# pre.cluster being to long? **URL:** \ **Category:** Commands in mothur\ **Created:** [December 1, 2016, 8:27pm UTC](https://forum.mothur.org/t/pre-cluster-being-to-long/3052 "2016-12-01T20:27:39Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![kimitas](https://avatars.discourse-cdn.com/v4/letter/k/f08c70/32.png) [@kimitas](https://forum.mothur.org/u/kimitas)\ **Post date:** [December 1, 2016, 8:27pm UTC](https://forum.mothur.org/t/pre-cluster-being-to-long/3052/1 "2016-12-01T20:27:39Z")
Hi, I am just a bit worried about how long should the pre.clustering should take? I have several sets (projects) of MiSeq (2 x 250) data. With a first set of samples: with 72 samples, the ‘pre clustering’ with my computer (so processors=1) was done overnight. But now I have a group of 6 samples that have been running for 24 hours and the pre.clustering has only advances for 2 samples … Then I have another set of samples : 42 samples, which I am running in better computer, using 16 processors and, and it still running since 3 days. Between yesterday and today it actually just analysed 1 sample… Is this slow process normal??? I am just worried since the first set of samples was done so quickly with more samples in it! Thanks ---
**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 5, 2016, 1:47pm UTC](https://forum.mothur.org/t/pre-cluster-being-to-long/3052/2 "2016-12-05T13:47:40Z")
It’s not about the number of samples. Rather, it’s about the number of sequences in the samples. I suspect you went through the small samples and are now stuck on the bigger samples. Pat ---
**Author:** ![kimitas](https://avatars.discourse-cdn.com/v4/letter/k/f08c70/32.png) [@kimitas](https://forum.mothur.org/u/kimitas)\ **Post date:** [December 7, 2016, 9:07pm UTC](https://forum.mothur.org/t/pre-cluster-being-to-long/3052/3 "2016-12-07T21:07:56Z")
Hi there, Well actually there is a problem with the filter.seqs that I realised and when I changed it it fixed the problem and the pre.cluster runned as normal in less than 1 day So I was rumnning : mothur \> filter.seqs(fasta=stability.trim.contigs.good.good.unique.good.filter.fasta, trump=. ) Unable to open /media/melissa/ExtraDrive1/KIM/Argonne\_Oct2016\_WIP/De. Trying default /usr/bin/De Unable to open /usr/bin/De. It will be disregarded. And I got this message because actually my folder De. was called “De-multiplexed” …and for some reason it didn’t like the ‘-’ ! So I changed it to “De\_multiplexed” (underscore ‘\_’) and it worked! What happened at the beginning is that because it was not working in the first place I just did: filter.seqs() And that was was working… But then I went and removed the ‘.’ myself : melissa@mprice:/media/melissa/ExtraDrive1/KIM/Argonne\_Oct2016\_WIP/De-multiplexed$ head stability.trim.contigs.good.good.unique.good.filter.fasta > HWI-M04771\_60\_000000000-AURUP\_1\_1101\_15771\_1813 > …T–AC–GG-AG-GGT—GCA-A-G–C–G-T-T–AT-C-CGG-AA–TC-A–T-T–GG-GT–TT-A–AA-GG-GT-CC–G-CA-G-G-C-G–G–T-CA-A-T-T–AA—G-T-C-A-----G-A-G-G–TG–A-AA-TC–C-C-AT-A-G----CT-T-AA—C-T-A-T-G-G-A–A-C–T-G–C-C–T–T—T–GA-T-A–C–T–G-G–TT–G-A-C—T-T-G-A-G-T–T—A-TA–CG-G-A---------A-G-T-A—GA-T-----AG–A–ATA—A-G-T-A-GT–GT-A-G-CG-GT–G–A–A-A------TG-C-AT-AG–AT-A-TT------------------------A-C—T-T–A-G-A-AT-A-CC----GA–T–T–GC-GAA-G–G-C–A—G–T-C-T-A—CTA-----C–GT-A-T------A-T-----A-C-T–GA–CG----C–T-C–A-TG–G-A-CG-A–AA-G-C—G-TG–GG-G–AG-C-G-AA-CA-GG… > HWI-M04771\_60\_000000000-AURUP\_1\_1101\_15030\_1835 > …G–AC–GG-AG-GAT—GCA-A-G–T–G-T-T–AT-C-CGG-AA–TC-A–C-T–GG-GC–GT-A–AA-GC-GT-CT–G-TA-G-G-T-G–G–T-TT-A-A-T–AA—G-T-C-A-----A-C-T-G–TT–A-AA-TC–T-T-GA-A-G----CT-C-AA—C-T-T-C-A-A-A–A-T–C-G–C-A–G–T—C–GA-A-A–C–T–A-T–TA–G-A-C—T-A-G-A-G-T–A—T-AG–TA-G-G---------G-G-T-A—AG-G-----GG–A–ATT—T-C-C-A-GT–GG-A-G-CG-GT–G–A–A-A------TG-C-GT-AG–AG-A-TT------------------------G-G—A-A–A-G-A-AC-A-CC----GA–T–G–GC-GAA-G–G-C–A—C–T-T-T-A—CTG-----G–GC-T-A------T-T-----A-C-T–AA–CA----C–T-C–A-GA–G-A-CG-A–AA-G-C—T-AG–GG-T–AG-C-A-AA-TG-GG… ~$ cat stability.trim.contigs.good.good.unique.good.filter.fasta | sed ‘s/.//g’ > stability.trim.contigs.good.good.unique.good.filter2.fasta melissa@mprice:/media/melissa/ExtraDrive1/KIM/Argonne\_Oct2016\_WIP/De-multiplexed$ head stability.trim.contigs.good.good.unique.good.filter2.fasta > HWI-M04771\_60\_000000000-AURUP\_1\_1101\_15771\_1813 > T–AC–GG-AG-GGT—GCA-A-G–C–G-T-T–AT-C-CGG-AA–TC-A–T-T–GG-GT–TT-A–AA-GG-GT-CC–G-CA-G-G-C-G–G–T-CA-A-T-T–AA—G-T-C-A-----G-A-G-G–TG–A-AA-TC–C-C-AT-A-G----CT-T-AA—C-T-A-T-G-G-A–A-C–T-G–C-C–T–T—T–GA-T-A–C–T–G-G–TT–G-A-C—T-T-G-A-G-T–T—A-TA–CG-G-A---------A-G-T-A—GA-T-----AG–A–ATA—A-G-T-A-GT–GT-A-G-CG-GT–G–A–A-A------TG-C-AT-AG–AT-A-TT------------------------A-C—T-T–A-G-A-AT-A-CC----GA–T–T–GC-GAA-G–G-C–A—G–T-C-T-A—CTA-----C–GT-A-T------A-T-----A-C-T–GA–CG----C–T-C–A-TG–G-A-CG-A–AA-G-C—G-TG–GG-G–AG-C-G-AA-CA-GG > HWI-M04771\_60\_000000000-AURUP\_1\_1101\_15030\_1835 > G–AC–GG-AG-GAT—GCA-A-G–T–G-T-T–AT-C-CGG-AA–TC-A–C-T–GG-GC–GT-A–AA-GC-GT-CT–G-TA-G-G-T-G–G–T-TT-A-A-T–AA—G-T-C-A-----A-C-T-G–TT–A-AA-TC–T-T-GA-A-G----CT-C-AA—C-T-T-C-A-A-A–A-T–C-G–C-A–G–T—C–GA-A-A–C–T–A-T–TA–G-A-C—T-A-G-A-G-T–A—T-AG–TA-G-G---------G-G-T-A—AG-G-----GG–A–ATT—T-C-C-A-GT–GG-A-G-CG-GT–G–A–A-A------TG-C-GT-AG–AG-A-TT------------------------G-G—A-A–A-G-A-AC-A-CC----GA–T–G–GC-GAA-G–G-C–A—C–T-T-T-A—CTG-----G–GC-T-A------T-T-----A-C-T–AA–CA----C–T-C–A-GA–G-A-CG-A–AA-G-C—T-AG–GG-T–AG-C-A-AA-TG-GG So I am not sure what happened there I haven’t gone back to figure it out… But i was taking over 1 week to do pre.cluster!