# classify.seqs **URL:** \ **Category:** Commands in mothur\ **Created:** [March 10, 2017, 8:24pm UTC](https://forum.mothur.org/t/classify-seqs/3161 "2017-03-10T20:24:47Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![tiagovitor](https://avatars.discourse-cdn.com/v4/letter/t/c6cbf5/32.png) [@tiagovitor](https://forum.mothur.org/u/tiagovitor)\ **Post date:** [March 10, 2017, 8:24pm UTC](https://forum.mothur.org/t/classify-seqs/3161/1 "2017-03-10T20:24:47Z")
Hi, I am doing the pipeline of my Illumina paired end samples, but I got some unclear issues. First, I don’t know why, but when I try to search for some topic in the forum and I go to Google, it shows me some results. However, I can’t access and it has been showing me the following message: “Information Sorry but you are not permitted to use the search system.” So, basically I have to check page by page in order to check if I find a topic related to mine, but this is though. Moving to my main issue… I am using the version v.1.39.4 and I amfollowing Myseq SOP tutorial. I ran align.seqs and in the end I got a lot of unclassified sequences. This was the command I ran: classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count\_table, reference=trainset14\_032015.pds.fasta, taxonomy=trainset14\_032015.pds.tax, cutoff=80) When I openned the tax summary file, I got it: taxlevel rankID taxon daughterlevels total Day\_01 Day\_12 Day\_17 Day\_29 Day\_30 Day\_38 Day\_42 Day\_56 Day\_68 0 0 Root 1 392548 43739 44545 43862 43225 54282 43321 34222 39640 45712 1 0.1 Bacteria 3 392548 43739 44545 43862 43225 54282 43321 34222 39640 45712 2 0.1.1 Actinobacteria 1 487 19 188 132 40 64 21 7 12 4 3 0.1.1.1 Actinobacteria 2 487 19 188 132 40 64 21 7 12 4 4 0.1.1.1.1 Actinobacteria\_unclassified 1 1 0 0 0 0 1 0 0 0 0 5 0.1.1.1.1.1 Actinobacteria\_unclassified 1 1 0 0 0 0 1 0 0 0 0 6 0.1.1.1.1.1.1 Actinobacteria\_unclassified 0 1 0 0 0 0 1 0 0 0 0 4 0.1.1.1.2 Actinomycetales 1 486 19 188 132 40 63 21 7 12 4 5 0.1.1.1.2.1 Actinomycetales\_unclassified 1 486 19 188 132 40 63 21 7 12 4 6 0.1.1.1.2.1.1 Actinomycetales\_unclassified 0 486 19 188 132 40 63 21 7 12 4 2 0.1.2 Bacteria\_unclassified 1 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 3 0.1.2.1 Bacteria\_unclassified 1 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 4 0.1.2.1.1 Bacteria\_unclassified 1 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 5 0.1.2.1.1.1 Bacteria\_unclassified 1 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 6 0.1.2.1.1.1.1 Bacteria\_unclassified 0 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 2 0.1.3 Proteobacteria 1 769 88 43 64 71 100 76 72 87 168 3 0.1.3.1 Proteobacteria\_unclassified 1 769 88 43 64 71 100 76 72 87 168 4 0.1.3.1.1 Proteobacteria\_unclassified 1 769 88 43 64 71 100 76 72 87 168 5 0.1.3.1.1.1 Proteobacteria\_unclassified 1 769 88 43 64 71 100 76 72 87 168 6 0.1.3.1.1.1.1 Proteobacteria\_unclassified 0 769 88 43 64 71 100 76 72 87 168 I guess this is not normal ☹ What could I try to do? Is this a command error or a bug in this version? Thank you! ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [March 13, 2017, 1:19pm UTC](https://forum.mothur.org/t/classify-seqs/3161/2 "2017-03-13T13:19:30Z")
What region? What mothur version? Do you have an example sequence that you think should be getting classified but isn’t? Pat