Rarefaction.single sample mixup win 64

mothur bugs
1

Hi
don’t know if it is a true bug or my sample names are illegal in some way, but I’m reporting it anyway:
If I use sample names in shared file as in an example:

label Group numOtus 1 2 3 4 5 6 7 8 9 10 11 12 13 14
0.03 1_B0_S96 14 100 0 0 0 0 0 0 0 0 0 0 0 0 0
0.03 10_B0_S103 14 100 100 100 100 100 100 100 100 100 100 0 0 0 0
0.03 12_B0_S104 14 100 100 100 100 100 100 100 100 100 100 100 100 0 0
0.03 14_B0_S178 14 100 100 100 100 100 100 100 100 100 100 100 100 100 100
0.03 2_B0_S97 14 100 100 0 0 0 0 0 0 0 0 0 0 0 0
0.03 3_B0_S98 14 100 100 100 0 0 0 0 0 0 0 0 0 0 0
0.03 4_B0_S99 14 100 100 100 100 0 0 0 0 0 0 0 0 0 0
0.03 7_B0_S100 14 100 100 100 100 100 100 100 0 0 0 0 0 0 0
0.03 8_B0_S101 14 100 100 100 100 100 100 100 100 0 0 0 0 0 0
0.03 9_B0_S102 14 100 100 100 100 100 100 100 100 100 0 0 0 0 0

results of rarefaction.single are mixed up. Sample order stays the same, but results from sample 1_BO_S96 are in a column under the sample label 14_B0_S178. The same behaviour in 1.32.1 and 1.33.1


Luka
2

Thanks for reporting this bug. Mothur is not printing the column labels in the correct order. This will be fixed in our next release. There are 2 workarounds. You can use mothur to create your shared file, or run the rarefaction command with groupmode=f. If you use mothur to create your shared file, mothur will sort the groups in the shared file. The data columns in the *groups.rarefaction are being printed in sorted order, so if the groups in your shared file are listed in alphabetical order the labels will match. The groupmode=f will create individual rarefaction file for you instead of a *group.rarefaction file.