A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
Home Page: http://fragpipe.nesvilab.org
License: Other
Hello,
I've tried to run MSFragger with a 4 protein FASTA file (Uniprot Format, with decoys appended) against spectra from a sample consisting of the 4 proteins in the FASTA file. While theoretical peptides do appear to be produced, msfragger does not generate any slices of the pepindex through which to search spectra against fragments/precursors.
Here's the output:
Removing duplicates and compacting...
Reduced to 669 peptides in 190ms
Generating modified peptides...DONE in 22ms
Generated 931 modified peptides
Merging peptide pools from threads... DONE in 3ms
Sorting modified peptides by mass...DONE in 2ms
Peptide index written in 215ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 10831.99MB
73968 fragments to be searched in 0 slices (0.00GB total)
This also needs to be hosted somewhere and the link should be included in the Fragger manual.
This is the same as #14
Hi Dmitry
I am using MSfragger to look for previously unrecognised peptide modifications in my samples.
For this, the interactive delta-mass distribution plot has proven to be very useful. So thank you for that!
However, I could use some help in interpreting the psm.tsv file MSfragger is giving me:
Many thanks for answering my questions
Maik
Hello,
I am trying to use this protein database in MSFragger: ProteomeDatabase.txt. Here is the output from running MSFragger:
Will execute 12 commands:
java -jar -Xmx14G D:\AlexStuff\MSFragger\MSFraggerApp\MSFragger.jar D:\AlexStuff\MSFragger\TestData\fragger.params D:\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.mzXML
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database D:\AlexStuff\MSFragger\TestData\ProteomeDatabase.txt D:\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate D:\AlexStuff\MSFragger\TestData\ProteomeDatabase.txt
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml D:\AlexStuff\MSFragger\TestData --protxml D:\AlexStuff\MSFragger\TestData\interact.prot.xml
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
~~~~~~~~~~~~~~~~~~~~~~
Executing command:
$> java -jar -Xmx14G D:\AlexStuff\MSFragger\MSFraggerApp\MSFragger.jar D:\AlexStuff\MSFragger\TestData\fragger.params D:\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.mzXML
Process started
Sequence database filtered and tagged in 16ms
Digestion completed in 156ms
Merged digestion results in 63ms
Sorting digested sequences...
of length 7: 82785
of length 8: 79879
of length 9: 76694
of length 10: 72803
of length 11: 69520
of length 12: 66345
of length 13: 62466
of length 14: 58788
of length 15: 55719
of length 16: 52347
of length 17: 49455
of length 18: 46152
of length 19: 42980
of length 20: 40571
of length 21: 37623
of length 22: 35227
of length 23: 32702
of length 24: 30325
of length 25: 28228
of length 26: 26685
of length 27: 24462
of length 28: 22891
of length 29: 21091
of length 30: 19170
of length 31: 18030
of length 32: 16572
of length 33: 15429
of length 34: 14309
of length 35: 13437
of length 36: 12410
of length 37: 11298
of length 38: 10680
of length 39: 9656
of length 40: 8620
of length 41: 6718
of length 42: 4864
of length 43: 2860
of length 44: 1311
of length 45: 453
of length 46: 127
of length 47: 24
of length 48: 6
DONE
Removing duplicates and compacting...
Reduced to 1281677 peptides in 702ms
Generating modified peptides...
DONE in 624ms
Generated 3466429 modified peptides
Merging peptide pools from threads... DONE in 78ms
Sorting modified peptides by mass...
