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qiime2 / q2-dada2

QIIME 2 plugin wrapping DADA2
BSD 3-Clause "New" or "Revised" License
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trunc_len=0 can't be used #67

Closed gregcaporaso closed 7 years ago

gregcaporaso commented 7 years ago 
$ qiime dada2 denoise-single   --i-demultiplexed-seqs demux.qza   --p-trim-left 10   --p-trunc-len 0   --o-representative-sequences rep-seqs.qza   --o-table table.qza

Plugin error from dada2:

  trim_left (10) must be smaller than trunc_len (0)

Debug info has been saved to /var/folders/b6/g3p2lswj2153q21x12mjlfwh0000gn/T/qiime2-q2cli-err-oeeswhd9.log

$ qiime dada2 denoise-single   --i-demultiplexed-seqs demux.qza  --p-trunc-len 0   --o-representative-sequences rep-seqs.qza   --o-table table.qza

Plugin error from dada2:

  trim_left (0) must be smaller than trunc_len (0)

Debug info has been saved to /var/folders/b6/g3p2lswj2153q21x12mjlfwh0000gn/T/qiime2-q2cli-err-8zcjto_1.log.
benjjneb commented 7 years ago

Oops, the condition-checks on the python side need to be updated to not enforce trunc-len > trim-left when trunc-len = 0.

https://github.com/qiime2/q2-dada2/blob/master/q2_dada2/_denoise.py#L115 https://github.com/qiime2/q2-dada2/blob/master/q2_dada2/_denoise.py#L148 https://github.com/qiime2/q2-dada2/blob/master/q2_dada2/_denoise.py#L151