.qza --p-metric shannon --p-group-categories Domain,PAC --p-state-column Time_h --p-individual-id-column Individual_ID --o-visualization linear_mixed_effects_round2.qzv --verbose

I've attached the shannon_vector.qza and sample metadata files.

PAC_domain_sample_metadata_repeatedmeasurestest.txt (6.3 KB)

shannon_vector.qza (20.3 KB)

Is this a sample name issue?

Thanks in advance!

[Nicholas_Bokulich]

Hi @tbranck1,
Thank you for posting this error, thank you for researching this error prior to posting, and thank you for sharing your data so we can debug!

@tbranck1

Is this a sample name issue?

That was my initial assumption. However, I cannot replicate your error locally. I run into a number of other errors, however, in this order:

1. It looks like you are running an older version of QIIME 2 (2017.9). Please install the latest version (2018.4) — --p-group-categories is an old parameter name.
2. Time_h contains non-numeric values ("inoculum") that must be converted prior to running. This makes me wonder — did you give me the correct metadata file? (this could also be due to the older QIIME 2 version that you are running)
3. Finally:

Linear model will not compute due to singular matrix error. This may occur if input variables correlate closely or exhibit zero variance. Please check your input variables. Removing potential covariates may resolve this issue.

That last issue is caused by the inoculum samples, which contain unique Individual_ID values and hence break the model. Removing those samples fixes this issue, and I obtain the expected output:

linear_mixed_effects_round2.qzv (315.4 KB)

So it sounds like you may just be running an outdated version of QIIME2 and maybe sent the wrong metadata file? Please install the latest version and let us know what you see!