DONE in 343ms
Peptide index written in 265ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 9343.86MB
295713248 fragments to be searched in 1 slices (2.20GB total)
Operating on slice 1 of 1:
8351ms
b1906_293T_proteinID_01A_QE3_122212.mzXML
62746ms
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 1883/41820 (4.50%) - 369.07 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 3874/41820 (9.26%) - 395.20 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 5789/41820 (13.84%) - 376.52 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 7748/41820 (18.53%) - 388.77 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 9754/41820 (23.32%) - 394.49 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 11659/41820 (27.88%) - 380.39 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 13315/41820 (31.84%) - 324.64 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 15184/41820 (36.31%) - 367.48 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 16990/41820 (40.63%) - 355.16 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 18759/41820 (44.86%) - 346.73 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 20546/41820 (49.13%) - 350.32 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 22293/41820 (53.31%) - 344.58 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 24038/41820 (57.48%) - 347.40 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 25776/41820 (61.64%) - 340.72 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 27455/41820 (65.65%) - 332.08 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 29135/41820 (69.67%) - 329.35 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 30820/41820 (73.70%) - 334.39 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 32516/41820 (77.75%) - 336.64 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 34185/41820 (81.74%) - 333.27 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 35876/41820 (85.79%) - 333.53 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 37658/41820 (90.05%) - 347.98 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 39408/41820 (94.23%) - 347.29 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 41181/41820 (98.47%) - 350.81 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 62746ms [progress: 41820/41820 (100.00%) - 153.98 spectra/s]
- completed 120968ms
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[15:16:13] Creating workspace
INFO[15:16:13] Done
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database D:\AlexStuff\MSFragger\TestData\ProteomeDatabase.txt D:\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
Process started
file 1: D:\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
processed altogether 23682 results
INFO: Results written to file: D:\AlexStuff\MSFragger\TestData\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
- D:\AlexStuff\MSFragger\TestData\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
init with X! Tandem trypsin
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 10553 2+, 10301 3+, 2524 4+, 245 5+, 56 6+, and 2 7+ spectra.
Found 11808 Decoys, and 11873 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
INFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .
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10
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20
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WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (2+).
.
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 26 iterations
INFO[15:17:01] Done
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[15:17:01] Removing workspace
WARN[15:17:01] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[15:17:01] Done
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[15:17:02] Creating workspace
WARN[15:17:02] existing workspace detected, will not overwrite
INFO[15:17:02] Done
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
Process started
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:/AlexStuff/MSFragger/TestData/interact-b1906_293T_proteinID_01A_QE3_122212.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
WARNING: no data - output file will be empty
INFO[15:17:02] Done
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[15:17:03] Removing workspace
WARN[15:17:03] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[15:17:03] Done
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[15:17:03] Creating workspace
WARN[15:17:03] existing workspace detected, will not overwrite
INFO[15:17:03] Done
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate D:\AlexStuff\MSFragger\TestData\ProteomeDatabase.txt
Process started
INFO[15:17:03] Processing database
FATA[15:17:03] Cannot identify the database type
Process finished, exit value: 1
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml D:\AlexStuff\MSFragger\TestData --protxml D:\AlexStuff\MSFragger\TestData\interact.prot.xml
Process started
INFO[15:17:03] Processing peptide identification files
FATA[15:17:03] no PSMs were found
Process finished, exit value: 1
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
Process started
INFO[15:17:04] Creating PSM report
INFO[15:17:04] Creating peptide Ion report
INFO[15:17:04] Creating peptide report
INFO[15:17:04] Done
Process finished, exit value: 0
Executing command:
$> D:\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[15:17:04] Removing workspace
WARN[15:17:04] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[15:17:04] Done
Process finished, exit value: 0
=========================
===
=== Done
===
=========================
I was able to successfully run MSFragger using a different database. I believe the only difference between the two databases were in the labeling of the amino acid sequences. Here is an example sequence from the database that worked on MSFragger:
>sp|A0A075B6H9|LV469_HUMAN Immunoglobulin lambda variable 4-69 OS=Homo sapiens GN=IGLV4-69 PE=1 SV=1
IGTGWTQCYYDAEDESQLSSITLYREAGSSSGSFRDPIGDGKSHSGDSNLKMLYRPGKEPQQQHWAIAYSSHGSSLTCTLKVSAGLSASASPSQTLVLQSLSGTCHLLLTLFLLPTWAM
Here is an example sequence from the database that is not working on MSFragger:
>Sequence0
VMITCCCRVEYQVDTAQLWIAWKQITMNVWGLSFRREWHAVVTLTTELGVWPCHYTWMHDFTWKNFYDRQGFWINNTFLKPQDLADYLMWNLMTRYRSQGKFEINGYAHNLCLIYSRHPANDSFIQNPKSQEKMCVESQWKSFTKTTKEFLDNCCIVDRGFDYWFIPVHCGWTGMMVMCVLCSFEWDPPIWQSTVKNPSYATQDIMPDHCISDGCRPTFDPQQPTESLARQDHVRIIIHRGIEKCCPADINFDAEVFSKGWCGYIYEWIPFPVDQYIQMTNHQCIWFEQWLNVEVGDFYHGVINIIWPPCPTVVRTWSGFLWYPMPESRGSNWIIQFTGWCMEAVEGWPC
If the issue with the latter database lies in the labeling of the sequences, I don't understand why that would cause an issue in MSFragger. Aren't both databases in fasta format?
