no PSMs found during identification \ filter phase

assafkacen commented 6 years ago

I keep getting fatal results which I can't find the reason to. attached is my output:

MSFragger version MSFragger-20171106
(c) University of Michigan

Sequence database filtered and tagged in 88ms
Digestion completed in 1303ms
Merged digestion results in 684ms
Sorting digested sequences...
        of length 6: 4394968
        of length 7: 4444979
        of length 8: 4438403
        of length 9: 4426976
        of length 10: 4414855
        of length 11: 4402736
        of length 12: 4390621
        of length 13: 4378510
        of length 14: 4366405
        of length 15: 4354300
        of length 16: 4342201
        of length 17: 4330104
        of length 18: 4318007
        of length 19: 4305912
        of length 20: 4293817
        of length 21: 4281722
        of length 22: 4269627
        of length 23: 4257534
        of length 24: 4245441
        of length 25: 4233359
        of length 26: 4221301
        of length 27: 4209245
        of length 28: 4197194
        of length 29: 4185151
        of length 30: 4173112
        of length 31: 4161079
        of length 32: 4149050
        of length 33: 4137021
        of length 34: 4124996
        of length 35: 4112966
        of length 36: 4100895
        of length 37: 4088203
        of length 38: 4073054
        of length 39: 4054230
        of length 40: 4018156
        DONE
Removing duplicates and compacting...
Reduced to 140014920  peptides in 125735ms
Generating modified peptides...DONE in 15185ms
Generated 225536543 modified peptides
Merging peptide pools from threads... DONE in 636ms
Sorting modified peptides by mass...DONE in 23610ms
Peptide index written in 20938ms
Selected fragment tolerance 0.05 Da and maximum fragment slice size of 41535.15MB
21592034992 fragments to be searched in 4 slices (160.87GB total)
Operating on slice 1 of 4: 336162ms
        QEP2_6816_YMER_1272_1_080218.mzML 30600ms [progress: 19299/19299 (100.00%) - 10152.03 spectra/s] - completed 1957ms
        QEP2_6816_YMER_1295_1_080218.mzML 41912ms [progress: 18836/18836 (100.00%) - 16923.63 spectra/s] - completed 1155ms
Operating on slice 2 of 4: 422698ms
        QEP2_6816_YMER_1272_1_080218.mzML 29361ms [progress: 19299/19299 (100.00%) - 17528.61 spectra/s] - completed 1143ms
        QEP2_6816_YMER_1295_1_080218.mzML 32019ms [progress: 18836/18836 (100.00%) - 20928.89 spectra/s] - completed 936ms
Operating on slice 3 of 4: 195457ms
        QEP2_6816_YMER_1272_1_080218.mzML 33156ms [progress: 19299/19299 (100.00%) - 20662.74 spectra/s] - completed 979ms
        QEP2_6816_YMER_1295_1_080218.mzML 26713ms [progress: 18836/18836 (100.00%) - 26908.57 spectra/s] - completed 737ms
Operating on slice 4 of 4: 213900ms
        QEP2_6816_YMER_1272_1_080218.mzML 31984ms [progress: 19299/19299 (100.00%) - 24123.75 spectra/s] - completed 843ms
        QEP2_6816_YMER_1295_1_080218.mzML 24931ms [progress: 18836/18836 (100.00%) - 26908.57 spectra/s] - completed 738ms
INFO[16:11:51] Creating workspace
INFO[16:11:51] Done
INFO[16:11:51] Executing PeptideProphet
 file 1: D:\reference_data_experiment\parallel-test\MSFragger\group_2\QEP2_6816_YMER_1272_1_080218.pepXML
Failed to open input file 'D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1272_1_080218.mzXML'.
WARNING: cannot open data file D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1272_1_080218.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1272_1_080218.mzML'.
WARNING: CANNOT correct data file D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1272_1_080218.mzML in msms_run_summary tag...
Failed to open input file 'D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1272_1_080218.mzXML'.
WARNING: cannot open data file D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1272_1_080218.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1272_1_080218.mzML'.
WARNING: CANNOT correct data file D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1272_1_080218.mzML in msms_run_summary tag...
 processed altogether 344 results
INFO: Results written to file: D:\reference_data_experiment\parallel-test\MSFragger\group_2\interact-QEP2_6816_YMER_1272_1_080218.pep.xml

