Make.biom picrust option doesnt handle unclassified?

mothur bugs
21

Hi,

I think the part “unclassified” is not a problem, since it´s normal to have some unclassify- I also have them in my biom file. And it´s strange, because if you haven´t got any error while generating files, they are supposed to be fine. Are you sure the problem is comming from mothur output file and not from some bugg in picrust webpage? You can also post your question in their forum, maybe they could help you.

22

I’m getting an error message when I try to make a biom file. I tried to use remove.lineage to correct this, but I received the same error message. Any suggestions would be appreciated, thanks.

make.biom(shared=s4s650ana.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.shared,constaxonomy=s4s650ana.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.pick.taxonomy, reftaxonomy=gg_13_8_99.gg.tax, picrust=97_otu_map.txt)
0.03
[ERROR]: could not find OTUId for unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);. Its reference sequences are .

mothur >
remove.lineage(constaxonomy=s4s650ana.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.taxonomy, list=s4s650ana.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list, taxon=‘unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);’, label=0.03)
Your constaxonomy file contains OTUs only from unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);.
Removed 0 OTUs from your list file.

23

The remove.lineage command reported the following "Your constaxonomy file contains OTUs only from unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);.” meaning all the OTUs had no consensus taxonomy. Could you have inputted the wrong file into classify.seqs or classify.otu?

24

The same problem continues with the latest mother version (1.38). I had to manually modify the constaxonomy file by removing the “xxxx-unclassifieds”.

Nezar

25

Hi sarah,

I don’t really want to run PICRUST, but I would like to have a look of each OTU potential genome function based on PICRUST precalculated file.
I did the following steps and just realized that the output .biom file contain otu ids, which is not matched with the greengenes id (which present in picrust precalculated file ).
Do you have an idea how to match my OTUs with greengene ids?

Thanks,
Junnan