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.