If the user selects MBR for IonQuant, but supplies just one file/experiment, then IonQuant crashes and FragPipe stops - but it should rather check for such cases and simply ignore MBR in these cases (in my case, it was an accident, as I reused an old query for a new, single file and forgot to tick off MBR in the IonQuant tab).
`System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
Version info:
FragPipe version 15.0
MSFragger version 3.2
Philosopher version 3.4.13 (build 1611589727)
20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw 139.2 s | deisotoping 0.7 s
[progress: 40816/40816 (100%) - 19002 spectra/s] 2.1s | postprocessing 0.2 s
***FIRST SEARCH DONE IN 3.765 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION
-----
---------------
---------------
---------------
---------------
MS1 (Old)
MS1 (New)
MS2 (Old)
MS2 (New)
Run
Median MAD
Median MAD
Median MAD
Median MAD
001
4.07 2.39
-0.19 1.70
2.41 3.45
-0.07 3.32
-----
---------------
---------------
---------------
---------------
Finding the optimal parameters:
-------
-------
-------
-------
-------
-------
-------
-------
-------
MS2
5
7
10
15
20
25
30
50
Count
19626
21152
22157
22662
22693
22540
skip rest
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
Peaks
500_0
300_0
200_0
175_0
150_1
125_1
100_1
-------
-------
-------
-------
-------
-------
-------
-------
Count
22700
22685
skip rest
-------
-------
-------
-------
-------
-------
-------
-------
-------
-------
Int.
1
-------
-------
Count
22940
-------
-------
-------
-------
Rm P.
1
-------
-------
Count
22688
-------
-------
New fragment_mass_tolerance = 20 PPM
New use_topN_peaks = 500
New minimum_ratio = 0.000000
New intensity_transform = 1
New remove_precursor_peak = 0
****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 3.173 MIN*****
20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.mzBIN_calibrated 0.6 s
[progress: 37923/37923 (100%) - 56099 spectra/s] 0.7s | postprocessing 2.3 s
MAIN SEARCH DONE IN 0.105 MIN
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0
init with X! Tandem stricttrypsin
PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 13434 2+, 12029 3+, 3402 4+, 656 5+, 93 6+, and 0 7+ spectra.
Found 2702 Decoys, and 26912 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
INFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .........10.........20.....WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
INFO[07:33:37] Done
Process 'PeptideProphet' finished, exit code: 0
PeptideProphet: Delete temp
C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp
Process 'PeptideProphet: Delete temp' finished, exit code: 0
Rewrite pepxml [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES]
C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib/* com.dmtavt.fragpipe.util.RewritePepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw
Fixing pepxml: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml
Writing output to: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml12015410115015550458.temp-rewrite
Deleting file: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml
Moving rewritten file to original location: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml12015410115015550458.temp-rewrite] -> [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
ProteinProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml
INFO[07:33:39] Executing ProteinProphet v3.4.13
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64))
(no FPKM) (using degen pep info)
Reading in E:/20210329_HeLa_Inverted-uPAC/MSFragger_Default_Closed_by_RAW/HeLa_Triple_LOW_RES/interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml...
...read in 0 1+, 10257 2+, 9316 3+, 2556 4+, 422 5+, 49 6+, 0 7+ spectra with min prob 0.05
Initializing 12499 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database e:/PHILOSOPHER_FASTA/2021-03-17-decoys-reviewed-contam-UP000005640.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U
MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG
...:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U
MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG
......:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:...... Total: 40860
Computing degenerate peptides for 3246 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing 3010 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
INFO: mu=7.33977e-06, db_size=45499165
Computing MU for 3358 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Finished.
