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Process make_SILVA_132_16S_classifier slipped our test runs.
Test command for fast processing e.g.:
`nextflow run rrna-ampliseq -profile test,singularity --classifier false --dereplication 90`
f…
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Specifically, the call `rarefaction(sad, 'indiv')` will return an error like `Error: cannot allocate vector of size 24.7 Gb` if the sad is of a size that is often seen in microbial communities S > 20K…
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@rob-knight requested additional `Table` methods be made available:
- filterLowAbundanceSamples(min_, relative=True/False)
- filterLowAbundanceObservations(min_, relative=True/False)
- filterHighAbund…
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Hello Benjamin,
I finally managed to go through the whole pipeline for big data with the `'pseudo'-pooling` + `collapseNoMismatch()`.
However, we are still encountering the same issue that we ob…
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```
Traceback (most recent call last):
File “/gpfs/software/python/anaconda/4.2/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py”, line 246, in call
results = action(**arg…
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test with real data on binac
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Metadata is handled differently depending on underlying file format (JSON or HDF5).
This is related to a previous issue (#585) and fix (#589). The original issue occurred in QIIME's rarefaction unit …
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q2-longitudinal volatility should be on there. Alpha rarefaction too.
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Hi there,
I am trying to run several very large microbial datasets using the MOB package (data has 370 obsv. and > 14500 variables). So far everything has run smoothly, but then I get (?a computation…