here’s the error, it’s weird because it started classifying. I see that you have a newer version, I’ll ask that be put on the server
mothur > classify.seqs(fasta=current, count=current, reference=silva.nr_v119.v4.align, taxonomy=silva.nr_v119.tax, cutoff=80)
Using JARFSoilFfu.trim.contigs.good.unique.good.filter.precluster.denovo.uchime.pick.pick.count_table as input file for the count parameter.
Using JARFSoilFfu.trim.contigs.good.unique.good.filter.precluster.pick.fasta as input file for the fasta parameter.
Using 1 processors.
Reading template taxonomy... DONE.
Reading template probabilities... DONE.
It took 19 seconds get probabilities.
Classifying sequences from JARFSoilFfu.trim.contigs.good.unique.good.filter.precluster.pick.fasta ...
[WARNING]: M03075_93_000000000-AY5YC_1_1101_14210_3327 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_12068_4915 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_19834_6357 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.
Using 1 processors.
Reading template taxonomy... DONE.
Reading template probabilities... DONE.
It took 21 seconds get probabilities.
Classifying sequences from JARFSoilFfu.trim.contigs.good.unique.good.filter.precluster.pick.fasta ...
[WARNING]: M03075_93_000000000-AY5YC_1_1101_14210_3327 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_12068_4915 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_19834_6357 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_15485_2061 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_14256_3479 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_14358_4881 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_21563_4702 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_14511_3150 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_14340_2055 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_22730_4770 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_6530_5556 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_19876_7645 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_21293_7368 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_14497_3280 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_19123_3574 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_19587_5096 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.
Under a time crunch with this analysis, so restarted in 1.38.0
Still getting the error but it doesn’t seem to be killing the processing
[WARNING]: M03075_93_000000000-AY5YC_1_1108_13515_2053 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_1114_17192_7687 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.
Mismatch with taxonomy and template files. Cannot continue.
[WARNING]: M03075_93_000000000-AY5YC_1_1101_12068_4915 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M03075_93_000000000-AY5YC_1_2103_2391_14354 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.