Hi all,
I’m trying to use the make.biom command with the Picrust option without success. This is what I’m typing, and the message that I’m getting:
make.biom(shared=subset_all.ren.redundant.unique.gg.wang.tx3.shared, reftaxonomy=gg_13_8_99.gg.tax, constaxonomy=subset_all.ren.redundant.unique.gg.wang.tx.1.cons3.taxonomy, picrust=./picrust/GG_13_5_otuMapTable/99_otu_map.txt)
1
Baron2014_T is not a valid group, and will be disregarded.
You provided no valid groups. I will run the command using all the groups in your file.
Output File Names:
subset_all.ren.redundant.unique.gg.wang.tx3.1.biom
subset_all.ren.redundant.unique.gg.wang.tx3.1.biom_shared
The output files *.biom only have the first sample of the shared file in them (Baron2014_T), there’s 5 other samples that don’t appear in the boom files.
What am I doing wrong?
The error you are getting appears to be a problem with the format of your shared file, if you send your input files to mothur.bugs@gmail.com I can take a look. One other issue that you didn’t hit yet, but will once the error you are currently facing is resolved is the mismatch in versions of the GreenGenes references. The reftaxonomy is version 8, but the mapping is version 5. These must match and be the same as the version you used to classify the sequences in the classify.seqs command.
make.biom(shared=subset_all.ren.redundant.unique.gg.wang.tx3.shared, reftaxonomy=gg_13_8_99.gg.tax, constaxonomy=subset_all.ren.redundant.unique.gg.wang.tx.1.cons3.taxonomy, picrust=./picrust/GG_13_5_otuMapTable/99_otu_map.txt)
Thank you! I re-did the whole thing again and used GG reftaxonomy and mapping version 5 and it worked perfectly. I think the problem was that I edited the .shared file with excel and a text editor (and I’ve done this plenty of times before without any issues on downstream analyses) but this time around it may have altered the file somehow and I couldn’t spot it . Thanks again!