INFO[07:33:52] Done
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES]
C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev
INFO[07:33:52] Executing Database v3.4.13
INFO[07:33:52] Processing database
INFO[07:33:56] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev
INFO[07:33:56] Executing Database v3.4.13
INFO[07:33:56] Processing database
INFO[07:33:59] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOWRES]
C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES --protxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\combined.prot.xml
INFO[07:33:59] Executing Filter v3.4.13
INFO[07:33:59] Processing peptide identification files
INFO[07:34:02] 1+ Charge profile decoy=0 target=0
INFO[07:34:02] 2+ Charge profile decoy=70 target=10187
INFO[07:34:02] 3+ Charge profile decoy=43 target=9273
INFO[07:34:02] 4+ Charge profile decoy=12 target=2544
INFO[07:34:02] 5+ Charge profile decoy=2 target=420
INFO[07:34:02] 6+ Charge profile decoy=0 target=49
INFO[07:34:02] Database search results ions=12482 peptides=10743 psms=22600
INFO[07:34:02] Converged to 0.56 % FDR with 22473 PSMs decoy=127 threshold=0.0503 total=22600
INFO[07:34:02] Converged to 1.00 % FDR with 10622 Peptides decoy=107 threshold=0.0573 total=10729
INFO[07:34:02] Converged to 0.91 % FDR with 12369 Ions decoy=113 threshold=0.0504 total=12482
INFO[07:34:03] Protein inference results decoy=143 target=2867
INFO[07:34:03] Converged to 1.02 % FDR with 2449 Proteins decoy=25 threshold=0.8943 total=2474
INFO[07:34:04] Applying sequential FDR estimation ions=12267 peptides=10529 psms=22360
INFO[07:34:04] Converged to 0.12 % FDR with 22332 PSMs decoy=28 threshold=0.0503 total=22360
INFO[07:34:04] Converged to 0.20 % FDR with 10507 Peptides decoy=22 threshold=0.0511 total=10529
INFO[07:34:05] Converged to 0.18 % FDR with 12245 Ions decoy=22 threshold=0.0511 total=12267
INFO[07:34:05] Post processing identifications
INFO[07:34:06] Mapping modifications
INFO[07:34:10] Processing protein inference
INFO[07:34:14] Assigning protein identifications to layers
INFO[07:34:15] Updating razor PSM assignment to proteins
INFO[07:34:15] Calculating spectral counts
INFO[07:34:15] Saving
INFO[07:34:17] Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES]
C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe report
INFO[07:34:17] Executing Report v3.4.13
INFO[07:34:19] Creating reports
INFO[07:34:20] Done
Process 'PhilosopherReport' finished, exit code: 0
IonQuant [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW]
C:\MSPrograms\fragpipe-15\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\thermo" -cp "C:\MSPrograms\fragpipe-15\tools\ionquant-1.5.5.jar;C:\MSPrograms\fragpipe-15\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 0 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm HeLa_Triple_LOW_RES\psm.tsv --multidir . --specdir E:\20210329_HeLa_Inverted-uPAC HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML
IonQuant version IonQuant-1.5.5
Batmass-IO version 1.22.1
timsdata library version timsdata-2-7-0
(c) University of Michigan
System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 108 GB memory
2021-03-30 07:34:21 [WARNING] - There are only 1 experiments. Using Top-N protein intensity calculation algorithm with min exps = 1.
2021-03-30 07:34:21 [WARNING] - proteinquant == 1 but minions > 1. Changing minions to 1.
