# classify.seqs with greenegenes tax and fasta gives 100% unclassified **URL:** \ **Category:** Commands in mothur\ **Created:** [November 5, 2015, 8:12pm UTC](https://forum.mothur.org/t/classify-seqs-with-greenegenes-tax-and-fasta-gives-100-unclassified/2592 "2015-11-05T20:12:04Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![gwidmer](https://avatars.discourse-cdn.com/v4/letter/g/a8b319/32.png) [@gwidmer](https://forum.mothur.org/u/gwidmer)\ **Post date:** [November 5, 2015, 8:12pm UTC](https://forum.mothur.org/t/classify-seqs-with-greenegenes-tax-and-fasta-gives-100-unclassified/2592/1 "2015-11-05T20:12:04Z")
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 ---
**Author:** ![gwidmer](https://avatars.discourse-cdn.com/v4/letter/g/a8b319/32.png) [@gwidmer](https://forum.mothur.org/u/gwidmer)\ **Post date:** [November 6, 2015, 5:34pm UTC](https://forum.mothur.org/t/classify-seqs-with-greenegenes-tax-and-fasta-gives-100-unclassified/2592/2 "2015-11-06T17:34:27Z")
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