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