What does this error mean?

[danielsebas (Daniel)]

Dear Friends,

When running rare fraction, I get this below error:

qiime diversity alpha-rarefaction --i-table Ionexpress_1to11-dada2-rep-seqs-table2.qza --i-phylogeny Ionexpress_1to11_dada2-rep-seqs-rooted-tree.qza --p-max-depth 10 --m-metadata-file cDNA_1to11_metadat.tsv --o-visualization Ionexpress_1to11-dada2-rep-seqs-alpha-rarefaction-10.qzv

Plugin error from diversity:

Provided number of steps (10) is greater than the steps possible between min_depth and max_depth (9).

Debug info has been saved to /data/deepak-data/NPRP-11-data/qiime-results/qiime-tmp/qiime2-q2cli-err-b8j4tz2k.log

Can you please tell me what does this error signify? Thanks!

[thermokarst]

That error message could probably stand to be modified a bit, but what it is saying is that given your max_depth of 10, the maximum possible number of steps is only 9. The default number of steps though, is 10 (which is greater than 9), and since you didn’t specify a parameter for the number of steps set at 9, well, this error popped up. Toss in a --p-steps 9 and you will be good to go. I must ask though - this is an absurdly low sequencing depth - I am skeptical that there will be much value in these data…

[danielsebas (Daniel)]

Yes, I agree, and I should discard the corresponding sample with such low feature count from the denoised data, right?

[thermokarst]

Probably, but you don’t need to worry about that when generating the alpha rarefaction plot. Are you setting the max_depth param to 10 for the sake of that low-abundance sample? If so - don’t! Set the max value to the max of the greatest abundance sample. The viz will take care of dropping samples from the plot as they are subsampled away.