mothur

Remove.rare: Your count table does not have group info

Hi,

I am upgrading a workflow that I made in v1.39.1 to v1.43.0 and ran into a problem when using remove.rare. In the workflow, I have a single sample that I want to classify so I do not have any group information. However, when I try to run remove.rare with a list file and a count table, I get the error ‘Your count table does not have group info. Please correct’. This never happened with v1.39.1 and running the command with that version works fine. Is there anything that I can do to add this group information in order to make remove.rare work again when only using a single sample?

Best regards
Raf

Thanks for reporting this issue. I have fixed the problem and the change will be part of our 1.44.0 release. In the meantime, here’s a workaround for you:

  1. Create a fake group. Open your count table in excel and copy and paste the total column into a new column.
Representative_Sequence total dummy
M00967_43_000000000-A3JHG_1_1101_20262_22075 1 1
M00967_43_000000000-A3JHG_1_1109_24493_23253 1 1
M00967_43_000000000-A3JHG_1_2105_6287_22914 1 1
M00967_43_000000000-A3JHG_1_2101_4780_15092 1 1
M00967_43_000000000-A3JHG_1_2106_8030_23327 1 1
M00967_43_000000000-A3JHG_1_1102_6774_6343 1 1
M00967_43_000000000-A3JHG_1_2108_7751_22068 1 1
M00967_43_000000000-A3JHG_1_2101_4159_12177 1 1
M00967_43_000000000-A3JHG_1_1114_19835_4993 5 5

mothur > remove.rare(list=yourListFile, count=dummy.count_table, nseqs=xxx) - remove rare seqs

mothur > list.seqs(list=current) - list sequences in good list file

mothur > get.seqs(count=yourOriginalCountFileWithoutDummyGroup, accnos=current) - select good sequences from the original file

Great, thanks for the workaround!

Best regards
Raf

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