Mothur error in the MothurOut class function mothurConvert-int

mothur bugs
1

Hello everone,

I got a problem trying to classify the representative sequences from my OTUs (1066 in total) using the silva database silva.nr_v123.align (renamed below):

mothur >
classify.seqs(fasta=Eukarya.opti_mcc.0.03.abund.0.03.pick.0.03.rep.fasta, count=Eukarya.opti_mcc.0.03.abund.0.03.pick.0.03.rep.count_table, reference=silva.align, taxonomy=silva.tax, cutoff=0.80)

The error is:

Using 1 processors.
[ERROR]: 0.80RAM used: 1.51879Gigabytes . Total Ram: 3.90992Gigabytes.
has occurred in the MothurOut class function mothurConvert-int.

Can you help me?.
Many thanks in advance!!!

Frederic

2

The error is due to the cutoff value. Mothur expects the cutoff to be an integer. For example to set the cutoff to 80% bootstrapped value, you would run the following:

mothur >
classify.seqs(fasta=Eukarya.opti_mcc.0.03.abund.0.03.pick.0.03.rep.fasta, count=Eukarya.opti_mcc.0.03.abund.0.03.pick.0.03.rep.count_table, reference=silva.align, taxonomy=silva.tax, cutoff=80)

The default value for the cutoff is 80, so you could run the command without providing the cutoff.

mothur >
classify.seqs(fasta=Eukarya.opti_mcc.0.03.abund.0.03.pick.0.03.rep.fasta, count=Eukarya.opti_mcc.0.03.abund.0.03.pick.0.03.rep.count_table, reference=silva.align, taxonomy=silva.tax)