  - D:\reference_data_experiment\parallel-test\MSFragger\group_2\interact-QEP2_6816_YMER_1272_1_080218.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
 PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 52 2+, 188 3+, 92 4+, 9 5+, 3 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 149 Decoys, and 195 Non-Decoys
Iterations: .........10.........20.....
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
INFO[16:12:58] Done
INFO[16:12:58] Executing PeptideProphet
 file 1: D:\reference_data_experiment\parallel-test\MSFragger\group_2\QEP2_6816_YMER_1295_1_080218.pepXML
Failed to open input file 'D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1295_1_080218.mzXML'.
WARNING: cannot open data file D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1295_1_080218.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1295_1_080218.mzML'.
WARNING: CANNOT correct data file D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1295_1_080218.mzML in msms_run_summary tag...
Failed to open input file 'D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1295_1_080218.mzXML'.
WARNING: cannot open data file D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1295_1_080218.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1295_1_080218.mzML'.
WARNING: CANNOT correct data file D:\reference_data_experiment\parallel-test\MSFragger\group_2/QEP2_6816_YMER_1295_1_080218.mzML in msms_run_summary tag...
 processed altogether 61 results
INFO: Results written to file: D:\reference_data_experiment\parallel-test\MSFragger\group_2\interact-QEP2_6816_YMER_1295_1_080218.pep.xml

  - D:\reference_data_experiment\parallel-test\MSFragger\group_2\interact-QEP2_6816_YMER_1295_1_080218.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
 PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
 read in 0 1+, 13 2+, 40 3+, 5 4+, 3 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 31 Decoys, and 30 Non-Decoys
Iterations: .........10.........20....
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (3+).
WARNING: Mixture model quality test failed for charge (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 25 iterations
INFO[16:12:59] Done
INFO[16:13:01] Removing workspace
INFO[16:13:01] Done
INFO[16:13:02] Creating workspace
INFO[16:13:02] Done
INFO[16:13:03] Executing ProteinProphet
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64))
 (no FPKM) (using degen pep info)
Reading in D:/reference_data_experiment/parallel-test/MSFragger/group_2/interact-QEP2_6816_YMER_1272_1_080218.pep.xml...
...read in 0 1+, 28 2+, 29 3+, 18 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Reading in D:/reference_data_experiment/parallel-test/MSFragger/group_2/interact-QEP2_6816_YMER_1295_1_080218.pep.xml...
did not find any PeptideProphet results in input data!  Did you forget to run PeptideProphet?
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 63 peptide weights: 0%...20%...60%...90%
Calculating protein lengths and molecular weights from database d:/reference_data_experiment/parallel-test/MSFragger/group_2/group_2_decoy.fasta
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
  Total: 8000
Computing degenerate peptides for 42 proteins: 0%...30%...40%...90%
Computing probabilities for 44 proteins.  Loop 1: 0%...20%...40%  Loop 2: 0%...20%...40%
Computing probabilities for 44 proteins.  Loop 1: 0%...20%...40%  Loop 2: 0%...20%...40%
Computing probabilities for 44 proteins.  Loop 1: 0%...20%...40%  Loop 2: 0%...20%...40%
Computing probabilities for 44 proteins.  Loop 1: 0%...20%...40%  Loop 2: 0%...20%...40%
Computing probabilities for 44 proteins.  Loop 1: 0%...20%...40%  Loop 2: 0%...20%...40%
Computing 40 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
Computing MU for 44 proteins: 0%...20%...40%...90%
INFO: mu=1.89845e-006, db_size=8725387

Finished
INFO[16:13:04] Done
INFO[16:13:05] Removing workspace
INFO[16:13:06] Done
INFO[16:13:07] Creating workspace
INFO[16:13:07] Done
INFO[16:13:07] Processing database
INFO[16:13:10] Done
INFO[16:13:10] Executing filter
INFO[16:13:10] Processing peptide identification files
FATA[16:13:10] no PSMs were found
INFO[16:13:10] Executing report
FATA[16:13:10] cannot restore serialized data structures: invalid argument
INFO[16:13:12] Removing workspace
INFO[16:13:12] Done

why don't I get PSMs? thanks

anesvi commented 6 years ago

You are running MSFragger-Philosopher on a very small dataset (just a thousand of spectra I think) . Perhaps there is not enough for PeptideProphet and ProteinProphet to work with. Please test your pipeline using more ‘normal’ data first. If it is running fine, then you should tell us more about your data so we can understand what you are trying to do.

