# pre.cluster problem

**URL:** <https://forum.mothur.org/t/pre-cluster-problem/2043>\
**Category:** mothur bugs\
**Created:** [September 23, 2014, 4:45pm UTC](https://forum.mothur.org/t/pre-cluster-problem/2043 "2014-09-23T16:45:53Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![davevanh](https://avatars.discourse-cdn.com/v4/letter/d/df788c/32.png) [@davevanh](https://forum.mothur.org/u/davevanh)\
**Post date:** [September 23, 2014, 4:45pm UTC](https://forum.mothur.org/t/pre-cluster-problem/2043/1 "2014-09-23T16:45:53Z")

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I’m getting the following error when I run the pre.cluster command:

_Your name file contains 40766 valid sequences, and your groupfile contains 81532, please correct._

The command was executed as follows:

_pre.cluster(fasta=MDVExhaustive\_Mothur\_Mod.unique.good.filter.unique.fasta, name=MDVExhaustive\_Mothur\_Mod.unique.good.filter.unique.accnos, group=GroupFile\_Unique.group, diffs=2, processors=8)_

I created my name file by using the list.seqs command with my fasta:

\_list.seqs(fasta=MDVExhaustive\_Mothur\_Mod.unique.good.filter.unique.fasta)

Output File Names:  
MDVExhaustive\_Mothur\_Mod.unique.good.filter.unique.accnos\_

I then used R to create my group file from my name file.

My fasta, name, and group files all have the same number of sequences as verified using grep:

_grep -o '_’ MDVExhaustive\_Mothur\_Mod.unique.good.filter.unique.accnos | wc -l  
(81,532)

grep -o ‘\_’ GroupFile\_Unique.group | wc -l  
(81,532)

grep -o ‘\>’ MDVExhaustive\_Mothur\_Mod.unique.good.filter.unique.fasta | wc -l  
(81,532)\_

The output gives me a list of all of the missing names, however, when I check my names file those names are actually present. The names it tells me are missing are distributed throughout my names file - they are not in a single cluster. Any help would be greatly appreciated!

Dave

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**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:** [September 25, 2014, 5:33pm UTC](https://forum.mothur.org/t/pre-cluster-problem/2043/2 "2014-09-25T17:33:02Z")

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Dave-

You appear to be giving pre.cluster your accnos file, not a names file. Can you try again?

pat

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**Author:** ![guangbin1980](https://avatars.discourse-cdn.com/v4/letter/g/919ad9/32.png) [@guangbin1980](https://forum.mothur.org/u/guangbin1980)\
**Post date:** [October 13, 2014, 2:02am UTC](https://forum.mothur.org/t/pre-cluster-problem/2043/3 "2014-10-13T02:02:05Z")

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I meet the same problem in pre.cluster commond, the result show as below:  
"Processing group MID1.archaea:  
Error: diffs is greater than your sequence length.

[ERROR]: Your name file contains 0 valid sequences, and your groupfile contains 423, please correct.

[ERROR]: Your name file contains 0 valid sequences, and your groupfile contains 564, please correct.

[ERROR]: Your name file contains 0 valid sequences, and your groupfile contains 564, please correct.  
[ERROR]: process 0 only processed 1 of 3 groups assigned to it, quitting.  
[ERROR]: process 1 only processed 1 of 3 groups assigned to it, quitting.  
[ERROR]: process 2 only processed 1 of 3 groups assigned to it, quitting. "  
The commond I used was “pre.cluster(fasta=njsys.shhh.trim.unique.good.filter.unique.fasta, name=njsys.shhh.trim.unique.good.filter.names, group=njsys.shhh.good.groups, diffs=2)”, which is same as SOP, but my sample comtains both bacteria and archaea sequences.  
we used the mixed reference file include silva.bacteria.fasta and silva.archaea.fasta.

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<div class="post-metadata">

**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:** [October 20, 2014, 9:26pm UTC](https://forum.mothur.org/t/pre-cluster-problem/2043/4 "2014-10-20T21:26:36Z")

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> "Processing group MID1.archaea:  
> Error: diffs is greater than your sequence length.

That’s your problem. I suspect this comes from your screen.seqs command. If you could start a new thread and post summary.seqs output before and after screen.seqs as well as what you are doing for screen.seqs that would be great.

Pat