I tried this command earlier today:
mothur > parsimony(tree=stability.tx.thetayc.1.lt.tre, group=design.file, groups=all)
Just a portion of the error message I received:
Your groupfile contains more than 1 sequence named AF, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named 3287, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named 2, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named unspun, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named AF, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named 2, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named unspun, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named AF, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named unspun, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named AF, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named unspun, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named AF, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named 2280, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named 0, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named unspun, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named AF, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named 2280, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named 0, sequence names must be unique. Please correct.
Your groupfile contains more than 1 sequence named unspun, sequence names must be unique. Please correct.
The design file is also causing problems with the lefse command - here’s what the top few lines of the design file look like:
group subject tissue ptb afbactload gad mr afil6 spun afc
Oct_AF0701 Prosp335 AF PTB_mildIAI 3287 23.5 2 20.1 unspun Positive
Jan_AF0701 Prosp335 AF PTB_mildIAI 3287 23.5 2 20.1 unspun Positive
Oct_AF0702 Prosp336 AF PTB_mildIAI 1726 33.5 2 0.6 unspun Negative
Oct_AF0711 Prosp341 AF TB_noIAI 2419 40 1 0.6 unspun Negative
Oct_AF0714 Prosp344 AF PTB_noIAI 2280 31.2 0 1.0 unspun Negative
Jan_AF0714 Prosp344 AF PTB_noIAI 2280 31.2 0 1.0 unspun Negative
Jun_AF0714 Prosp344 AF PTB_noIAI 2280 31.2 0 1.0 unspun Negative
Jun_T843FM Prosp344 FM PTB_noIAI 2280 31.2 0 1.0 unspun Negative
Jun_T843plac Prosp344 PLAC PTB_noIAI 2280 31.2 0 1.0 unspun Negative
Oct_AF0723 Prosp347 AF PTB_noIAI 124 35.3 0 0.2 unspun Negative
Jun_AF0737 Prosp353 AF PTB_mildIAI 1710 25.4 2 7.1 unspun Positive
Jun_AF0737b Prosp353 AF PTB_mildIAI 5186 25.4 2 13.0 unspun Positive
Jun_T881FM Prosp353 FM PTB_mildIAI 5186 25.4 2 13.0 unspun Positive
Jun_T881plac Prosp353 PLAC PTB_mildIAI 5186 25.4 2 13.0 unspun Positive
Jun_AF0743 Prosp356 AF PTB_mildIAI 2620 25.0 2 17.3 unspun Negative
Oct_AF0743b Prosp356 AF PTB_severeIAI 29102 25.0 4 22.1 unspun Positive
Jan_AF0743b Prosp356 AF PTB_severeIAI 29102 25.0 4 22.1 unspun Positive
Jun_AF0743b Prosp356 AF PTB_severeIAI 29102 25.0 4 22.1 unspun Positive
Jun_T888FM Prosp356 FM PTB_mildIAI 2620 25 2 17.3 unspun Negative
Jun_T888plac Prosp356 PLAC PTB_mildIAI 2620 25 2 17.3 unspun Negative
Jun_AF0747 Prosp359 AF PTB_mildIAI 2720 30.4 2 3.5 unspun Negative
Jun_AF0747b Prosp359 AF PTB_severeIAI 19317 30.4 4 22.1 unspun Positive
Oct_AF0750 Prosp361 AF TB_noIAI 2769 38.1 0 0.2 unspun Negative
Jan_AF0750 Prosp361 AF TB_noIAI 2769 38.1 0 0.2 unspun Negative
Help?