pre.cluster being to long?

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

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

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!