mothur > sffinfo(sff=M1.sff, flow=T, inputdir=C:\Users\Roman\Desktop\AMOA\input4
mothur\input\, outputdir=C:\Users\Roman\Desktop\AMOA\input4mothur\output\)
=C:\Users\Roman\Desktop\AMOA\input4mothur\output\ directory does not exist or is
not writable.
=C:\Users\Roman\Desktop\AMOA\input4mothur\input\ directory does not exist or is
not writable.
Extracting info from C:\Users\Roman\Desktop\AMOA\input4mothur\input\M1.sff ...
10000
20000
30000
40000
50000
60000
70000
80000
90000
94754
It took 283 secs to extract 94754.
Output File Names:
C:\Users\Roman\Desktop\AMOA\input4mothur\output\M1.fasta
C:\Users\Roman\Desktop\AMOA\input4mothur\output\M1.qual
C:\Users\Roman\Desktop\AMOA\input4mothur\output\M1.flow
produces output at the correct directory, but gives error messages when you run it, =C:\Users\Roman\Desktop\AMOA\input4mothur\output\ directory does not exist or is not writable. Its obvious that this has to do with it interpreting the = as path component.
Another strange error with these options is you leave out the trailing backslash \ it also doesn’t work, but using the set.dir command, you can safely leave that out just fine. A bit of inconsistancy there which lead to further trial and error to get this to work, and the error message is non helpful.
Another error which my labmate just reminded me about, You can’t use processors=8 on trim.seqs as it corrupts the output, Seems that 1 or 4 work fine. Not a huge deal because even on 1 processor it still completes in a less than a minute for 400,000 sequences, but it was something that took me a bit to work out why that was happening.