Trim.seqs removing group info in counts file

mothur bugs
1

Not sure if it is me doing something wrong or the software but…

With the intention to remove short sequences, when I run

mothur > trim.seqs(fasta=current, minlength=120, count=current)

All group info is lost in the new count file. This makes mothur to fail in downstream analyses when counts/groups/names are needed.

The count infile (first few rows):
Representative_Sequence total BZ313D BZ316N
M03075_96_000000000-AVF08_1_1101_12073_1968 3788 2565 1223
M03075_96_000000000-AVF08_1_1101_18441_2028 2 2 0
M03075_96_000000000-AVF08_1_1101_14523_2077 2038 2030 8
M03075_96_000000000-AVF08_1_1101_18008_2134 10531 4124 6407
M03075_96_000000000-AVF08_1_1101_16243_2444 2128 2108 20

The count outfile:
Representative_Sequence total
M03075_96_000000000-AVF08_1_1101_12073_1968 3788
M03075_96_000000000-AVF08_1_1101_18441_2028 2
M03075_96_000000000-AVF08_1_1101_14523_2077 2038
M03075_96_000000000-AVF08_1_1101_18008_2134 10531
M03075_96_000000000-AVF08_1_1101_16243_2444 2128

I am using mothur 1.38.1 in CentOS (RedHat 7).

Thanks,

Leo

2

The trim.seqs command is designed to generate its own group information if an oligos file is given. Perhaps a better way to remove short sequences is the screen.seqs command.

mothur > screen.seqs(fasta=current, minlength=120, count=current)