# What is the meaning of increasing numbers from classify.seqs? **URL:** \ **Category:** Theory behind mothur\ **Created:** [May 12, 2021, 1:10pm UTC](https://forum.mothur.org/t/what-is-the-meaning-of-increasing-numbers-from-classify-seqs/20979 "2021-05-12T13:10:23Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![weu](https://avatars.discourse-cdn.com/v4/letter/w/f08c70/32.png) [@weu](https://forum.mothur.org/u/weu)\ **Post date:** [May 12, 2021, 1:10pm UTC](https://forum.mothur.org/t/what-is-the-meaning-of-increasing-numbers-from-classify-seqs/20979/1 "2021-05-12T13:10:24Z")
Hi, I am running classify.seqs using Ezbiocloud edited v3v4 reference sequences, but classifying sequences took a very long time (currently running more than 24 hours) and the numbers showing are still increasing. May I know what does this mean? And is there a way to predict the duration? If my laptop went to sleep does the process get hindered? 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:** [May 13, 2021, 5:46pm UTC](https://forum.mothur.org/t/what-is-the-meaning-of-increasing-numbers-from-classify-seqs/20979/2 "2021-05-13T17:46:20Z")
Hi, How many unique sequences do you have? If you’re sequencing V3-V4 or aren’t following our MiSeqSOP, you might want to check out this post… > **[Why do I have such a large distance matrix](https://mothur.org/blog/2014/Why-such-a-large-distance-matrix/)** > > 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:** ![weu](https://avatars.discourse-cdn.com/v4/letter/w/f08c70/32.png) [@weu](https://forum.mothur.org/u/weu)\ **Post date:** [May 14, 2021, 4:04am UTC](https://forum.mothur.org/t/what-is-the-meaning-of-increasing-numbers-from-classify-seqs/20979/3 "2021-05-14T04:04:21Z")
There are 194520 sequences classified from classify.seqs command. Im using Macbook Air M1 chip, but couldn’t find any details of comparison on RAM or so for mothur analysis. I did follow the SOP as much as I can understand 😁 😁 and added large=T as well as putting taxlevel=3. May I know what are the use of those different dist files produced? ---
**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:** [May 14, 2021, 4:51pm UTC](https://forum.mothur.org/t/what-is-the-meaning-of-increasing-numbers-from-classify-seqs/20979/4 "2021-05-14T16:51:48Z")
That’s a lot of uniques. What region are you sequencing? I suspect you have so many because of low sequence quality from sequencing V3-V4 or V4-V5 (i.e. something longer than ~250 nt). I certainly wouldn’t try to process this on a laptop. The `large=T` option should not be used and you probably want to use `taxlevel=5` or 6 and possibly increase the `diffs` value in `pre.cluster` to the integer that is just less than your sequence length divided by 100, Pat ---
**Author:** ![weu](https://avatars.discourse-cdn.com/v4/letter/w/f08c70/32.png) [@weu](https://forum.mothur.org/u/weu)\ **Post date:** [May 15, 2021, 2:03pm UTC](https://forum.mothur.org/t/what-is-the-meaning-of-increasing-numbers-from-classify-seqs/20979/5 "2021-05-15T14:03:31Z")
Yes its V3-V4 region.Thousand thanks for all great suggestions, everything worked fine after increasing diffs to 5, and changed taxlevel to 6. I also changed the reference database to silvaseed instead of the larger silva reference sequences, may I know if size of the reference database affects? ---
**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:** [May 17, 2021, 5:25pm UTC](https://forum.mothur.org/t/what-is-the-meaning-of-increasing-numbers-from-classify-seqs/20979/6 "2021-05-17T17:25:19Z")
the seed version should be good enough for most purposes 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:** [May 27, 2021, 5:26pm UTC](https://forum.mothur.org/t/what-is-the-meaning-of-increasing-numbers-from-classify-seqs/20979/7 "2021-05-27T17:26:07Z")
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