Hi Brian, Yes, this would be a good optimization to make, but I think it would make sense to create an additional separate option for this. So in addition to having an option to compute the ratio from only the CID charge state, we would have an option to not try to compute the other ratios at all. Does this sound reasonable?
-David On Wed, Jan 21, 2009 at 3:21 PM, Brian Pratt <brian.pr...@insilicos.com> wrote: > > Hi Oded, > > This would seem to be a simple enough code change, but there's presumably > some reason for the current behavior (why have a "used=0" tag when you could > just omit the entries for the non-CID charge states altogether?). I'd feel > better if someone closer to the code would weigh in on this. > > Brian > > -----Original Message----- > From: spctools-discuss@googlegroups.com > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Oded > Sent: Wednesday, January 21, 2009 7:18 AM > To: spctools-discuss > Subject: [spctools-discuss] Re: ASAPRatio - multi-threading > > > Hi Brian, > I'm also experiencing very long analysis times with ASAPratio (On dual- > core Mac with 4G RAM). For me it can go up to 48 hours using 12 mzXML > files (or 700M to 1G each) of Orbitrap data. > This is still better than what it used to be with TPP before the > integration of IPP - but still this is very slow processes. I wonder > if it is possible to make ASAPratio do less calculations in order to > speed it up. For example I prefer to calculate the ratio only where > the CID occur - if this option is selected ASAPratio present the ratio > of the CID state but still calculate (or try to calculate it for all > the other states and they can be added later on. This is something > that makes the calculation 3 or 4 times slower (depending on the > number of charge states) and usually provide not very essential input. > If you want I can send you one of my files etc. > Thanks, > Oded > On Jan 21, 11:09 am, Kelly Hogue <kelly.ho...@gmail.com> wrote: >> I am fairly certain it is ASAPRatio that is the bottleneck but don't quote >> me on that. >> >> Here are the commands from the run so far: >> # Commands for session DPBYHSST7 on Thu Jan 15 12:19:15 2009 >> # BEGIN COMMAND BLOCK >> ###### BEGIN Command Execution ###### >> [Thu Jan 15 12:19:15 2009] EXECUTING: run_in >> c:/Inetpub/wwwroot/ISB/data/G041L10; xinteract >> -NG041L10_arthur_interact.pep.xml -p0.05 -l7 -x20 -OANp -dREV_ >> -X-m0.05-nK,8.014199 -A-lK-F-B-r0.05-mK136.109161 >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_35_G041L10_F11.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_36_G041L10_F12.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_37_G041L10_G01.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_38_G041L10_G02.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_39_G041L10_G03.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_40_G041L10_G04.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_41_G041L10_G05.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_42_G041L10_G06.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_43_G041L10_G07.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_44_G041L10_G08.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_45_G041L10_G09.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_46_G041L10_G10.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_47_G041L10_G11.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_48_G041L10_G12.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_49_G041L10_H01.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_50_G041L10_H02.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_51_G041L10_H03.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_52_G041L10_H04.tandem.pep.xml >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_53_G041L10_H05.tandem.pep.xml >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_51_G041L10_F11_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_52_G041L10_F12_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_53_G041L10_G01_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_54_G041L10_G02_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_55_G041L10_G03_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_56_G041L10_G04_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_57_G041L10_G05_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_58_G041L10_G06_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_59_G041L10_G07_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_60_G041L10_G08_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_61_G041L10_G09_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_62_G041L10_G10_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_63_G041L10_G11_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_64_G041L10_G12_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_65_G041L10_H01_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_66_G041L10_H02_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_67_G041L10_H03_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_68_G041L10_H04_R2.tandem.pep.xm > l >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_69_G041L10_H05_R2.tandem.pep.xm > l >> >> OUTPUT: >> >> xinteract (TPP v4.1 JETSTREAM rev 1, Build 200811121809 (MinGW)) >> >> running: "C:/Inetpub/tpp-bin/InteractParser >> "G041L10_arthur_interact.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_35_G041L10_F11.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_36_G041L10_F12.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_37_G041L10_G01.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_38_G041L10_G02.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_39_G041L10_G03.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_40_G041L10_G04.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_41_G041L10_G05.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_42_G041L10_G06.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_43_G041L10_G07.