2021-03-30 07:34:21 [INFO] - Parameters:
2021-03-30 07:34:21 [INFO] - threads = 48
2021-03-30 07:34:21 [INFO] - mztol = 10.0
2021-03-30 07:34:21 [INFO] - rttol = 0.4
2021-03-30 07:34:21 [INFO] - imtol = 0.05
2021-03-30 07:34:21 [INFO] - seedmz = 0
2021-03-30 07:34:21 [INFO] - minisotopes = 2
2021-03-30 07:34:21 [INFO] - minscans = 3
2021-03-30 07:34:21 [INFO] - psm = E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\psm.tsv
2021-03-30 07:34:21 [INFO] - multidir = E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW.\
2021-03-30 07:34:21 [INFO] - excludemods =
2021-03-30 07:34:21 [INFO] - minions = 1
2021-03-30 07:34:21 [INFO] - proteinquant = 1
2021-03-30 07:34:21 [INFO] - normalization = 1
2021-03-30 07:34:21 [INFO] - minexps = 1
2021-03-30 07:34:21 [INFO] - minfreq = 0.5
2021-03-30 07:34:21 [INFO] - tp = 3
2021-03-30 07:34:21 [INFO] - mbr = 1
2021-03-30 07:34:21 [INFO] - mbrrttol = 1.0
2021-03-30 07:34:21 [INFO] - mbrimtol = 0.05
2021-03-30 07:34:21 [INFO] - mbrtoprun = 10
2021-03-30 07:34:21 [INFO] - mbrmincorr = 0.0
2021-03-30 07:34:21 [INFO] - ionmobility = 0
2021-03-30 07:34:21 [INFO] - ionfdr = 0.01
2021-03-30 07:34:21 [INFO] - peptidefdr = 1.0
2021-03-30 07:34:21 [INFO] - proteinfdr = 1.0
2021-03-30 07:34:21 [INFO] - light =
2021-03-30 07:34:21 [INFO] - medium =
2021-03-30 07:34:21 [INFO] - heavy =
2021-03-30 07:34:21 [INFO] - requantify = 0
2021-03-30 07:34:21 [INFO] - writeindex = 0
2021-03-30 07:34:21 [INFO] - specdir = E:\20210329_HeLa_Inverted-uPAC
2021-03-30 07:34:21 [INFO] - E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML
2021-03-30 07:34:21 [INFO] - Checking E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw...
2021-03-30 07:34:24 [INFO] - Loading E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw...
2021-03-30 07:36:45 [INFO] - 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES has 3 compensation voltages: -70.0, -43.0, -30.0
2021-03-30 07:36:45 [INFO] - Building index...
2021-03-30 07:36:46 [INFO] - Writing index to E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.quantindex
2021-03-30 07:36:46 [INFO] - Loading E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML...
2021-03-30 07:36:47 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2021-03-30 07:36:47 [INFO] - Quantifying...
2021-03-30 07:36:49 [INFO] - Updating Philosopher's tables...
2021-03-30 07:36:51 [INFO] - Matching-between-runs: 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES...
2021-03-30 07:36:51 [INFO] - Calculating correlations between all other runs...
2021-03-30 07:36:51 [WARNING] - There is no run passing the minimum correlation threshold 0.0
2021-03-30 07:36:51 [WARNING] - Run 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES got nothing matched.
2021-03-30 07:36:51 [INFO] - Estimating match-between-runs FDR...
2021-03-30 07:36:51 [WARNING] - There is no mbr file for run E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES. May be because it failed in MBR.
2021-03-30 07:36:51 [WARNING] - There is no MBR result.
2021-03-30 07:36:51 [INFO] - Combining experiments and estimating protein intensity...
java.lang.Exception: The intensity columns don't match the experiments.
at l.a(Unknown Source)
at l.(Unknown Source)
at ionquant.IonQuant.main(Unknown Source)
2021-03-30 07:36:52 [ERROR] - The intensity columns don't match the experiments.