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

assafkacen commented 6 years ago

Thanks. Do you know about minimum number of spectrums that should cause such a problem? ... so I can check it a head of time...

נשלח מה-iPhone שלי

‫ב-20 במרץ 2018, בשעה 16:49, ‏‏Alexey Nesvizhskii ‏notifications@github.com<mailto:notifications@github.com> כתב/ה:‬

You are running MSFragger-Philosopher on a very small dataset (just a thousand of spectra I think) . Perhaps there is not enough for PeptideProphet and ProteinProphet to work with. Please test your pipeline using more ‘normal’ data first. If it is running fine, then you should tell us more about your data so we can understand what you are trying to do.

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/chhh/MSFragger-GUI/issues/51#issuecomment-374625594, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aj2G2wsA1CoQpTqdDfVQAEOQZXVtmksiks5tgRbhgaJpZM4SyBMB.

anesvi commented 6 years ago

Any modern instrument should generate much more than minimum necessary. What instrument are you using? I would expect at least 5-10,000 PSMs in a single MS run

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assafkacen commented 6 years ago

I am using a QE , I think I have problems with my samples which produce low number of spectrum - I will check it in the raw files. I just didn’t know there a lower bound to the spectra numbers which cause the peptide prophet to fail

נשלח מה-iPhone שלי

‫ב-20 במרץ 2018, בשעה 20:03, ‏‏Alexey Nesvizhskii ‏notifications@github.com<mailto:notifications@github.com> כתב/ה:‬

Any modern instrument should generate much more than minimum necessary. What instrument are you using? I would expect at least 5-10,000 PSMs in a single MS run

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— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/chhh/MSFragger-GUI/issues/51#issuecomment-374698570, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aj2G200HiEo_NysGS-FcxSiBze0f_4BTks5tgURFgaJpZM4SyBMB.

assafkacen commented 6 years ago

I changed to a raw data with more than 10000 spectra. now it create a PSM file with only headers, the ions and peptide files looks OK. I am attaching the log

INFO[22:09:32] Executing Workspace 20180317
INFO[22:09:34] Creating workspace
INFO[22:09:34] Done
INFO[22:09:34] Executing PeptideProphet 20180317
 file 1: /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.pepXML
Failed to open input file '/home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.mzXML'.
WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.mzXML in msms_run_summary tag... trying .mzML ...
SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.mzML in msms_run_summary tag...
 processed altogether 10856 results
INFO: Results written to file: /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_191_1_170516.pep.xml

  - /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_191_1_170516.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
 PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB
 read in 0 1+, 2042 2+, 5137 3+, 2763 4+, 637 5+, 193 6+, and 37 7+ spectra.
Initialising statistical models ...
Found 4864 Decoys, and 5945 Non-Decoys
Iterations: .........10.........20.......
WARNING: Mixture model quality test failed for charge (1+).
model complete after 28 iterations
INFO[22:09:51] Done
INFO[22:09:51] Executing PeptideProphet 20180317
 file 1: /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.pepXML
Failed to open input file '/home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.mzXML'.
WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.mzXML in msms_run_summary tag... trying .mzML ...
SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.mzML in msms_run_summary tag...
 processed altogether 9895 results
INFO: Results written to file: /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_190_1_170516.pep.xml