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_44_G041L10_G08.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_45_G041L10_G09.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_46_G041L10_G10.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_47_G041L10_G11.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_48_G041L10_G12.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_49_G041L10_H01.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_50_G041L10_H02.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_51_G041L10_H03.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_52_G041L10_H04.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_53_G041L10_H05.tandem.pep.xml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_51_G041L10_F11_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_52_G041L10_F12_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_53_G041L10_G01_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_54_G041L10_G02_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_55_G041L10_G03_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_56_G041L10_G04_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_57_G041L10_G05_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_58_G041L10_G06_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_59_G041L10_G07_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_60_G041L10_G08_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_61_G041L10_G09_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_62_G041L10_G10_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_63_G041L10_G11_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_64_G041L10_G12_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_65_G041L10_H01_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_66_G041L10_H02_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_67_G041L10_H03_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_68_G041L10_H04_R2.tandem.pep.x > ml" >> > "c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_69_G041L10_H05_R2.tandem.pep.x > ml" >> -L"7"" >> file 1: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_35_G041L10_F11.tandem.pep.xml >> file 2: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_36_G041L10_F12.tandem.pep.xml >> file 3: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_37_G041L10_G01.tandem.pep.xml >> file 4: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_38_G041L10_G02.tandem.pep.xml >> file 5: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_39_G041L10_G03.tandem.pep.xml >> file 6: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_40_G041L10_G04.tandem.pep.xml >> file 7: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_41_G041L10_G05.tandem.pep.xml >> file 8: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_42_G041L10_G06.tandem.pep.xml >> file 9: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_43_G041L10_G07.tandem.pep.xml >> file 10: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_44_G041L10_G08.tandem.pep.xml >> file 11: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_45_G041L10_G09.tandem.pep.xml >> file 12: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_46_G041L10_G10.tandem.pep.xml >> file 13: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_47_G041L10_G11.tandem.pep.xml >> file 14: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_48_G041L10_G12.tandem.pep.xml >> file 15: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_49_G041L10_H01.tandem.pep.xml >> file 16: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_50_G041L10_H02.tandem.pep.xml >> file 17: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_51_G041L10_H03.tandem.pep.xml >> file 18: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_52_G041L10_H04.tandem.pep.xml >> file 19: >> c:/Inetpub/wwwroot/ISB/data/G041L10/B_081030_53_G041L10_H05.tandem.pep.xml >> file 20: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_51_G041L10_F11_R2.tandem.pep.xm > l >> file 21: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_52_G041L10_F12_R2.tandem.pep.xm > l >> file 22: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_53_G041L10_G01_R2.tandem.pep.xm > l >> file 23: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_54_G041L10_G02_R2.tandem.pep.xm > l >> file 24: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_55_G041L10_G03_R2.tandem.pep.xm > l >> file 25: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_56_G041L10_G04_R2.tandem.pep.xm > l >> file 26: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_57_G041L10_G05_R2.tandem.pep.xm > l >> file 27: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_58_G041L10_G06_R2.tandem.pep.xm > l >> file 28: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_59_G041L10_G07_R2.tandem.pep.xm > l >> file 29: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_60_G041L10_G08_R2.tandem.pep.xm > l >> file 30: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_61_G041L10_G09_R2.tandem.pep.xm > l >> file 31: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_62_G041L10_G10_R2.tandem.pep.xm > l >> file 32: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_63_G041L10_G11_R2.tandem.pep.xm > l >> file 33: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_64_G041L10_G12_R2.tandem.pep.xm > l >> file 34: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_65_G041L10_H01_R2.tandem.pep.xm > l >> file 35: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_66_G041L10_H02_R2.tandem.pep.xm > l >> file 36: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_67_G041L10_H03_R2.tandem.pep.xm > l >> file 37: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_68_G041L10_H04_R2.tandem.pep.xm > l >> file 38: >> > c:/Inetpub/wwwroot/ISB/data/G041L10/B_081103_69_G041L10_H05_R2.tandem.pep.xm > l >> processed altogether 569337 results >> ... >> >> read more ยป > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
