set.dir cannot have different input and output directories

mothur bugs
1

Hi!

I am using mothur 1.22.

I have the problem that if I set the input dir, the output goes to the same place as the input, and vice versa.

Example:

mothur > set.dir(input=/usit/titan/u1/karinlag)

Mothur’s directories:
inputDir=/usit/titan/u1/karinlag/

mothur > set.dir(output=.)

Mothur’s directories:
outputDir=/xanadu/home/karinlag/tmp/

mothur > summary.seqs(fasta=makeseq.fasta)

Unable to open makeseq.fasta. Trying output directory /xanadu/home/karinlag/tmp/makeseq.fasta
Unable to open /xanadu/home/karinlag/tmp/makeseq.fasta
[ERROR]: did not complete summary.seqs.

mothur >


And now for the other way:

mothur > set.dir(output=/xanadu/home/karinlag/tmp/)

Mothur’s directories:
outputDir=/xanadu/home/karinlag/tmp/

mothur > set.dir(input=.)

Mothur’s directories:
inputDir=/xanadu/home/karinlag/

mothur > summary.seqs(fasta=makeseq.fasta)


Start End NBases Ambigs Polymer NumSeqs Minimum: 1 800 800 0 6 1 2.5%-tile: 1 800 800 0 6 1 25%-tile: 1 800 800 0 6 1 Median: 1 800 800 0 6 1 75%-tile: 1 800 800 0 6 1 97.5%-tile: 1 800 800 0 6 1 Maximum: 1 800 800 0 6 1 Mean: 1 800 800 0 6 # of Seqs: 1

Output File Name:
/xanadu/home/karinlag/makeseq.fasta.summary


mothur >
This is quite annoying.....

Karin

2

When you run the set.dir(input=someDirectory), mothur clears the saved input and output directories and then sets input=someDirectory. If you want to set both the input and output directories, run set.dir(input=/usit/titan/u1/karinlag, output=.).

3

Ah, that clears up a lot! I was convinced I had to set them separately.

Thanks!