Talked to Yaamini this morning about her Pecan run being done already and it looks like something didn’t work right. Pecan claims to have run correctly, but produced no .feature files for Percolator to operate on.
I’m running a single instance of Pecan now with the command
/home/shared/pecan/bin/pecan -b /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt --minCharge 2 --maxCharge 3 --ionTypes y 2017_January_23_envtstress_oyster1.mzML /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt 400.0 405.0 2017_January_23_envtstress_oyster123
and the only output given by Pecan is
Pecan does produce a log file which says
PECAN|WARNING| ====== Initiating PECAN|INFO| # /home/shared/pecan/bin/pecan -b /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt --minCharge 2 --maxCharge 3 --ionTypes y 2017_January_23_envtstress_oyster1.mzML /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt 400.0 405.0 2017_January_23_envtstress_oyster123 PECAN|INFO| # 2017-03-04T08:54:49.835533 PECAN|INFO| # host = roadrunner PECAN|INFO| # minElutionTime = 12.00 PECAN|INFO| # maxElutionTime = 30.00 PECAN|INFO| # minCharge = 2 PECAN|INFO| # maxCharge = 3 PECAN|INFO| # topX peaks = 1 PECAN|INFO| # decoyTag = decoy PECAN|INFO| # bgDecoyNumber = 2000 PECAN|INFO| # isoWindowWidth = 5.00 PECAN|INFO| # idotpThreshold = 0.00 PECAN|INFO| # ms1Tolerance = 10 ppm PECAN|INFO| # ms2Tolerance = 10 ppm PECAN|INFO| # overlapPercentage = 0 PECAN|INFO| # alpha = 1.80 PECAN|INFO| # beta = 0.40 PECAN|INFO| # fixedMod = C=C[+57.021464] PECAN|INFO| # logFile = 2017_January_23_envtstress_oyster123.402.5.log PECAN|INFO| # mzBoundaries = [58.0, 870.0] PECAN|INFO| # ionTypes = ('y',) PECAN|INFO| # backgroundProteome = /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt PECAN|INFO| # SCIEX mzML? False PECAN|WARNING| ====== Checking ms2 PECAN.Chromatogram|INFO| Scanned 0 MS2 scans with precursor m/z 400.0 - 405.0 PECAN.Chromatogram|INFO| Cycle time for the first 100 cycles: 0.000000 seconds PECAN.Chromatogram|INFO| 0 MS2 scans! Quit now
I’m not sure if this means there’s an issue with the mzML file or what.