Hi,
I’ve recently downloaded Mothur v.1.34.0 and encountered a problem with classify.seqs command.
Normally the classify.seqs command gives 2 output files, named *.taxonomy and *.tax.summary.
However this is my output …
mothur > classify.seqs(fasta=current, count=current, reference=db.fasta, taxonomy=db.tax, cutoff=80, processors=4)
Using 1.uchime.pick.count_table as input file for the count parameter.
Using 1.fasta as input file for the fasta parameter.
Using 4 processors.
Generating search database… DONE.
It took 3 seconds generate search database.
Reading in the db.tax taxonomy… HM108361.1.1446 has an error in the taxonomy. This may be due to a ;;
DONE.
AB000389.1 is in your taxonomy file and is not in your template file. Please correct.
AB001518.1 is in your taxonomy file and is not in your template file. Please correct.
…
Z96096.1 is in your taxonomy file and is not in your template file. Please correct.
Z99997.1 is in your taxonomy file and is not in your template file. Please correct.
DONE.
It took 4 seconds get probabilities.
As you can see, no output files are generated.
Is there an incompatibility with the new Mothur v.1.34.0 or am I overlooking something?
Kind regards,
Anneleen
Generally errors like this are related to a formatting issue in the taxonomy file. You can see what mothur is reading by using the debug flag.
mothur > set.dir(debug=t)
mothur > classify.seqs(…)
After loading this into mothur
mothur > set.dir(debug=t)
mothur > classify.seqs(…)
I get the following
mothur > set.dir(debug=t)
Setting [DEBUG] flag.
mothur > classify.seqs(fasta=x.fasta, count=x.count_table, reference=db.fasta, taxonomy=db.tax, cutoff=80, processors=4)
Using 4 processors.
Generating search database… DONE.
It took 6 seconds generate search database.
unknown unknown
Reading in the db.tax taxonomy… [DEBUG]: Taxonomies read in…
[DEBUG]: name = ‘AB000389.1’ tax = ‘Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Pseudoalteromonadaceae;Pseudoalteromonas;’
[DEBUG]: name = ‘AB000699.1’ tax = ‘Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas;’
…
Z96096.1 is in your taxonomy file and is not in your template file. Please correct.
Z99997.1 is in your taxonomy file and is not in your template file. Please correct.
[DEBUG]: about to generateWordPairDiffArr
[DEBUG]: done generateWordPairDiffArr
DONE.
It took 11 seconds get probabilities.
The debug flag worked fine, but did not give me any output data files after the classify.seqs command.
But a .tree.sum and .8mer are generated (as I’ve observed before).
Any other solutions?
Kind regards,
Anneleen