Get.otus results in error

1

Hi,

I have been trying to follow Pats advice to convert mothur output to allow its use in picrust. Link here: Mothur file to biom

When I do the get.otus(constaxonomy= stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.cons.taxonomy, accnos= stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.list) step I get the following error.

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used: 0.017601Gigabytes . Total Ram: 125.364Gigabytes.

has occurred in the Utils class function mothurConvert-int. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.

Could you please advise on how to proceed?
Thanks
Paul

2

The issue is the accnos file. It looks like you provided a list file instead of a file containing the OTU labels.

get.otus(constaxonomy= stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.cons.taxonomy, accnos= stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.list)

The list.otus command will generate the accnos file for you. Try this:

list.otus(list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.list)
get.otus(accnos=current, constaxonomy= stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.cons.taxonomy)

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