# Error with classify.seqs: XXX could not be classified/is bad/it has no kmers of lenght 8 **URL:** \ **Category:** Commands in mothur\ **Created:** [December 15, 2022, 3:14pm UTC](https://forum.mothur.org/t/error-with-classify-seqs-xxx-could-not-be-classified-is-bad-it-has-no-kmers-of-lenght-8/21668 "2022-12-15T15:14:18Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![cgini31](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/cgini31/32/429_2.png) [@cgini31](https://forum.mothur.org/u/cgini31)\ **Post date:** [December 15, 2022, 3:14pm UTC](https://forum.mothur.org/t/error-with-classify-seqs-xxx-could-not-be-classified-is-bad-it-has-no-kmers-of-lenght-8/21668/1 "2022-12-15T15:14:18Z")
Dear all, I ask your support for classify.seqs command. I am running the command in a container (until now very well functioning) containing mothur v.1.48.0, and analyzing mock communities sequences. I give the command as following: mothur \> classify.seqs(fasta=stability.trim.contigs.unique.filter.fasta, count=stability.trim.contigs.unique.filter.count\_table, reference=Databases/silva\_v132.fasta, taxonomy=Databases/silva.nr\_v132.tax, outputdir=XXX). I receive this message: Using 16 processors. Reading template taxonomy… DONE. Reading template probabilities… DONE. It took 30 seconds get probabilities. Classifying sequences from Analysis/mock\_communities/mothur/stability.trim.contigs.unique.filter.fasta … _M02765\_22\_000000000-AJBRW\_1\_2107\_4690\_15120 is bad. It has no kmers of length 8._ _[WARNING]: M02765\_22\_000000000-AJBRW\_1\_2107\_4690\_15120 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences._ Lines in italic repeate themselves and give me a final message of 2 error messages and 82126 warning messages. Problem is I am not understanding what is wrong with them. NOTE: before classify.seqs I ran the commands make.files, make.contigs, unique.seqs, align.seqs, filter.seqs, unique.seqs, cluster.split with label 0.20 as suggested in SOP and manual, make.shared, and stop here in classify.otu. (I am not interested in screen.seqs as I work on server, so no worries about my computer melting down for the effort) Thanks in advance to those that will try to help! Cheers ---
**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:** [December 15, 2022, 6:58pm UTC](https://forum.mothur.org/t/error-with-classify-seqs-xxx-could-not-be-classified-is-bad-it-has-no-kmers-of-lenght-8/21668/2 "2022-12-15T18:58:10Z")
Hey there - I think you’re getting these warning messages because the sequences are bad. You would remove those if you used `screen.seqs`. I’m wondering where you got your protocol from since it’s been some time since we suggested a cutoff of 0.20. The `screen.seqs` step isn’t about conserving RAM, it’s really about removing sequences that a problems Here’s our current protocol… > **[MiSeq SOP](https://mothur.org/wiki/miseq_sop/)** > > The website that supports the mothur software program - one of the most widely used tools for analyzing 16S rRNA gene sequence data. Step inside to learn how to use the software, get help, and join our community! Pat ---
**Author:** ![cgini31](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/cgini31/32/429_2.png) [@cgini31](https://forum.mothur.org/u/cgini31)\ **Post date:** [December 19, 2022, 4:09pm UTC](https://forum.mothur.org/t/error-with-classify-seqs-xxx-could-not-be-classified-is-bad-it-has-no-kmers-of-lenght-8/21668/3 "2022-12-19T16:09:26Z")
Hello @pschloss, thank you very much for your response. I took the protocol from same address you are sending me, just trying to make it a little lighter with only the commands I strictly need (having kinda fun!). I found the 0.03 cutoff in SOP, while only saw 0.20 cutoff suggested in cluster.split: I assume it is so because SOP have a special dataset to work with then 🙂 Since I have added screen.seqs I am retrieving errors that say: _[ERROR]: M02765\_22\_000000000-AJBRW\_1\_1114\_19191\_6585 is not in your count table. Please correct._ I checked and in fact, I see this code (M02765\_22\_000000000-AJBRW\_1\_1114\_19191\_6585, but it is an example) in count\_table but not in fasta file. Can you texplain me why or address me on this issue as well? Should I modify my fasta file manually? Thanks in advance, Chiara ---
**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:** [December 20, 2022, 7:34pm UTC](https://forum.mothur.org/t/error-with-classify-seqs-xxx-could-not-be-classified-is-bad-it-has-no-kmers-of-lenght-8/21668/4 "2022-12-20T19:34:36Z")
You should only use 0.03 for the cutoff regardless of the dataset I’d suggest going back to previous steps until you don’t get the error message. This typically happens because you are using the wrong fasta and count\_tables - one of them has been processed more than the other. Hope this helps, Pat ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [December 30, 2022, 7:34pm UTC](https://forum.mothur.org/t/error-with-classify-seqs-xxx-could-not-be-classified-is-bad-it-has-no-kmers-of-lenght-8/21668/5 "2022-12-30T19:34:48Z")
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