mothur

MAKE.BIOM in Mothur

Hello, could someone help me to generate a biom file, which I require to work in PICRUST, it does not accept the files that I need on the command line, generate the files as follows

mothur > classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, reference=gg_13_8_99.fasta, taxonomy=gg_13_8_99.gg.tax, cutoff=80)

Using 64 processors.

Generating search database… DONE.

It took 133 seconds generate search database.

Reading in the /home/equiroz/Jurel/gg_13_8_99.gg.tax taxonomy… DONE.

Calculating template taxonomy tree… DONE.

Calculating template probabilities… DONE.

It took 333 seconds get probabilities.

Classifying sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta …

It took 39 secs to classify 37365 sequences.

It took 39 secs to classify 37365 sequences.

It took 3 secs to create the summary file for 37365 sequences.

Output File Names:

stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.gg.wang.taxonomy

stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.gg.wang.tax.summary

make.biom(shared= Âż???

@chjicu can you help? I know you’ve done piecrust recently

Hi Equiroz,
Would you pleas try the following code?

mothur > classify.otu(list=stability.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.list, count=stability.trim.contigs.good.unique.good.filter.precluster.denovo.vsearch.pick.pick.count_table, taxonomy=stability.trim.contigs.good.unique.good.filter.precluster.pick.gg.wang.pick.taxonomy)

mothur > make.biom(shared=stability.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.shared, label=0.03, reftaxonomy=gg_13_8_99.gg.tax, constaxonomy=stability.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.0.03.cons.taxonomy, picrust=97_otu_map.txt)

Our group applied make.biom and PICRUSt in serval projects. Our codes worked well.

Please let me know if I can be of any further help: jie.2.chen@uconn.edu.

Best,
Jie

1 Like

Dear Jie

Thank you very much for your tip, it was very useful to me. I have the biom file to work in PICRUSt

Kind regards

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.