  - /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_190_1_170516.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
 PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB
 read in 0 1+, 1728 2+, 4652 3+, 2548 4+, 680 5+, 197 6+, and 45 7+ spectra.
Initialising statistical models ...
Found 4523 Decoys, and 5327 Non-Decoys
Iterations: .........10.........20.......
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 28 iterations
INFO[22:10:08] Done
INFO[22:10:08] Executing Workspace 20180317
INFO[22:10:09] Removing workspace
INFO[22:10:09] Done
INFO[22:10:10] Executing Workspace 20180317
INFO[22:10:11] Creating workspace
INFO[22:10:11] Done
INFO[22:10:11] Executing ProteinProphet 20180317
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705221614-exported (Linux-x86_64))
 (no FPKM) (using degen pep info)
Reading in /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_191_1_170516.pep.xml...
...read in 0 1+, 688 2+, 620 3+, 197 4+, 47 5+, 22 6+, 4 7+ spectra with min prob 0.05

Reading in /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_190_1_170516.pep.xml...
...read in 0 1+, 567 2+, 469 3+, 180 4+, 50 5+, 19 6+, 0 7+ spectra with min prob 0.05

Initializing 1979 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/group_9_decoy.fasta
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
  Total: 8000
Computing degenerate peptides for 1024 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 1123 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1123 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1123 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing 900 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
Computing MU for 1123 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO: mu=0.000157192, db_size=4346325

Finished
INFO[22:10:12] Done
INFO[22:10:12] Executing Workspace 20180317
INFO[22:10:14] Removing workspace
INFO[22:10:14] Done
INFO[22:10:14] Executing Workspace 20180317
INFO[22:10:15] Creating workspace
INFO[22:10:15] Done
INFO[22:10:15] Executing Database 20180317
INFO[22:10:15] Processing database
INFO[22:10:18] Done
INFO[22:10:18] Executing Filter 20180317
INFO[22:10:18] Processing peptide identification files
INFO[22:10:18] 1+ Charge profile                             decoy=0 target=0
INFO[22:10:18] 2+ Charge profile                             decoy=280 target=981
INFO[22:10:18] 3+ Charge profile                             decoy=251 target=843
INFO[22:10:18] 4+ Charge profile                             decoy=36 target=343
INFO[22:10:18] 5+ Charge profile                             decoy=7 target=91
INFO[22:10:18] 6+ Charge profile                             decoy=2 target=39
INFO[22:10:18] Database search results                       ions=1979 peptides=1724 psms=2877
INFO[22:10:18] Converged to 0.98 % FDR with 1118 PSMs        decoy=11 threshold=0.959 total=1129
INFO[22:10:18] Converged to 0.99 % FDR with 503 Peptides     decoy=5 threshold=0.9704 total=508
INFO[22:10:18] Converged to 0.92 % FDR with 648 Ions         decoy=6 threshold=0.9703 total=654
INFO[22:10:18] Post processing identifications
INFO[22:10:18] Processing Protein Inference
INFO[22:10:18] Correcting PSM to Protein mappings
INFO[22:10:18] Mapping Ion status to PSMs
INFO[22:10:18] Updating razor PSM assingment to Proteins
INFO[22:10:18] Calculating Spectral Counts
INFO[22:10:19] Done
INFO[22:10:19] Executing Report 20180317
INFO[22:10:19] Creating PSM report
INFO[22:10:19] Creating peptide report
INFO[22:10:19] Creating peptide Ion report
INFO[22:10:19] Done
INFO[22:10:20] Executing Workspace 20180317
INFO[22:10:21] Removing workspace
INFO[22:10:22] Done

anesvi commented 6 years ago

Certainly looks better, except I noticed a few unusual things:

1) Why are you not using ntt and nmc models? Did you turn them off (in PeptideProphet command)?

Not using ntt model Not using nmc model 2) What was your philosopher report command? I do not see 1% protein level filter applied. Did you have --protxml interact.prot.xml In your filter command specified? Or did you remove it on purpose because you do not want to apply any protein level FDR filter?

