# Pre.cluster is very lslow and the fasta file which it produce is blank **URL:** \ **Category:** Uncategorized\ **Created:** [April 23, 2023, 1:21am UTC](https://forum.mothur.org/t/pre-cluster-is-very-lslow-and-the-fasta-file-which-it-produce-is-blank/21794 "2023-04-23T01:21:36Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![DYH](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@DYH](https://forum.mothur.org/u/DYH)\ **Post date:** [April 23, 2023, 1:21am UTC](https://forum.mothur.org/t/pre-cluster-is-very-lslow-and-the-fasta-file-which-it-produce-is-blank/21794/1 "2023-04-23T01:21:36Z")
mothur \> pre.cluster(fasta=stability.trim.contigs.subsample.good.unique.good.filter.unique.fasta,count=stability.trim.contigs.subsample.good.unique.good.filter.count\_table, diffs=2) Using 64 processors. When using running without group information mothur can only use 1 processor, continuing. 1108681 505548 603133 Total number of sequences before precluster was 1108681. pre.cluster removed 603133 sequences. /\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/ [WARNING]: stability.trim.contigs.subsample.good.unique.good.filter.unique.fasta does not contain any sequence from the .accnos file. Selected 0 sequences from stability.trim.contigs.subsample.good.unique.good.filter.unique.fasta. Output File Names: stability.trim.contigs.subsample.good.unique.good.filter.unique.precluster.fasta I had the above error while running pre.cluster and the size of the generated fasta file was 0, so I could not proceed to the next step ---
**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:** [April 24, 2023, 4:19pm UTC](https://forum.mothur.org/t/pre-cluster-is-very-lslow-and-the-fasta-file-which-it-produce-is-blank/21794/2 "2023-04-24T16:19:49Z")
It looks like mothur is only seeing one group in your data. Normally it operates on each group separately and then pools the results at the end. I suspect you might be running into memory issues or something else weird. Do you mean to only have one group? Pat ---
**Author:** ![Somebodyatthedoor](https://avatars.discourse-cdn.com/v4/letter/s/a3d4f5/32.png) [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)\ **Post date:** [May 2, 2023, 12:59pm UTC](https://forum.mothur.org/t/pre-cluster-is-very-lslow-and-the-fasta-file-which-it-produce-is-blank/21794/3 "2023-05-02T12:59:30Z")
Hi Pat, I am having the same problem. I am using the conda version of mothur (v1.48.0). My data should have groups, but this info seems to be lost at some point during my pipeline. After make.contigs I get a count of all of the groups, so the input to that is fine. However, in my previous analyses make.contigs used to output samples.contigs.groups file, which I noticed it did not this time. Usually I would use this file as input for commands such as count.seqs but I haven’t been able to this time. So, I tried following the newest version of the Miseq SOP, which doesn’t seem to use any group files as input to commands. The commands I have ran are: make.contigs(file=samples.txt, processors=16) summary.seqs(fasta=samples.trim.contigs.fasta, processors=16) screen.seqs(fasta=samples.trim.contigs.fasta, count=samples.contigs.count\_table, maxambig=0, maxlength=254, processors=16) unique.seqs(fasta=samples.trim.contigs.good.fasta) summary.seqs(count=samples.trim.contigs.good.count\_table) align.seqs(fasta=samples.trim.contigs.good.unique.fasta, reference=references/silva.nr\_v138\_1.align, processors=16) summary.seqs(fasta=samples.trim.contigs.good.unique.align, count=samples.trim.contigs.good.count\_table, processors=16) screen.seqs(fasta=samples.trim.contigs.good.unique.align, count=samples.trim.contigs.good.count\_table, summary=samples.trim.contigs.good.unique.summary, start=13862, end=22107, maxhomop=9) summary.seqs(fasta=samples.trim.contigs.good.unique.good.align, count=samples.trim.contigs.good.good.count\_table) filter.seqs(fasta=samples.trim.contigs.good.unique.good.align, vertical=T, trump=., processors=16) unique.seqs(fasta=samples.trim.contigs.good.unique.good.filter.fasta, count=samples.trim.contigs.good.good.count\_table) summary.seqs(fasta=samples.trim.contigs.good.unique.good.filter.unique.fasta, count=samples.trim.contigs.good.unique.good.filter.count\_table, processors=16) pre.cluster(fasta=samples.trim.contigs.good.unique.good.filter.unique.fasta, count=samples.trim.contigs.good.unique.good.filter.count\_table, diffs=2, processors=16) chimera.vsearch(fasta=samples.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=samples.trim.contigs.good.unique.good.filter.unique.precluster.count\_table, dereplicate=t, processors=16) The output of pre.cluster is: Total number of sequences before precluster was 244215. pre.cluster removed 191544 sequences. /\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/ [WARNING]: samples.trim.contigs.good.unique.good.filter.unique.fasta does not contain any sequence from the .accnos file. Selected 0 sequences from samples.trim.contigs.good.unique.good.filter.unique.fasta. Output File Names: samples.trim.contigs.good.unique.good.filter.unique.precluster.fasta /\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/ Done. It took 455 secs to cluster 244215 sequences. Using 16 processors. Output File Names: samples.trim.contigs.good.unique.good.filter.unique.precluster.fasta samples.trim.contigs.good.unique.good.filter.unique.precluster.count\_table samples.trim.contigs.good.unique.good.filter.unique.precluster.map Thanks for your help, Laura ---
**Author:** ![Somebodyatthedoor](https://avatars.discourse-cdn.com/v4/letter/s/a3d4f5/32.png) [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)\ **Post date:** [May 2, 2023, 1:20pm UTC](https://forum.mothur.org/t/pre-cluster-is-very-lslow-and-the-fasta-file-which-it-produce-is-blank/21794/4 "2023-05-02T13:20:14Z")
Hi Pat, Sorry please ignore my last post. As usual, as soon as you post a query online you find the answer yourself… Looks like I’d forgot to input a count table file to unique.seqs. Cheers, Laura ---
**Author:** ![tripitakit](https://avatars.discourse-cdn.com/v4/letter/t/bc79bd/32.png) [@tripitakit](https://forum.mothur.org/u/tripitakit)\ **Post date:** [November 30, 2023, 11:17am UTC](https://forum.mothur.org/t/pre-cluster-is-very-lslow-and-the-fasta-file-which-it-produce-is-blank/21794/5 "2023-11-30T11:17:47Z")
> [@Somebodyatthedoor](#): > > Looks like I’d forgot to input a count table file to unique.seqs. I just did the same mistake, thank you for the time saving solution 🙇‍♂️ ---
**Author:** ![DYH](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@DYH](https://forum.mothur.org/u/DYH)\ **Post date:** [February 15, 2024, 3:31pm UTC](https://forum.mothur.org/t/pre-cluster-is-very-lslow-and-the-fasta-file-which-it-produce-is-blank/21794/6 "2024-02-15T15:31:27Z")
I would like to know how you specifically solved this problem ---
**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:** [February 20, 2024, 4:41pm UTC](https://forum.mothur.org/t/pre-cluster-is-very-lslow-and-the-fasta-file-which-it-produce-is-blank/21794/7 "2024-02-20T16:41:20Z")
You should be getting a `count_table` file from `make.contigs` or from `unique.seqs` Pat