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PNNL-Comp-Mass-Spec / Informed-Proteomics

Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data
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Error computing FDR: Cannot compute FDR Scores; target file is empty #15

Open Arrow-V opened 5 years ago

Arrow-V commented 5 years ago

I directly use MSPathFinderT to analyze my data(Thermo .raw), however, it goes wrong. I don't know know how to fix it, could anybody help me?

C:\Users\Neal\Documents>MSPathFinderT.exe -s D:\10_26data\Chem2-2-1.raw -d D:\10_26data\all.fasta -o D:\10_26data\new -t 10 -f 10 -m 1 -tda 1 -minLength 21 -maxLength 300 -minCharge 2 -maxCharge 30 -minFragCharge 1 -maxFragCharge 15 -minMass 3000 -maxMass 50000 -mod D:\10_26data\MSPathFinder_Mods.txt MSPathFinderT version 1.0.6510 (Oct. 28, 2017) MaxThreads: 6 SpectrumFilePath: D:\10_26data\Chem2-2-1.raw DatabaseFilePath: D:\10_26data\all.fasta FeatureFilePath: N/A OutputDir: D:\10_26data\new InternalCleavageMode: SingleInternalCleavage Tag-based search: True Tda: Target+Decoy PrecursorIonTolerancePpm: 10 ProductIonTolerancePpm: 10 MinSequenceLength: 21 MaxSequenceLength: 300 MinPrecursorIonCharge: 2 MaxPrecursorIonCharge: 30 MinProductIonCharge: 1 MaxProductIonCharge: 15 MinSequenceMass: 3000 MaxSequenceMass: 50000 MaxDynamicModificationsPerSequence: 4 Modifications: C(0) H(0) N(0) O(1) S(0),M,opt,Everywhere,Oxidation C(0) H(-1) N(0) O(0) S(0),C,opt,Everywhere,Dehydro C(2) H(2) N(0) O(1) S(0),*,opt,ProteinNTerm,Acetyl Creating and loading pbf file... Total Progress: 0.00%, 0d 0h 0.00m elapsed, Current Task: Reading spectra file Elapsed Time: 5.2 sec Reading Fasta File Generating D:\10_26data\all.icseq and Generating D:\10_26data\all.icanno ... Done Reading ProMex results... 3155/3155 features loaded...Elapsed Time: 2.0 sec Generating deconvoluted spectra for MS/MS spectra... Elapsed Time: 0.0 sec Generating sequence tags for MS/MS spectra... Number of spectra: 0 Generated sequence tags: 0 Elapsed Time: 0.0 sec Caching peaks in MS1 spectra: 25329 scans Sorting MS1 peaks: 54,689,404 peaks Reading the target database... Elapsed Time: 0.3 sec Tag-based searching the target database Number of spectra containing sequence tags: 0 Collected candidate matches: 0 Target database tag-based search elapsed Time: 35.5 sec Searching the target database Generating D:\10_26data\all.icplcp ... Done Estimated Sequences: 37,834,838 Processing, 0 proteins done, 0.0% complete, 0.0 sec elapsed Processing, 106315 proteins done, 0.3% complete, 15.1 sec elapsed Processing, 118028 proteins done, 0.3% complete, 30.1 sec elapsed Processing, 216527 proteins done, 0.6% complete, 45.1 sec elapsed Processing, 323031 proteins done, 0.9% complete, 60.1 sec elapsed Processing, 427459 proteins done, 1.1% complete, 75.1 sec elapsed Total Progress: 42.70%, 0d 0h 5.00m elapsed, Current Task: Searching the target database Processing, 532183 proteins done, 1.4% complete, 90.1 sec elapsed Processing, 637148 proteins done, 1.7% complete, 105.1 sec elapsed Processing, 768883 proteins done, 2.0% complete, 135.1 sec elapsed Processing, 953651 proteins done, 2.5% complete, 165.1 sec elapsed Processing, 1101862 proteins done, 2.9% complete, 195.9 sec elapsed Processing, 1285452 proteins done, 3.4% complete, 225.9 sec elapsed Processing, 1422493 proteins done, 3.8% complete, 255.9 sec elapsed Processing, 1510383 proteins done, 4.0% complete, 285.9 sec elapsed Processing, 1672899 proteins