Best Alexey

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assafkacen commented 6 years ago

Hi Alexey,

I do not use ntt and nmc models because my peptide are natural peptide (no enzyme cutting), therefore I thought those models will no fit my data. I would love to hear your opinion on the matter.
My filter command is: philosopher filter --razor --sequential –pepxml my_working_folder
My report command is just philosopher report
I do get an output file: interact.prot.xml among other…

Does it make sense to you? Thanks Assaf

From: Alexey Nesvizhskii [mailto:notifications@github.com] Sent: Wednesday, March 21, 2018 10:34 PM To: chhh/MSFragger-GUI MSFragger-GUI@noreply.github.com Cc: Assaf Kacen assaf.kacen@weizmann.ac.il; Author author@noreply.github.com Subject: Re: [chhh/MSFragger-GUI] no PSMs found during identification \ filter phase (#51)

Certainly looks better, except I noticed a few unusual things:

1) Why are you not using ntt and nmc models? Did you turn them off (in PeptideProphet command)?

Not using ntt model Not using nmc model 2) What was your philosopher report command? I do not see 1% protein level filter applied. Did you have --protxml interact.prot.xml In your filter command specified? Or did you remove it on purpose because you do not want to apply any protein level FDR filter?

Best Alexey

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— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/chhh/MSFragger-GUI/issues/51#issuecomment-375086199, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Aj2G21e3QlPbF9toEdl-I-Y9UUUbo8oyks5tgrkxgaJpZM4SyBMB.

anesvi commented 6 years ago

Ok, what you described makes sense for natural peptides. No enzyme and no protein filter is needed. What did you specify in fragger.params file for the enzyme?

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assafkacen commented 6 years ago

Msfragger.params I put num_enzyme_termini = 0

I am attaching the output log again with my commands embedded in it. Hope it will help you make sense out of it and find my problem:

command :/home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --init
INFO[23:11:07] Executing Workspace 20180317
INFO[23:11:08] Creating workspace
INFO[23:11:08] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 peptideprophet --decoy rev --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/group_9_decoy.fasta /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.pepXML
INFO[23:11:08] Executing PeptideProphet 20180317
file 1: /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.pepXML
Failed to open input file '/home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.mzXML'.
WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.mzXML in msms_run_summary tag... trying .mzML ...
SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_191_1_170516.mzML in msms_run_summary tag...
processed altogether 10856 results
INFO: Results written to file: /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_191_1_170516.pep.xml

  - /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_191_1_170516.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB
read in 0 1+, 2042 2+, 5137 3+, 2763 4+, 637 5+, 193 6+, and 37 7+ spectra.
Initialising statistical models ...
Found 4864 Decoys, and 5945 Non-Decoys
Iterations: .........10.........20.......
WARNING: Mixture model quality test failed for charge (1+).
model complete after 28 iterations
INFO[23:11:25] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 peptideprophet --decoy rev --decoyprobs --ppm --accmass --nonparam --expectscore --nonmc --nontt --database /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/group_9_decoy.fasta /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.pepXML
INFO[23:11:25] Executing PeptideProphet 20180317
file 1: /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.pepXML
Failed to open input file '/home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.mzXML'.
WARNING: cannot open data file /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.mzXML in msms_run_summary tag... trying .mzML ...
SUCCESS: CORRECTED data file /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/QEP2_YMER_190_1_170516.mzML in msms_run_summary tag...
processed altogether 9895 results
INFO: Results written to file: /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_190_1_170516.pep.xml

  - /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_190_1_170516.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)

adding ACCMASS mixture distribution
init with X! Tandem trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB
read in 0 1+, 1728 2+, 4652 3+, 2548 4+, 680 5+, 197 6+, and 45 7+ spectra.
Initialising statistical models ...
Found 4523 Decoys, and 5327 Non-Decoys
Iterations: .........10.........20.......
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 28 iterations
INFO[23:11:42] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --clean
INFO[23:11:43] Executing Workspace 20180317
INFO[23:11:44] Removing workspace
INFO[23:11:44] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --init
INFO[23:11:44] Executing Workspace 20180317
INFO[23:11:45] Creating workspace
INFO[23:11:46] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 proteinprophet --output interact /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_191_1_170516.pep.xml /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_190_1_170516.pep.xml
INFO[23:11:46] Executing ProteinProphet 20180317
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705221614-exported (Linux-x86_64))
(no FPKM) (using degen pep info)
Reading in /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_191_1_170516.pep.xml...
...read in 0 1+, 688 2+, 620 3+, 197 4+, 47 5+, 22 6+, 4 7+ spectra with min prob 0.05

