# Issue with cluster not making a list file when using method=agc

**URL:** <https://forum.mothur.org/t/issue-with-cluster-not-making-a-list-file-when-using-method-agc/22280>\
**Category:** mothur bugs\
**Created:** [January 25, 2025, 3:50am UTC](https://forum.mothur.org/t/issue-with-cluster-not-making-a-list-file-when-using-method-agc/22280 "2025-01-25T03:50:03Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![nohayoussef](https://avatars.discourse-cdn.com/v4/letter/n/ccd318/32.png) [@nohayoussef](https://forum.mothur.org/u/nohayoussef)\
**Post date:** [January 25, 2025, 3:50am UTC](https://forum.mothur.org/t/issue-with-cluster-not-making-a-list-file-when-using-method-agc/22280/1 "2025-01-25T03:50:03Z")

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I am having issues when using cluster with the vsearch (method=agc). My fasta file is aligned and preclustered. It is huge (~7M sequences). Vsearch finishes clustering and produces the .uc and .log files. The largest cluster has over 3.7M sequences. The list is not created and it looks like it is just sitting there doing nothing.

Here is what is in the log file:  
vsearch v2.17.1\_linux\_x86\_64, 92.9GB RAM, 32 cores  
/opt/mothur/1.48.0/prebuilt//vsearch --maxaccepts=16 --threads=32 --usersort --id=0.94 --minseqlength=30 --wordlength=8 --uc=Beavers\_B.trim.contigs.good.filter.good.precluster.fasta.sorted.fasta.temp.clustered.uc --cluster\_smallmem=Beavers\_B.trim.contigs.good.filter.good.precluster.fasta.sorted.fasta.temp --maxrejects=64 --strand=both --log=Beavers\_B.trim.contigs.good.filter.good.precluster.fasta.sorted.fasta.temp.clustered.log --sizeorder  
Started Wed Jan 22 11:58:40 2025  
2224429547 nt in 7324114 seqs, min 240, max 602, avg 304

```
  Alphabet nt
Word width 8
 Word ones 8
    Spaced No
    Hashed No
     Coded No
   Stepped No
     Slots 65536 (65.5k)
   DBAccel 100%

```

Clusters: 9309 Size min 1, max 3790290, avg 786.8  
Singletons: 4966, 0.1% of seqs, 53.3% of clusters

Finished Wed Jan 22 12:20:41 2025  
Elapsed time 22:01  
Max memory 6.0GB

The fasta file is 26.8 GB and the count is close to 0.8 GB. Do you think this is a memory issue?

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [January 27, 2025, 7:09pm UTC](https://forum.mothur.org/t/issue-with-cluster-not-making-a-list-file-when-using-method-agc/22280/2 "2025-01-27T19:09:59Z")

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It looks like vsearch completed the clustering, but the creation of the list file from the .uc file is either hanging or taking a very long time. Could you send Beavers\_B.trim.contigs.good.filter.good.precluster.fasta.sorted.fasta.temp.clustered.uc and Beavers\_B.trim.contigs.good.filter.good.precluster.fasta.sorted.fasta.temp.clustered.log to [mothur.westcott@gmail.com](mailto:mothur.westcott@gmail.com) so I can troubleshoot the issue for you?

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**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [February 6, 2025, 7:10pm UTC](https://forum.mothur.org/t/issue-with-cluster-not-making-a-list-file-when-using-method-agc/22280/3 "2025-02-06T19:10:45Z")

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