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.