make.groups problem


I’m trying to make a group file out of 169 fasta files but failed and I don’t know why.

I followed the instructions, so that my code looks like that (I’ll just put it for 3 samples):, groups=final.S1.filter-final.S2.filter-final.S3.filter)

Strangely, I get an outpu tfile called “mergegroups”.

What did I do wrong?

Thanks, C.

Are you using version 1.34? Also, mothur renames the output file merge.groups when there are 3 or more files to avoid a filename that is too long for the OS.


I’m using mothur v.1.33.3. Actually, it’s not producing merge.groups but mergegroups, so without a dot.
That’s looks strange to me.

Hm, but when I look at the first lines it looks normal:

HWI-M01755_45__1_1101_8467_1850 final.S1
HWI-M01755_45__1_1101_12550_1955 final.S1
HWI-M01755_45__1_1101_24116_2000 final.S1
HWI-M01755_45__1_1101_24178_2049 final.S1
HWI-M01755_45__1_1101_11583_2068 final.S1
HWI-M01755_45__1_1101_9304_2088 final.S1
HWI-M01755_45__1_1101_17701_2131 final.S1
HWI-M01755_45__1_1101_12612_2135 final.S1
HWI-M01755_45__1_1101_16322_2144 final.S1
HWI-M01755_45__1_1101_7300_2193 final.S1

I’m still not sure if I should make the group names final.S1, final.S2… or final.S1.filter, final.S2.filter, since my fasta files are called final.S1.filter.fasta and so on.


Can you try it with our current version? I am not seeing the issues you are describing with 1.34.

mothur >, groups=a.2.3-b.1.4-d.5.1)
Unable to open amazon.fasta. Trying default /Users/sarahwestcott/desktop/release/amazon.fasta
Unable to open abrecovery.fasta. Trying default /Users/sarahwestcott/desktop/release/abrecovery.fasta
Unable to open final.fasta. Trying default /Users/sarahwestcott/desktop/release/final.fasta

Output File Names: /Users/sarahwestcott/desktop/release/

U68589 a.2.3
U68590 a.2.3
U68591 a.2.3
U68592 a.2.3
U68593 a.2.3
U68594 a.2.3
U68595 a.2.3
U68596 a.2.3
U68597 a.2.3