done, 4.4% complete, 346.0 sec elapsed Total Progress: 43.36%, 0d 0h 10.00m elapsed, Current Task: Searching the target database Processing, 2041036 proteins done, 5.4% complete, 406.0 sec elapsed Processing, 2368429 proteins done, 6.3% complete, 466.0 sec elapsed Processing, 2683408 proteins done, 7.1% complete, 527.5 sec elapsed Processing, 2991146 proteins done, 7.9% complete, 587.5 sec elapsed Processing, 3309509 proteins done, 8.7% complete, 647.5 sec elapsed Total Progress: 44.12%, 0d 0h 15.04m elapsed, Current Task: Searching the target database Processing, 3681335 proteins done, 9.7% complete, 707.5 sec elapsed Processing, 4036809 proteins done, 10.7% complete, 767.5 sec elapsed Processing, 4308919 proteins done, 11.4% complete, 827.6 sec elapsed Processing, 4548002 proteins done, 12.0% complete, 887.8 sec elapsed Processing, 4752700 proteins done, 12.6% complete, 947.8 sec elapsed Total Progress: 44.75%, 0d 0h 20.09m elapsed, Current Task: Searching the target database Processing, 4939771 proteins done, 13.1% complete, 1007.8 sec elapsed Processing, 4939772 proteins done, 13.1% complete, 1007.8 sec elapsed Processing, 4939773 proteins done, 13.1% complete, 1007.8 sec elapsed Processing, 5122628 proteins done, 13.5% complete, 1069.0 sec elapsed Processing, 5122627 proteins done, 13.5% complete, 1069.0 sec elapsed Processing, 5328186 proteins done, 14.1% complete, 1129.0 sec elapsed Processing, 5535302 proteins done, 14.6% complete, 1191.3 sec elapsed Total Progress: 45.21%, 0d 0h 25.09m elapsed, Current Task: Searching the target database Processing, 6754622 proteins done, 17.9% complete, 1492.6 sec elapsed Total Progress: 45.77%, 0d 0h 30.09m elapsed, Current Task: Searching the target database Processing, 7896082 proteins done, 20.9% complete, 1792.6 sec elapsed Total Progress: 46.38%, 0d 0h 35.14m elapsed, Current Task: Searching the target database Processing, 9470041 proteins done, 25.0% complete, 2092.6 sec elapsed Total Progress: 47.03%, 0d 0h 40.14m elapsed, Current Task: Searching the target database Processing, 10584900 proteins done, 28.0% complete, 2393.7 sec elapsed Total Progress: 47.50%, 0d 0h 45.19m elapsed, Current Task: Searching the target database Processing, 11487978 proteins done, 30.4% complete, 2694.0 sec elapsed Total Progress: 47.98%, 0d 0h 50.21m elapsed, Current Task: Searching the target database Processing, 12217755 proteins done, 32.3% complete, 2994.0 sec elapsed Total Progress: 48.23%, 0d 0h 55.22m elapsed, Current Task: Searching the target database Processing, 12725499 proteins done, 33.6% complete, 3296.6 sec elapsed Total Progress: 48.39%, 0d 1h 0.26m elapsed, Current Task: Searching the target database Total Progress: 48.39%, 0d 1h 5.27m elapsed, Current Task: Searching the target database Total Progress: 48.39%, 0d 1h 10.29m elapsed, Current Task: Searching the target database Total Progress: 48.39%, 0d 1h 15.31m elapsed, Current Task: Searching the target database Total Progress: 48.39%, 0d 1h 20.32m elapsed, Current Task: Searching the target database Total Progress: 48.39%, 0d 1h 25.34m elapsed, Current Task: Searching the target database Processing, 12725500 proteins done, 33.6% complete, 5000.6 sec elapsed Total Progress: 48.84%, 0d 1h 30.34m elapsed, Current Task: Searching the target database Processing, 14227281 proteins done, 37.6% complete, 5300.6 sec elapsed Total Progress: 49.45%, 0d 1h 35.38m elapsed, Current Task: Searching the target database Processing, 