Error running LEFSE - can't open design file

Commands in mothur
1

I just tried running:

lefse(shared=stability.tx.shared,design=design.file)

I got this error:

Unable to open design.file. Trying default /opt/mothur/1.39.5/mothur/design.file
Unable to open /opt/mothur/1.39.5/mothur/design.file. Trying mothur’s location /opt/mothur/1.39.5/mothurdesign.file
Unable to open /opt/mothur/1.39.5/mothurdesign.file
[ERROR]: did not complete lefse.

The design.file is in the same directory as the shared file, and it is a tab-delimited text file whose first 25 lines look something like this:

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

2

And I finally figured this out - had to hard-code the path to the design file, e.g. ~/mydir/design.file

Seems like a bug?

3

I don’t think it’s a bug. Where are you running this from? What is the path to the shared file? I suspect the shared and design files are in different directories.

Pat