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hildebra / lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
http://lotus2.earlham.ac.uk/
GNU General Public License v3.0
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Lotus2 not reading #35

Closed thecrobe closed 1 year ago

thecrobe commented 1 year ago

Hello,

I am trying to use Lotus2 to process ITS2 reads. I have tried to set the taxAligner to blast but it does not want to read it, have you encountered this issue? It seems that Lotus2 is not reading multiple of my commands? My code is below.

Error: "RefDB UNITE requested, but -taxAligner set to "0": therefore RDP classification of reads will be done"

It also puts out this error sometimes: zsh: command not found: -amplicon_type zsh: command not found: -tax_group zsh: command not found: -taxAligner zsh: command not found: -clustering

My Code:

lotus2 -i Seqs \ -o lotus2 \ -m TestMap.txt \ -refDB UNITE \ -amplicon_type ITS2 \ -tax_group fungi \ -taxAligner blast \ -clustering vsearch \ -id 0.97

hildebra commented 1 year ago

Hey, I think there is a mistake in the bash code: lotus2 -i Seqs -o lotus2 -m TestMap.txt -refDB UNITE \ -amplicon_type ITS2 \ -tax_group fungi \ -taxAligner blast -clustering vsearch -id 0.97

is missing in some cases the " \ " as a line ending. So I guess some flags are not correctly reported to LotuS2. Can you try to run this command as single command line?