15403529 proteins done, 40.7% complete, 5600.7 sec elapsed Total Progress: 49.87%, 0d 1h 40.38m elapsed, Current Task: Searching the target database Processing, 16221767 proteins done, 42.9% complete, 5900.7 sec elapsed Total Progress: 50.28%, 0d 1h 45.39m elapsed, Current Task: Searching the target database Processing, 17104889 proteins done, 45.2% complete, 6203.2 sec elapsed Total Progress: 50.69%, 0d 1h 50.39m elapsed, Current Task: Searching the target database Processing, 18226901 proteins done, 48.2% complete, 6505.3 sec elapsed Total Progress: 51.20%, 0d 1h 55.39m elapsed, Current Task: Searching the target database Processing, 19098473 proteins done, 50.5% complete, 6806.7 sec elapsed Total Progress: 51.62%, 0d 2h 0.42m elapsed, Current Task: Searching the target database Processing, 20256051 proteins done, 53.5% complete, 7106.7 sec elapsed Total Progress: 52.17%, 0d 2h 5.42m elapsed, Current Task: Searching the target database Processing, 21211621 proteins done, 56.1% complete, 7406.7 sec elapsed Total Progress: 52.57%, 0d 2h 10.43m elapsed, Current Task: Searching the target database Processing, 22091816 proteins done, 58.4% complete, 7708.7 sec elapsed Total Progress: 53.12%, 0d 2h 15.48m elapsed, Current Task: Searching the target database Processing, 23624794 proteins done, 62.4% complete, 8008.7 sec elapsed Total Progress: 53.93%, 0d 2h 20.48m elapsed, Current Task: Searching the target database Processing, 25145852 proteins done, 66.5% complete, 8311.5 sec elapsed Total Progress: 54.50%, 0d 2h 25.51m elapsed, Current Task: Searching the target database Processing, 26387047 proteins done, 69.7% complete, 8613.3 sec elapsed Total Progress: 55.08%, 0d 2h 30.54m elapsed, Current Task: Searching the target database Processing, 27652102 proteins done, 73.1% complete, 8913.3 sec elapsed Total Progress: 55.66%, 0d 2h 35.54m elapsed, Current Task: Searching the target database Processing, 28895951 proteins done, 76.4% complete, 9215.1 sec elapsed Total Progress: 56.24%, 0d 2h 40.58m elapsed, Current Task: Searching the target database Processing, 30139855 proteins done, 79.7% complete, 9515.2 sec elapsed Total Progress: 56.80%, 0d 2h 45.59m elapsed, Current Task: Searching the target database Processing, 31342528 proteins done, 82.8% complete, 9815.2 sec elapsed Total Progress: 57.34%, 0d 2h 50.59m elapsed, Current Task: Searching the target database Processing, 32435944 proteins done, 85.7% complete, 10117.8 sec elapsed Total Progress: 57.87%, 0d 2h 55.59m elapsed, Current Task: Searching the target database Processing, 33930982 proteins done, 89.7% complete, 10417.8 sec elapsed Total Progress: 58.68%, 0d 3h 0.61m elapsed, Current Task: Searching the target database Processing, 35360872 proteins done, 93.5% complete, 10717.8 sec elapsed Total Progress: 59.19%, 0d 3h 5.62m elapsed, Current Task: Searching the target database Processing, 36518054 proteins done, 96.5% complete, 11017.8 sec elapsed Total Progress: 59.74%, 0d 3h 10.67m elapsed, Current Task: Searching the target database Processing, 37390107 proteins done, 98.8% complete, 11319.5 sec elapsed Collected candidate matches: 0 Target database search elapsed Time: 11399.8 sec Calculating spectral E-values for target-spectrum matches Estimated matched sequences: 0 Target-spectrum match E-value calculation elapsed Time: 0.1 sec Creating D:\10_26data\all.icsfldecoy.fasta Generating D:\10_26data\all.icsfldecoy.icseq and Generating D:\10_26data\all.icsfldecoy.icanno ... Done Reading the decoy database... Elapsed Time: 0.5 sec Tag-based searching the decoy database Number of spectra containing sequence tags: 0 Collected candidate matches: 0 Decoy database tag-based search elapsed Time: 12.1 sec Searching the decoy database Generating D:\10_26data\all.icsfldecoy.icplcp ... Done Estimated Sequences: 37,834,838 Processing, 0 proteins done, 0.0% complete, 0.0 sec elapsed Processing, 91058 proteins done, 0.2% complete, 15.0 sec elapsed Processing, 104777 proteins done, 0.3% complete, 36.5 sec elapsed Processing, 104775 proteins done, 0.3% complete, 36.5 sec elapsed Processing, 104780 proteins done, 0.3% complete, 36.5 sec elapsed Processing, 199050 proteins done, 0.5% complete, 51.5 sec elapsed Processing, 299404 proteins done, 0.8% complete, 66.5 sec elapsed Processing, 399679 proteins done, 1.1% complete, 81.6 sec elapsed Processing, 473324 proteins done, 1.3% complete, 99.3 sec elapsed Total Progress: 77.72%, 0d 3h 15.70m elapsed, Current Task: Searching the decoy database Processing, 473827 proteins done, 1.3% complete, 116.2 sec elapsed Processing, 473826 proteins done, 1.3% complete, 116.2 sec elapsed Processing, 473828 proteins done, 1.3% complete, 116.2 sec elapsed Processing, 474920 proteins done, 1.3% complete, 147.2 sec elapsed Processing, 576058 proteins done, 1.5% complete, 177.2 sec elapsed Processing, 776854 proteins done, 2.1% complete, 207.2 sec elapsed Processing, 978487 proteins done, 2.6% complete, 237.2 sec elapsed Processing, 1122059 proteins done, 3.0% complete, 267.2 sec elapsed Processing, 1322696 proteins done, 3.5% complete, 297.2 sec elapsed Processing, 1707488 proteins done, 4.5% complete, 357.2 sec elapsed Total Progress: 78.42%, 0d 3h 20.70m elapsed, Current Task: Searching the decoy database Processing, 2026830 proteins done, 5.4% complete, 417.3 sec elapsed Processing, 2367141 proteins done, 6.3% complete, 478.8 sec elapsed Processing, 2721653 proteins done, 7.2% complete, 538.8 sec elapsed Processing, 3082872 proteins done, 8.1% complete, 598.8 sec elapsed Processing, 3434130 proteins done, 9.1% complete, 658.8 sec elapsed Total Progress: 79.22%, 0d 3h 25.70m elapsed, Current Task: Searching the decoy database Processing, 3745457 proteins done, 9.9% complete, 718.8 sec elapsed Processing, 3996486 proteins done, 10.6% complete, 778.8 sec elapsed Processing, 4350716 proteins done, 11.5% complete, 838.9 sec elapsed Processing, 4716227 proteins done, 12.5% complete, 904.6 sec elapsed Processing, 4716229 proteins done, 12.5% complete, 904.6 sec elapsed Processing, 5132499 proteins done, 13.6% complete, 964.6 sec elapsed Total Progress: 80.00%, 0d 3h 30.71m elapsed, Current Task: Searching the decoy database Processing, 5520902 proteins done, 14.6% complete, 1024.6 sec elapsed Processing, 6057630 proteins done, 16.0% complete, 1084.6 sec elapsed Processing, 6560208 proteins done, 17.3% complete, 1144.6 sec elapsed Total Progress: 81.24%, 0d 3h 35.71m elapsed, Current Task: Searching the decoy database Processing, 9229408 proteins done, 24.4% complete, 1444.6 sec elapsed Total Progress: 82.43%, 0d 3h 40.71m elapsed, Current Task: Searching the decoy database Processing, 11711076 proteins done, 31.0% complete, 1744.7 sec elapsed Total Progress: 83.50%, 0d 3h 45.71m elapsed, Current Task: Searching the decoy database Processing, 13778610 proteins done, 36.4% complete, 2044.7 sec elapsed Total Progress: 84.34%, 0d 3h 50.71m elapsed, Current Task: Searching