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March 8, 2017 14:53
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percolator_concat_stderr
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Percolator version 3.01, Build Date Nov 16 2016 14:58:22 | |
Copyright (c) 2006-9 University of Washington. All rights reserved. | |
Written by Lukas Käll (lukall@u.washington.edu) in the | |
Department of Genome Sciences at the University of Washington. | |
Issued command: | |
percolator -t 0.02 -m test.concat.psm.tsv -r test.concat.pep.tsv test.concat.pin | |
Started Wed Mar 8 08:48:30 2017 | |
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 | |
Reading tab-delimited input from datafile test.concat.pin | |
Features: | |
lnrSp deltLCn deltCn lnExpect Xcorr Sp IonFrac Mass PepLen Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 enzN enzC enzInt lnNumSP dM absdM | |
Found 19690 PSMs | |
Concatenated search input detected, skipping both target-decoy competition and mix-max. | |
Train/test set contains 13915 positives and 5775 negatives, size ratio=2.40952 and pi0=1 | |
Selecting Cpos by cross-validation. | |
Selecting Cneg by cross-validation. | |
Split 1: Selected feature 4 as initial search direction. Could separate 4623 training set positives in that direction. | |
Split 2: Selected feature 4 as initial search direction. Could separate 4701 training set positives in that direction. | |
Split 3: Selected feature 4 as initial search direction. Could separate 4650 training set positives in that direction. | |
Found 6974 test set positives with q<0.02 in initial direction | |
Reading in data and feature calculation took 0.288918 cpu seconds or 1 seconds wall clock time. | |
---Training with Cpos selected by cross validation, Cneg selected by cross validation, fdr=0.01 | |
Iteration 1: Estimated 7364 PSMs with q<0.02 | |
Iteration 2: Estimated 7370 PSMs with q<0.02 | |
Iteration 3: Estimated 7387 PSMs with q<0.02 | |
Iteration 4: Estimated 7400 PSMs with q<0.02 | |
Iteration 5: Estimated 7400 PSMs with q<0.02 | |
Iteration 6: Estimated 7398 PSMs with q<0.02 | |
Iteration 7: Estimated 7397 PSMs with q<0.02 | |
Iteration 8: Estimated 7405 PSMs with q<0.02 | |
Iteration 9: Estimated 7403 PSMs with q<0.02 | |
Iteration 10: Estimated 7402 PSMs with q<0.02 | |
Learned normalized SVM weights for the 3 cross-validation splits: | |
Split1 Split2 Split3 FeatureName | |
-0.3382 -0.6418 -0.5385 lnrSp | |
0.7802 0.9219 1.0173 deltLCn | |
-0.2933 -0.3049 -0.3753 deltCn | |
-1.4325 -0.8598 -0.9613 lnExpect | |
1.1402 1.6526 1.4503 Xcorr | |
0.8775 -0.0381 0.8188 Sp | |
-0.6558 0.0101 -0.2641 IonFrac | |
-0.0032 -0.0341 0.1013 Mass | |
-0.1820 0.0555 -0.0189 PepLen | |
0.0000 0.0000 0.0000 Charge1 | |
-0.0933 -0.0722 -0.1392 Charge2 | |
0.1316 0.1262 0.1372 Charge3 | |
-0.0964 -0.1331 -0.0123 Charge4 | |
0.0139 0.0091 0.0458 Charge5 | |
0.0193 0.0196 0.0146 Charge6 | |
0.1025 0.3099 0.3136 enzN | |
0.0000 0.0000 0.0000 enzC | |
-0.1095 -0.2527 -0.2502 enzInt | |
0.2132 0.1264 0.3269 lnNumSP | |
0.3171 0.6445 0.6229 dM | |
-0.7204 -0.7712 -0.9014 absdM | |
-0.7389 -0.9315 -0.7722 m0 | |
Found 7266 test set PSMs with q<0.02. | |
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. | |
Calculating q values. | |
Final list yields 5017 target peptides with q<0.02. | |
Calculating posterior error probabilities (PEPs). | |
Processing took 11.22 cpu seconds or 5 seconds wall clock time. |
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