I'm running remove.rare for more than 4 days

Commands in mothur
1

Hi, I’m trying to remove singletons using following command:
remove.rare(list=study.opti_mcc.list, count=study.count_table, nseqs=1, label=0.03)

It took 154053 secs (about 43 hours) for dist.seqs and only 17369 secs (about 5 hours) for cluster command. As far as I know, remove.rare should be much faster than these steps.

It is still running without showing any messages for more than 4 days.
When I try the remove.rare without count table, it finishes within a few seconds. However, I need to put count table for further analysis.

Could you please help me fix this problem?

Best,
Ho-kyung

2

Could you send your log, list and count file to mothur.bugs@gmail.com so I can troubleshoot the issue for you?

3

Thanks for reporting this issue and sending your files. I was able to find the source of the slowdown and have fixed it. The change will be part of our next release coming soon.

4

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