sff.multiple not using specified parameters

Commands in mothur
1

Hi - I am running two sff files and oligo’s files through sff.multiple, and I used the following command:

sff.multiple(file=mysfffiles.txt, minflows=360, maxflows=720, maxhomop=8, lookup=LookUp_Titanium.pat, minlength=200, maxlength=600, processors=16)

Though it read the sfffiles.txt file OK - and is working, the trim.flows, shhh.flows commands that are called are not using those parameters I specified,

trim.flows used: trim.flows(flow=ATL1.flow, oligos=ATL1_Oligos.txt, maxhomop=9, maxflows=450, minflows=450, pdiffs=0, bdiffs=0, ldiffs=0, sdiffs=0, tdiffs=0, signal=0.5, noise=0.7, order=TACG, processors=1)

similarly shhh.flows is running shhh.flows(file=ATL1.flow.files, lookup=LookUp_Titanium.pat, cutoff=0.01, sigma=60, mindelta=0.000001, order=TACG, processors=1)

Can you help clarify how I get the command to run with my parameters including the multiple processors? I should add that if I run the same sff file through the sequential steps sff.info, trim.flows, shhh.flows and trim.seqs with these parameters where appropriate it uses 16 processors where possible, and worked as far as I can tell; I wanted to use the sff.multiple command since I have two sff files to analyze here together.

Thanks, Alison

2

One step forward… there was an extra “space” at the end of the sfffiles.txt line that I found and it is working using the specified min and max flow parameters however the multiple processors (I specified 16) is not being used for an unknown reason.

my command was: sff.multiple(file=ATL_multiple.sfffiles2.txt, minflows=360, maxflows=720, maxhomop=8, lookup=LookUp_Titanium.pat, minlength=200, maxlength=600, processors=16)

and it is doing the following:
trim.flows(flow=ATL1.flow, oligos=ATL1_Oligos.txt, maxhomop=8, maxflows=720, minflows=360, pdiffs=0, bdiffs=0, ldiffs=0, sdiffs=0, tdiffs=0, signal=0.5, noise=0.7, order=TACG, processors=1)

shhh.flows(file=ATL1.flow.files, lookup=LookUp_Titanium.pat, cutoff=0.01, sigma=60, mindelta=0.000001, order=TACG, processors=1)

3

The processors option is implemented in sff.multiple by giving each processors a sff file to run the commands on. Each processor runs the commands with processors=1 to avoid spawning more processes than you have processors.