the decoy database Processing, 15581306 proteins done, 41.2% complete, 2344.7 sec elapsed Total Progress: 85.13%, 0d 3h 55.71m elapsed, Current Task: Searching the decoy database Processing, 17190416 proteins done, 45.4% complete, 2644.7 sec elapsed Total Progress: 85.85%, 0d 4h 0.71m elapsed, Current Task: Searching the decoy database Processing, 18745544 proteins done, 49.5% complete, 2944.7 sec elapsed Total Progress: 86.40%, 0d 4h 5.71m elapsed, Current Task: Searching the decoy database Processing, 19900230 proteins done, 52.6% complete, 3244.7 sec elapsed Total Progress: 87.10%, 0d 4h 10.71m elapsed, Current Task: Searching the decoy database Processing, 21381784 proteins done, 56.5% complete, 3546.7 sec elapsed Total Progress: 87.72%, 0d 4h 15.76m elapsed, Current Task: Searching the decoy database Processing, 22653945 proteins done, 59.9% complete, 3846.7 sec elapsed Total Progress: 88.33%, 0d 4h 20.76m elapsed, Current Task: Searching the decoy database Processing, 24074766 proteins done, 63.6% complete, 4147.1 sec elapsed Total Progress: 88.99%, 0d 4h 25.76m elapsed, Current Task: Searching the decoy database Processing, 25388499 proteins done, 67.1% complete, 4447.1 sec elapsed Total Progress: 89.56%, 0d 4h 30.81m elapsed, Current Task: Searching the decoy database Processing, 26602039 proteins done, 70.3% complete, 4748.9 sec elapsed Total Progress: 90.13%, 0d 4h 35.85m elapsed, Current Task: Searching the decoy database Processing, 27836037 proteins done, 73.6% complete, 5050.5 sec elapsed Total Progress: 90.70%, 0d 4h 40.86m elapsed, Current Task: Searching the decoy database Processing, 29086254 proteins done, 76.9% complete, 5351.3 sec elapsed Total Progress: 91.28%, 0d 4h 45.88m elapsed, Current Task: Searching the decoy database Processing, 30335458 proteins done, 80.2% complete, 5651.3 sec elapsed Total Progress: 91.84%, 0d 4h 50.88m elapsed, Current Task: Searching the decoy database Processing, 31534228 proteins done, 83.3% complete, 5951.9 sec elapsed Processing, 31534229 proteins done, 83.3% complete, 5951.9 sec elapsed Total Progress: 92.36%, 0d 4h 55.91m elapsed, Current Task: Searching the decoy database Processing, 32562446 proteins done, 86.1% complete, 6254.3 sec elapsed Total Progress: 92.87%, 0d 5h 0.93m elapsed, Current Task: Searching the decoy database Processing, 33775607 proteins done, 89.3% complete, 6557.1 sec elapsed Total Progress: 93.44%, 0d 5h 5.98m elapsed, Current Task: Searching the decoy database Processing, 34961566 proteins done, 92.4% complete, 6858.7 sec elapsed Total Progress: 93.96%, 0d 5h 11.00m elapsed, Current Task: Searching the decoy database Processing, 36073780 proteins done, 95.3% complete, 7160.8 sec elapsed Total Progress: 94.51%, 0d 5h 16.05m elapsed, Current Task: Searching the decoy database Processing, 37283875 proteins done, 98.5% complete, 7460.8 sec elapsed Collected candidate matches: 0 Decoy database search elapsed Time: 7626.0 sec Calculating spectral E-values for decoy-spectrum matches Estimated matched sequences: 0 Decoy-spectrum match E-value calculation elapsed Time: 0.0 sec

Warning: Error computing FDR: Cannot compute FDR Scores; target file is empty Error processing Chem2-2-1.raw: Cannot compute FDR Scores; target file is empty

FarmGeek4Life commented 5 years ago

The error is that you have no results for the target or the decoy search. The only part of the entire process that shows any results is ProMex, which reports only 3155 features.