Unfortunately I can't help you with Mayu as it's not a tool I use. You might consider re-posting your attachment as only a small portion of the top of the image is visible.
On Wed, Mar 11, 2015 at 10:58 PM, Rachel <rachel2005...@gmail.com> wrote: > HI David and Jimmy, > > It worked after removed ./. Thank you so much! > But when I run Mayu.pl on comet.iprophet.pep.xml. I got the following > error(pls see attached). And there is no output. I have run the same > dataset on tandem output and I am sure I should get some outputs. Why? > > Regards, > Rachel > > On Thursday, March 5, 2015 at 3:26:21 PM UTC+8, Rachel wrote: > >> Dear Eric, >> I have run spectrast successfully on tandem iprophet output, but not on >> comet output. (using following command) >> what can be the reason? >> spectrast -cNSpectralib -cP0.0001 -cODengue_id.txt -cIHCD -cf "Protein! ~ >> DECOY" -c_IRTiRTdefinition.txt -c_IRR comet.iprophet.pep.xml >> >> Below is the log file... I am sure I have put all mzXML files in the same >> folder. >> ========== >> START: (Thu Mar 05 14:49:48 2015) spectrast -cNSpectralib -cP0.0001 >> -cODengue_id.txt -cIHCD -cf Protein! ~ DECOY -c_IRTiRTdefinition.txt -c_IRR >> comet.iprophet.pep.xml >> GENERAL: File offset size is 8 bytes. Big library supported. >> GENERAL: Pointer size is 8 bytes. >> CREATE: Apply FILTER for Protein! ~ DECOY >> CREATE: Apply FILTER for entries in protein list "c:/Users/Administrator/ >> Dengue/Dengue_id.txt" >> CREATE: IMPORT FROM PepXML "c:/Users/Administrator/ >> Dengue/comet.iprophet.pep.xml", (Comet against >> "Human_reviewed_CON_Selected_Denguevirus_iRT_DECOY.fasta" (AA); ) >> [P=0.0001;q=9999;n=;g=FALSE;o=FALSE;I=HCD;_RNT=0;_RDR= >> 100000;_DCN=0;_NAA=6;_NPK=10;_MDF=9999;_CEN=FALSE;_XAN= >> FALSE;_BRK=FALSE;_BRM=FALSE;_IRT=c:/Users/Administrator/ >> Dengue/iRTdefinition.txt;_IRR=TRUE]; FILTER for Protein! ~ DECOY; FILTER >> for entries in protein list "c:/Users/Administrator/Dengue/Dengue_id.txt" >> PEPXML IMPORT: Total of 46372 read (46011 with PeptideProphet >> probability; 46011 with iProphet probability). >> PEPXML IMPORT: Total of 22230 spectra (46011 queries) have probability >= >> 0.0001. >> PEPXML IMPORT: Read RT landmarks from file >> "c:/Users/Administrator/Dengue/iRTdefinition.txt" >> : LGGNEQVTR (29.3) | GAGSSEPVTGLDAK (42.4) | VEATFGVDESNAK (52.7) | >> YILAGVENSK (50.6) | TPVISGGPYEYR (54.7) | TPVITGAPYEYR (58.1) | >> DGLDAASYYAPVR (68.9) | ADVTPADFSEWSK (69.1) | GTFIIDPGGVIR (77.9) | >> GTFIIDPAAVIR (86.1) | LFLQFGAQGSPFLK (87.8) | . >> PEPXML IMPORT: RT normalization by linear regression. Found 10 landmarks >> in MS run "". >> PEPXML_IMPORT: Final fitted equation: iRT = (rRT + 38.32) / (61.4); R^2 = >> 0.9956; 0 outliers removed. >> ERROR PEPXML IMPORT: Cannot open file ".mzXML|.mzML|.mzXML.gz|.mzML.gz|.mz5 >> in c:/Users/Administrator/Dengue/". No scan from this file will be >> imported. >> ========== >> Thank you! >> Rachel >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