Reading in /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/interact-QEP2_YMER_190_1_170516.pep.xml...
...read in 0 1+, 567 2+, 469 3+, 180 4+, 50 5+, 19 6+, 0 7+ spectra with min prob 0.05

Initializing 1979 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/group_9_decoy.fasta
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
  Total: 8000
Computing degenerate peptides for 1024 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 1123 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1123 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1123 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing 900 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
Computing MU for 1123 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO: mu=0.000157192, db_size=4346325

Finished
INFO[23:11:47] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --clean
INFO[23:11:47] Executing Workspace 20180317
INFO[23:11:48] Removing workspace
INFO[23:11:49] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --init
INFO[23:11:49] Executing Workspace 20180317
INFO[23:11:50] Creating workspace
INFO[23:11:50] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 database --annotate /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9/group_9_decoy.fasta
INFO[23:11:50] Executing Database 20180317
INFO[23:11:50] Processing database
INFO[23:11:53] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 filter --razor --sequential --pepxml /home/labs/yifatlab/assafk/modification/parallel-test/MSFragger/group_9
INFO[23:11:53] Executing Filter 20180317
INFO[23:11:53] Processing peptide identification files
INFO[23:11:53] 1+ Charge profile                             decoy=0 target=0
INFO[23:11:53] 2+ Charge profile                             decoy=280 target=981
INFO[23:11:53] 3+ Charge profile                             decoy=251 target=843
INFO[23:11:53] 4+ Charge profile                             decoy=36 target=343
INFO[23:11:53] 5+ Charge profile                             decoy=7 target=91
INFO[23:11:53] 6+ Charge profile                             decoy=2 target=39
INFO[23:11:53] Database search results                       ions=1979 peptides=1724 psms=2877
INFO[23:11:53] Converged to 0.98 % FDR with 1118 PSMs        decoy=11 threshold=0.959 total=1129
INFO[23:11:53] Converged to 0.99 % FDR with 503 Peptides     decoy=5 threshold=0.9704 total=508
INFO[23:11:53] Converged to 0.92 % FDR with 648 Ions         decoy=6 threshold=0.9703 total=654
INFO[23:11:53] Post processing identifications
INFO[23:11:53] Processing Protein Inference
INFO[23:11:53] Correcting PSM to Protein mappings
INFO[23:11:53] Mapping Ion status to PSMs
INFO[23:11:53] Updating razor PSM assingment to Proteins
INFO[23:11:53] Calculating Spectral Counts
INFO[23:11:54] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 report
INFO[23:11:54] Executing Report 20180317
INFO[23:11:54] Creating PSM report
INFO[23:11:54] Creating peptide report
INFO[23:11:54] Creating peptide Ion report
INFO[23:11:54] Done
command : /home/labs/yifatlab/assafk/tools/MSFragger_20170103/philosopher_linux_amd64 workspace --clean
INFO[23:11:56] Executing Workspace 20180317
INFO[23:11:57] Removing workspace
INFO[23:11:58] Done

chhh commented 6 years ago

@assafkacen Also looks like you're using old versions of GUI and MSFragger (possibly Philosopher as well). Could you please download the latest version of GUI from here: https://github.com/chhh/MSFragger-GUI/releases/latest

This version will notify you about updates to MSFragger, which you will be able to upgrade, and Philosopher. Just in case, Philosopher download page is https://github.com/prvst/philosopher/releases/latest.

The new version of GUI will print information about the environment at the start of each log (like OS, java version, MSFragger and Philospher versions), please post the full log, including that part of it as well.

Please re-run with the new GUI, MSFragger and Philosopher and post the output + the fragger.params file from the output directory. Please reply through the github website instead of replying by email to make sure the files get attached, here's the direct link to this issue thread: https://github.com/chhh/MSFragger-GUI/issues/51.

chhh commented 6 years ago

Closing due to no response in a month

Nesvilab / FragPipe

no PSMs found during identification \ filter phase #51