Process 'IonQuant' finished, exit code: 1
Process returned non-zero exit code, stopping
If the user selects MBR for IonQuant, but supplies just one file/experiment, then IonQuant crashes and FragPipe stops - but it should rather check for such cases and simply ignore MBR in these cases (in my case, it was an accident, as I reused an old query for a new, single file and forgot to tick off MBR in the IonQuant tab). `System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
Version info: FragPipe version 15.0 MSFragger version 3.2 Philosopher version 3.4.13 (build 1611589727)
LCMS files: Experiment/Group: HeLa_Triple_LOW_RES
19 commands to execute: WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx108G C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\MSFragger-3.2.jar E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\fragger.params E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw MSFragger move pepxml C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar;/C:/MSPrograms/fragpipe-15/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML MSFragger move tsv C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar;/C:/MSPrograms/fragpipe-15/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.tsv E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.tsv PeptideProphet: Workspace init [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWERRES.pepXML-temp] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database E:\PHILOSOPHER_FASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas ..\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML PeptideProphet: Delete temp C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp Rewrite pepxml [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib/* com.dmtavt.fragpipe.util.RewritePepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw ProteinProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOWRES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES --protxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\combined.prot.xml PhilosopherReport [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe report IonQuant [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\thermo" -cp "C:\MSPrograms\fragpipe-15\tools\ionquant-1.5.5.jar;C:\MSPrograms\fragpipe-15\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 0 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm HeLa_Triple_LOW_RES\psm.tsv --multidir . --specdir E:\20210329_HeLa_Inverted-uPAC HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML WorkspaceClean [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[07:25:23] Executing Workspace v3.4.13
INFO[07:25:23] Removing workspace
WARN[07:25:23] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:25:23] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[07:25:23] Executing Workspace v3.4.13
INFO[07:25:23] Creating workspace
INFO[07:25:23] Done
WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[07:25:24] Executing Workspace v3.4.13
INFO[07:25:24] Removing workspace
WARN[07:25:24] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[07:25:24] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[07:25:24] Executing Workspace v3.4.13
INFO[07:25:24] Creating workspace
INFO[07:25:24] Done
MSFragger [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx108G C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\MSFragger-3.2.jar E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\fragger.params E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw MSFragger version MSFragger-3.2 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 108 GB memory Checking database... Checking spectral files... E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw: Scans = 102005 ***FIRST SEARCH**** Parameters: num_threads = 48 database_name = E:\PHILOSOPHER_FASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 318543152 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.14 s
New fragment_mass_tolerance = 20 PPM New use_topN_peaks = 500 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 3.173 MIN*****
****MAIN SEARCH**** Checking database... Parameters: num_threads = 48 database_name = E:\PHILOSOPHER_FASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -50.0 precursor_mass_upper = 50.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = 0 isotope_error = 0/1/2/3 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 500 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (255.15829 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Selected fragment index width 0.10 Da. 318543152 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.45 s
***TOTAL TIME 7.043 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar;/C:/MSPrograms/fragpipe-15/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar;/C:/MSPrograms/fragpipe-15/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.tsv E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.tsv Process 'MSFragger move tsv' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'PeptideProphet: Workspace init' finished, exit code: 0 INFO[07:32:31] Executing Workspace v3.4.13
INFO[07:32:31] Creating workspace
INFO[07:32:31] Done
PeptideProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWERRES.pepXML-temp] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database E:\PHILOSOPHER_FASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas ..\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML INFO[07:32:32] Executing PeptideProphet v3.4.13
Unknown file type. No file loaded.E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES/20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw Unknown file type. No file loaded.E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES/20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw file 1: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML processed altogether 29614 results INFO: Results written to file: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml
using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem stricttrypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 13434 2+, 12029 3+, 3402 4+, 656 5+, 93 6+, and 0 7+ spectra. Found 2702 Decoys, and 26912 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10.........20.....WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (7+). model complete after 26 iterations INFO[07:33:37] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\fragpipe-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -cp C:\MSPrograms\fragpipe-15\lib/* com.dmtavt.fragpipe.util.RewritePepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw Fixing pepxml: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml Writing output to: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml12015410115015550458.temp-rewrite Deleting file: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml Moving rewritten file to original location: [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml12015410115015550458.temp-rewrite] -> [E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml INFO[07:33:39] Executing ProteinProphet v3.4.13
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) (no FPKM) (using degen pep info) Reading in E:/20210329_HeLa_Inverted-uPAC/MSFragger_Default_Closed_by_RAW/HeLa_Triple_LOW_RES/interact-20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pep.xml... ...read in 0 1+, 10257 2+, 9316 3+, 2556 4+, 422 5+, 49 6+, 0 7+ spectra with min prob 0.05
Initializing 12499 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database e:/PHILOSOPHER_FASTA/2021-03-17-decoys-reviewed-contam-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG ...:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:...WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG ......:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:...... Total: 40860 Computing degenerate peptides for 3246 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 3010 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... INFO: mu=7.33977e-06, db_size=45499165 Computing MU for 3358 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Finished. INFO[07:33:52] Done(Unknown Source)
at ionquant.IonQuant.main(Unknown Source)
2021-03-30 07:36:52 [ERROR] - The intensity columns don't match the experiments.
