# cluster.split problem

**URL:** <https://forum.mothur.org/t/cluster-split-problem/2183>\
**Category:** Theory behind mothur\
**Created:** [January 6, 2015, 7:13am UTC](https://forum.mothur.org/t/cluster-split-problem/2183 "2015-01-06T07:13:53Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Jamie](https://avatars.discourse-cdn.com/v4/letter/j/aca169/32.png) [@Jamie](https://forum.mothur.org/u/Jamie)\
**Post date:** [January 6, 2015, 7:13am UTC](https://forum.mothur.org/t/cluster-split-problem/2183/1 "2015-01-06T07:13:53Z")

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Hi,  
I am using mothur to analysis 24 samples which obtain from Illumina MiSeq original 16S Fastaq data.  
Raw data contains 13Gb, 2x300bp, V3 region (341-805R).  
Everything is great, but I face with a problem when command cluster.split running, it creat 806Gb data and it almost running for 7 days, now still in running process…  
Is there any problem? thank you~

Here is my command:  
make.contigs(file=stability.files, processors=4)  
summary.seqs(fasta=stability.trim.contigs.fasta); total 6866561 seqs  
screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, maxlength=480)  
get.current()  
summary.seqs(fasta=stability.trim.contigs.good.fasta); total 5431619 seqs  
unique.seqs(fasta=stability.trim.contigs.good.fasta); 2838557 unique seqs, total 5431619 seqs  
count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)  
summary.seqs(count=stability.trim.contigs.good.count\_table); 2838557 unique seqs, total 5431619 seqs  
pcr.seqs(fasta=silva.bacteria.fasta, oligos=pcrTest.oligos)  
align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.bacteria.pcr.fasta)  
summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count\_table); 2838557 unique seqs, total 5431619 sequence  
screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count\_table, summary=stability.trim.contigs.good.unique.summary, start=6388, end=25316, maxhomop=8)  
summary.seqs(fasta=current, count=current); 2710518 unique seqs, total 5276789 seqs  
filter.seqs(fasta=stability.trim.contigs.good.unique.good.align, vertical=T, trump=.)  
unique.seqs(fasta=stability.trim.contigs.good.unique.good.filter.fasta, count=stability.trim.contigs.good.good.count\_table)  
pre.cluster(fasta=stability.trim.contigs.good.unique.good.filter.unique.fasta, count=stability.trim.contigs.good.unique.good.filter.count\_table, diffs=2)  
summary.seqs(fasta=current, count=current); 1199095 unique seqs, total 5376789 seqs  
chimera.uchime(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count\_table, dereplicate=t)  
remove.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, accnos=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos)  
summary.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count\_table)  
966622 Unique sequences, total 4990158 seqs, 7.19% chimera  
classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count\_table, reference=silva.bacteria.ng.fasta, taxonomy=silva.bacteria.silva.tax, cutoff=80)  
remove.lineage(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count\_table, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.silva.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Eukaryota)  
959943 unique sequence, toal 4958696 seqs  
cluster.split(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count\_table, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.silva.wang.pick.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.15, processors=4)

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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:** [January 9, 2015, 3:48pm UTC](https://forum.mothur.org/t/cluster-split-problem/2183/2 "2015-01-09T15:48:16Z")

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[http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/](http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/)