mismatch between taxonomy and template

Hi,

I’m trying to run through some MiSeq data (1 sample, V4 target). When classifying the sequences I keep getting the following error:

Mismatch with taxonomy and template files. Cannot continue

and then Mothur will crash. I also tried using the pcr command to customize the alignment (used an e coli 16S sequence to make sure I had the correct start and end points).

Thank you for any insight! Probably missing something simple…

Here is the complete command and response sequence when I tried just using the full alignment space:

mothur > classify.seqs(fasta=DeMMO4_Jul2016.unique.good.filter.unique.precluster.pick.fasta, name=DeMMO4_Jul2016.unique.good.filter.unique.precluster.pick.names, template=silva.nr_v123.align, taxonomy=silva.nr_v123.tax, cutoff=80)

Using 1 processors.
Generating search database… DONE.
It took 247 seconds generate search database.

Reading in the silva.nr_v123.tax taxonomy… DONE.
Calculating template taxonomy tree… DONE.
Calculating template probabilities… DONE.
It took 365 seconds get probabilities.
Classifying sequences from DeMMO4_Jul2016.unique.good.filter.unique.precluster.pick.fasta …
[WARNING]: 25.24228.071116_851 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: 25.24228.071116_10820 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: 25.24228.071116_2064 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: 25.24228.071116_11819 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: 25.24228.071116_23068 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: 25.24228.071116_4524 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
Mismatch with taxonomy and template files. Cannot continue.

So not sure what’s going on here, but what version of mothur are you running?

Cheers
Richard

Hi Richard,

I’m running version:

mothur v.1.39.2
Last updated: 2/16/2017

Thanks
Haley

Try switching to 1.39.3
1.39.2 has a bug in classify

also, not that the cutoff is 80
if you drop it to a lower value, you’ll find some of those unknowns disappear

Thanks everyone! ran with the new release and no longer receive the error. Looks like this was reported as bug and has been corrected