classify.seqs with greenegenes tax and fasta gives 100% unclassified

Commands in mothur
1

Hi Pat and Sarah,
I am trying to generate a biom file for picrust. I downloaded Gg_13_5_99.taxonomy.tar and opened it with
$ tar -xvf Gg_13_5_99.taxonomy.tar

when I run:
classify.seqs(fasta=PhRats_84.subsample.chop.unique.good.filter.precluster.unique.fasta, name=PhRats_84.subsample.chop.unique.good.filter.precluster.unique.names, taxonomy=gg_13_5_99.gg.tax, template=gg_13_5_99.fasta, cutoff=70)

I get 100% unclassified:
My .tax.summary file looks like this:
taxlevel rankID taxon daughterlevels total
0 0 Root 1 162896
1 0.4 unknown 1 162896
2 0.4.1 unclassified 1 162896
3 0.4.1.1 unclassified 1 162896
4 0.4.1.1.1 unclassified 1 162896
5 0.4.1.1.1.1 unclassified 1 162896
6 0.4.1.1.1.1.1 unclassified 1 162896
7 0.4.1.1.1.1.1.1 unclassified 0 162896

I tried the same command with the abrecovery.fasta file, and same problem:
classify.seqs(fasta=abrecovery.fasta, taxonomy=gg_13_5_99.gg.tax, template=gg_13_5_99.fasta, cutoff=70)
taxlevel rankID taxon daughterlevels total
0 0 Root 1 242
1 0.4 unknown 1 242
2 0.4.1 unclassified 1 242
3 0.4.1.1 unclassified 1 242
4 0.4.1.1.1 unclassified 1 242
5 0.4.1.1.1.1 unclassified 1 242
6 0.4.1.1.1.1.1 unclassified 1 242
7 0.4.1.1.1.1.1.1 unclassified 0 242

I also checked the template file and I can’t see anything wrong:
mothur > summary.seqs(fasta=gg_13_5_99.fasta)
Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 1254 1254 0 4 1
2.5%-tile: 1 1330 1330 0 5 5061
25%-tile: 1 1383 1383 0 5 50606
Median: 1 1433 1433 0 5 101211
75%-tile: 1 1482 1482 0 6 151816
97.5%-tile: 1 1529 1529 6 8 197361
Maximum: 1 2333 2333 185 185 202421
Mean: 1 1430.99 1430.99 0.502463 5.65616

of Seqs: 202421

The accnos file in the first example contains 7077 files and in the second example 123 files. I have used classify.seqs may times with other template and tax file and I have never run into this problem. This is my first attempt at using GG. Any suggestions?

thanks,

Giovanni

2

I can answer the question myself… there was a memory issue and as a result one or multiple files created by classify.seqs: gg_13_5_99.gg.gg_13_5_99.8mer.numNonZero
gg_13_5_99.gg.tree.train
gg_13_5_99.gg.tree.sum
gg_13_5_99.8mer

were incomplete or otherwise corrupted. running classify.seqs in batch mode solved the problem

Giovanni