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.