Process 'IonQuant' finished, exit code: 1
Process returned non-zero exit code, stopping
Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[07:33:52] Executing Database v3.4.13
INFO[07:33:52] Processing database
INFO[07:33:56] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe database --annotate E:\PHILOSOPHERFASTA\2021-03-17-decoys-reviewed-contam-UP000005640.fas --prefix rev INFO[07:33:56] Executing Database v3.4.13
INFO[07:33:56] Processing database
INFO[07:33:59] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOWRES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --tag rev --pepxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES --protxml E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\combined.prot.xml INFO[07:33:59] Executing Filter v3.4.13
INFO[07:33:59] Processing peptide identification files
INFO[07:34:02] 1+ Charge profile decoy=0 target=0 INFO[07:34:02] 2+ Charge profile decoy=70 target=10187 INFO[07:34:02] 3+ Charge profile decoy=43 target=9273 INFO[07:34:02] 4+ Charge profile decoy=12 target=2544 INFO[07:34:02] 5+ Charge profile decoy=2 target=420 INFO[07:34:02] 6+ Charge profile decoy=0 target=49 INFO[07:34:02] Database search results ions=12482 peptides=10743 psms=22600 INFO[07:34:02] Converged to 0.56 % FDR with 22473 PSMs decoy=127 threshold=0.0503 total=22600 INFO[07:34:02] Converged to 1.00 % FDR with 10622 Peptides decoy=107 threshold=0.0573 total=10729 INFO[07:34:02] Converged to 0.91 % FDR with 12369 Ions decoy=113 threshold=0.0504 total=12482 INFO[07:34:03] Protein inference results decoy=143 target=2867 INFO[07:34:03] Converged to 1.02 % FDR with 2449 Proteins decoy=25 threshold=0.8943 total=2474 INFO[07:34:04] Applying sequential FDR estimation ions=12267 peptides=10529 psms=22360 INFO[07:34:04] Converged to 0.12 % FDR with 22332 PSMs decoy=28 threshold=0.0503 total=22360 INFO[07:34:04] Converged to 0.20 % FDR with 10507 Peptides decoy=22 threshold=0.0511 total=10529 INFO[07:34:05] Converged to 0.18 % FDR with 12245 Ions decoy=22 threshold=0.0511 total=12267 INFO[07:34:05] Post processing identifications
INFO[07:34:06] Mapping modifications
INFO[07:34:10] Processing protein inference
INFO[07:34:14] Assigning protein identifications to layers
INFO[07:34:15] Updating razor PSM assignment to proteins
INFO[07:34:15] Calculating spectral counts
INFO[07:34:15] Saving
INFO[07:34:17] Done
Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES] C:\MSPrograms\fragpipe-15\tools\philosopher\philosopher.exe report INFO[07:34:17] Executing Report v3.4.13
INFO[07:34:19] Creating reports
INFO[07:34:20] Done
Process 'PhilosopherReport' finished, exit code: 0 IonQuant [Work dir: E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW] C:\MSPrograms\fragpipe-15\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\bruker" -Dlibs.thermo.dir="C:\MSPrograms\fragpipe-15\tools\MSFragger-3.2\ext\thermo" -cp "C:\MSPrograms\fragpipe-15\tools\ionquant-1.5.5.jar;C:\MSPrograms\fragpipe-15\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 0 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm HeLa_Triple_LOW_RES\psm.tsv --multidir . --specdir E:\20210329_HeLa_Inverted-uPAC HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML IonQuant version IonQuant-1.5.5 Batmass-IO version 1.22.1 timsdata library version timsdata-2-7-0 (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 108 GB memory 2021-03-30 07:34:21 [WARNING] - There are only 1 experiments. Using Top-N protein intensity calculation algorithm with min exps = 1. 