Make.biom picrust option error

mothur bugs
1

Hi,

I ran make.biom command of picrust option but I’m facing persistent error as below.

0.03
[ERROR]: could not find OTUId for k__Bacteria(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);. Its reference sequences are .

I’ve tried

1- Using the same gg taxomony version of gg_13_5_99 for classify.seq and OUTid mapping - FAILED
2- Remove the error OTUId through remove.lineage command after classify.seq - FAILED

#remove.lineage
remove.lineage(constaxonomy=final.cons.taxonomy, list=ms.trim.contigs.good.unique.good.filter.unique.precluster.pick.abund.pick.an.unique_list.list, taxon='k__Bacteria(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100)', label=0.03)

What do you think could be the problem? Thanks.

2

You don’t want the confidence scores in remove.lineage, you don’t want quotes, and you have it looking for a very weird taxonomic group…

remove.lineage(constaxonomy=final.cons.taxonomy, list=ms.trim.contigs.good.unique.good.filter.unique.precluster.pick.abund.pick.an.unique_list.list, taxon=k__Bacteria_unclassified, label=0.03)
3

I ran into similar issues. (mothur 1.37.5)


I think the issue is with remove.lineage.

wc -l processed.agc.unique_list.0.03.cons.taxonomy
85276 processed.agc.unique_list.0.03.cons.taxonomy

mothur “#remove.lineage(list=processed.agc.unique_list.list, count=processed.count_table, taxonomy=processed.agc.unique_list.0.03.cons.taxonomy, taxon=unknown);quit()”

wc -l processed.agc.unique_list.0.03.cons.pick.taxonomy
127907 processed.agc.unique_list.0.03.cons.pick.taxonomy

As you can see the number of lines in the file has increased ~ 50%.

I think there is something wrong with the end of line character because when i try to reformat the file things get really weird.

hope this helps.

"quick fix from terminal:
awk ‘$3!=“unknown(100);unknown_unclassified(100);unknown_unclassified(100);unknown_unclassified(100);unknown_unclassified(100);unknown_unclassified(100);unknown_unclassified(100);”’ processed.agc.unique_list.0.03.cons.taxonomy > processed.agc.unique_list.0.03.cons.pick.taxonomy

4

Hi,

I managed to solve the problem by typing exactly the “k__Bacteria_unclassified” taxon as below as what have been suggested by Pat Hope this also helps for others. Thanks.

mothur > 
remove.lineage(constaxonomy=final.cons.taxonomy, shared=final.0.03.subsample.shared, taxon=k__Bacteria_unclassified, label=0.03)
Removed 176 OTUs from your shared file.

Output File Names: 
final.cons.pick.taxonomy
final.0.03.subsample.0.03.pick.shared


mothur > 
make.biom(shared=final.0.03.subsample.0.03.pick.shared, label=0.03, reftaxonomy=gg_13_5_99.gg.tax, constaxonomy=final.cons.pick.taxonomy, picrust=97_otu_map.txt)
0.03

Output File Names: 
final.0.03.subsample.0.03.pick.0.03.biom
final.0.03.subsample.0.03.pick.0.03.biom_shared