I just downloaded Mothur (version 1.20.2) yesterday. Running on a Windows 64-bit machine using Windows 7.
I cannot get trim.seqs to work. With this command
trim.seqs(fasta=1.TCA.454Reads.fna, maxhomop=10)
I get this error message:
Error opening file: Invalid arguement

The .fna file works with a variety of other mothur commands including summary and unique, so the file appears valid.
I also tried using sffinfo to create a fasta file from the sff file, but that does not help.
Using other options (oligos, maxambig) rather than homop does not help.

I’m sure I’m doing something really simple wrong, but I just can’t figure it out. Can anyone help me out?


It works on a Mac with exactly the same files, so I would guess the problem is incompatibility with Windows 7 (64-bit).

We are planning on releasing a 64bit version of mothur for WIndows 7 starting with version 1.21.0.

I’ve been using windows 32bit mothur on a 64 bit windows7 machine at home when working through my steps (with few samples)… i’m actually suprised at the speed it works at relative to using a windows xp machine at work that has faster specs (at least in CPU speed… my home computer is an older gaming machine)… of course the mac versions work even better…

i’ve never used your trim.seqs command in that fashion… I get the sff files from the lab, sffinfo and then trim.seqs the fasta and qual files…

trim.seqs(fasta=, qfile=, oligos=, maxambig=0, maxhomop=8, bdiffs=1, pdiffs=2, qwindowaverage=30, qwindowsize=50)

that works perfectly fine on a windows7 64 bit machine… do you have the option to get those files?


Hi Shaun,

I too have no problems using the 32bit on a 64bit win7. I also trim.seqs in the same fashion as you. However, I see you have lowered the qwindowaverage from the 35 (reconmended by Pat) to 30. Can I ask why you have done this?

I ask because I had a problem when using (the reconmended function) qwindowaverage=35 and qwindowsize=50 due to poor quality sequences and thus a large proportion of my samples were removed. To overcome this without lowering the average quality of the sequence to below 35 I set the qwindowsize=100. This allows more sequences of greater lenght to be included compared with the reconmended function. Pat has outlined in another thread that 30 compared with 35 will give and error rate od 0.55% compared with 0.1%, respectively. Food for thought…

Let me know what you think,