2021-03-30 07:34:21 [WARNING] - proteinquant == 1 but minions > 1. Changing minions to 1. 2021-03-30 07:34:21 [INFO] - Parameters: 2021-03-30 07:34:21 [INFO] - threads = 48 2021-03-30 07:34:21 [INFO] - mztol = 10.0 2021-03-30 07:34:21 [INFO] - rttol = 0.4 2021-03-30 07:34:21 [INFO] - imtol = 0.05 2021-03-30 07:34:21 [INFO] - seedmz = 0 2021-03-30 07:34:21 [INFO] - minisotopes = 2 2021-03-30 07:34:21 [INFO] - minscans = 3 2021-03-30 07:34:21 [INFO] - psm = E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\psm.tsv 2021-03-30 07:34:21 [INFO] - multidir = E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW.\ 2021-03-30 07:34:21 [INFO] - excludemods = 2021-03-30 07:34:21 [INFO] - minions = 1 2021-03-30 07:34:21 [INFO] - proteinquant = 1 2021-03-30 07:34:21 [INFO] - normalization = 1 2021-03-30 07:34:21 [INFO] - minexps = 1 2021-03-30 07:34:21 [INFO] - minfreq = 0.5 2021-03-30 07:34:21 [INFO] - tp = 3 2021-03-30 07:34:21 [INFO] - mbr = 1 2021-03-30 07:34:21 [INFO] - mbrrttol = 1.0 2021-03-30 07:34:21 [INFO] - mbrimtol = 0.05 2021-03-30 07:34:21 [INFO] - mbrtoprun = 10 2021-03-30 07:34:21 [INFO] - mbrmincorr = 0.0 2021-03-30 07:34:21 [INFO] - ionmobility = 0 2021-03-30 07:34:21 [INFO] - ionfdr = 0.01 2021-03-30 07:34:21 [INFO] - peptidefdr = 1.0 2021-03-30 07:34:21 [INFO] - proteinfdr = 1.0 2021-03-30 07:34:21 [INFO] - light = 2021-03-30 07:34:21 [INFO] - medium = 2021-03-30 07:34:21 [INFO] - heavy = 2021-03-30 07:34:21 [INFO] - requantify = 0 2021-03-30 07:34:21 [INFO] - writeindex = 0 2021-03-30 07:34:21 [INFO] - specdir = E:\20210329_HeLa_Inverted-uPAC 2021-03-30 07:34:21 [INFO] - E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML 2021-03-30 07:34:21 [INFO] - Checking E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw... 2021-03-30 07:34:24 [INFO] - Loading E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.raw... 2021-03-30 07:36:45 [INFO] - 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES has 3 compensation voltages: -70.0, -43.0, -30.0 2021-03-30 07:36:45 [INFO] - Building index... 2021-03-30 07:36:46 [INFO] - Writing index to E:\20210329_HeLa_Inverted-uPAC\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.quantindex 2021-03-30 07:36:46 [INFO] - Loading E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES.pepXML... 2021-03-30 07:36:47 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2021-03-30 07:36:47 [INFO] - Quantifying... 2021-03-30 07:36:49 [INFO] - Updating Philosopher's tables... 2021-03-30 07:36:51 [INFO] - Matching-between-runs: 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES... 2021-03-30 07:36:51 [INFO] - Calculating correlations between all other runs... 2021-03-30 07:36:51 [WARNING] - There is no run passing the minimum correlation threshold 0.0 2021-03-30 07:36:51 [WARNING] - Run 20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES got nothing matched. 2021-03-30 07:36:51 [INFO] - Estimating match-between-runs FDR... 2021-03-30 07:36:51 [WARNING] - There is no mbr file for run E:\20210329_HeLa_Inverted-uPAC\MSFragger_Default_Closed_by_RAW\HeLa_Triple_LOW_RES\20210329_HeLa_100ng_150mGENIII-FAIMS-70-43-30V-CV_FIXED_CE_500nL_5-30_LOWER_RES. May be because it failed in MBR. 2021-03-30 07:36:51 [WARNING] - There is no MBR result. 2021-03-30 07:36:51 [INFO] - Combining experiments and estimating protein intensity... java.lang.Exception: The intensity columns don't match the experiments. at l.a(Unknown Source) at l.