mothur

cluster vsearch; method=agc, no conversion of vsearch output to mothur list format

Hi all,

I’m using mothur:

Linux version
Using ReadLine
Running 64Bit Version
mothur v.1.39.5
Last updated: 3/20/2017

I’m trying to cluster a large environmental, highly diverse, highly multiplexed, nonaligned fungal ITS file with

cluster(fasta=MiSeq.pick.pick.fasta, count=MiSeq.pick.pick.count_table, method=agc, cutoff=0.03, processors=32)

Clustering progresses normally, outputs two files but then hangs.

output in mothur home directory:
MiSeq.pick.pick.fasta.sorted.fasta.temp.clustered.uc
MiSeq.pick.pick.fasta.sorted.fasta.temp.clustered.log


The log contains the vsearch log output:
vsearch v2.3.4_linux_x86_64, 252.2GB RAM, 32 cores
/mnt/shared/users/tf40403/mothur/mothur/vsearch --maxaccepts=16 --threads=32 --usersort --id=0.97 --minseqlength=30 --wordlength=8 --uc=MiSeq.pick.pick.fasta.sorted.fasta.temp.clustered.uc --cluster_smallmem=MiSeq.pick.pick.fasta.sorted.fasta.temp --maxrejects=64 --strand=both --log=MiSeq.pick.pick.fasta.sorted.fasta.temp.clustered.log --sizeorder
Started Sun Jul 2 15:14:57 20171629881570 nt in 5111917 seqs, min 150, max 403, avg 319
Alphabet nt
Word width 8
Word ones 8
Spaced No
Hashed No
Coded No
Stepped No
Slots 65536 (65.5k)
DBAccel 100%
Clusters: 753615 Size min 1, max 404079, avg 6.8
Singletons: 706642, 13.8% of seqs, 93.8% of clusters
Finished Sun Jul 2 17:12:51 2017
Elapsed time 117:54
Max memory 6.8GB

I’ve used the cluster- method=agc, module of this mothur installation before and it worked fine.

I’m not sure what is going on here:
Either, the size and complexity of the dataset completely prevents the conversion of the vsearch output to mothur list file or slows it down to snail pace. :frowning:

Any comments are greatly appreciated.

Tom

Update:
repeated clustering with cutoff=0.1 to reduce complexity of clustering output:

same result. Vsearch clustering completes after few hours but hangs with unconverted uc out file.
:?
Hmm…
will try and further reduce input file size.

Tom

Could you send your input files to mothur.bugs@gmail.com so I can take a look?

Hi Sarah,

I think I got the same issue that the Vsearch clustering was hanging there! So I am wondering what should I do?

Thanks,
Rain

12%20PM|690x307

Could you send the log, fasta and count files to mothur.bugs@gmail.com?