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

mothur bugs
1

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?

2

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 so I can troubleshoot the issue for you?

3

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