sffinfo

Commands in mothur
1

Hi all

I’m new to using mothur. The command I’m trying to run is

sffinfo(sff=seqs.sff, flow=T)

but I keep getting the following error returned:

/var/spool/slurm/job1656598/slurm_script: line 39: syntax error near unexpected token sff=seqs.sff' /var/spool/slurm/job1656598/slurm_script: line 39:sffinfo(sff=seqs.sff, flow=T)’

Has anyone had similar syntax issues? Is there another way of writing the command?

Thanks

2

Hi all

I figured it out after playing around. I needed to format the command as:

mothur "#sffinfo(sff=seqs.sff, flow=T)"

Thanks

3

You may download the example data and try. It will work if the sff file is right.

4

Hi everybody
I am new to mothur as well.
I did MiSeq SOP without any problem but starting the 454 SOP, I can not continue!
When I write this command:
mothur> sffinfo(sff=GQY1XT001.sff, flow=T)
It says:
Unable to open GQY1XT001.sff. It will be disregarded.
no valid files.
[ERROR]: you must provide a valid sff or sfftxt file.
[ERROR]: did not complete sffinfo.

and when write this one:
mothur> summary.seqs(fasta=GQY1XT001.fasta)
It says:
Unable to open GQY1XT001.fasta

and it is right! Becaus I can’t find them among the downloaded files as either.
I have downloaded all the four documents of the SOP plus the Mothur and have put them in one folder as the tutorial wants us to do and as I did for the MiSeq SOP.
I don’t know what is wrong! would you please help me?
Thanks

5

At the end of the bullet that says “Example data from Schloss Lab” there is a link to the full dataset:

http://www.mothur.org/w/images/2/27/SOP_SFF.bz2