Any comments and suggestions for how to fix the problem would be greatly appreciated!
Thanks,
-Alex
Hi,
I want to flag two minor suggestions for the MSFragger_GUI.
I noticed that when one clicks on to load "Defaults Open Search" in MSFragger tab of the GUI, then it loads the default parameters only in the MSFragger tab and Prophet tabs whereas when one clicks "Load Defaults Open Search" in the home tab, then it loads the parameters in all tabs including prophets and report tab. I think this difference in the behavior when clicked in the home tab versus the msfragger tab or other tabs could be made uniform.
Initially, I assumed that it makes no difference between loading default parameters for open or closed search from any tab but this not the case.
I realized that if one changes the decoy tag from "rev" to something else (e.g. XXX) in the peptideProphet then it should also be correspondingly changed in the report tag with the option "--tag XXX_". This tag option does not appear by default in the Filter option of the report tab. Not setting this correctly or modifying only in the peptideProphet tab will result in 0 decoys in the output from the "philosopher filter" step and thus in the final output files.
Please excuse me if the above suggestions are already known or flagged.
I would be happy to answer further questions if anything unclear.
Best Regards
Adithi
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
Dear MSFragger-Development Team,
I recently started working with your software and stumbled across a problem which i don't know how to solve:
Whenever i try to run PeptideProphet, the command "mv" will not be recognized. I seems like that it want to execute the linux command "mv", however i am working on windows. Tested with the latest versions of Philosopher for philosopher_windows_64_amd and 386. It could also be that i missed something obvious for which i apologize in advance, tho i didnt find anything else related in the issues.
As you probably already have seen i also strongly endorse that you make a tutorial with sample data to test the installation as in Issue #14 for bloody beginners like me.
The output of MSFraggerGUI is at the bottom.
Thanks for your efforts,
tom
Will execute 12 commands:
java -jar -Xmx8G D:\ProjectMQMSFRAG\MSFragger-20171106\MSFragger-20171106.jar D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\fragger.params D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\b1906_293T_proteinID_01A_QE3_122212.mzXML
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel 2 --database D:\ProjectMQMSFRAG\Philosopher\2018-01-22-td-UP000005640.fas D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\b1906_293T_proteinID_01A_QE3_122212.pepXML
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe proteinprophet --output interact --maxppmdiff 20 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe database --annotate D:\ProjectMQMSFRAG\Philosopher\2018-01-22-td-UP000005640.fas
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe filter --sequential --mapmods --pepxml D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test --protxml D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact.prot.xml
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe report
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
~~~~~~~~~~~~~~~~~~~~~~
Dry Run selected, not running the commands.
Will execute 12 commands:
java -jar -Xmx8G D:\ProjectMQMSFRAG\MSFragger-20171106\MSFragger-20171106.jar D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\fragger.params D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\b1906_293T_proteinID_01A_QE3_122212.mzXML
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel 2 --database D:\ProjectMQMSFRAG\Philosopher\2018-01-22-td-UP000005640.fas D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\b1906_293T_proteinID_01A_QE3_122212.pepXML
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe proteinprophet --output interact --maxppmdiff 20 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe database --annotate D:\ProjectMQMSFRAG\Philosopher\2018-01-22-td-UP000005640.fas
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe filter --sequential --mapmods --pepxml D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test --protxml D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact.prot.xml
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe report
D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
~~~~~~~~~~~~~~~~~~~~~~
Executing command:
$> java -jar -Xmx8G D:\ProjectMQMSFRAG\MSFragger-20171106\MSFragger-20171106.jar D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\fragger.params D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\b1906_293T_proteinID_01A_QE3_122212.mzXML
Process started
MSFragger version MSFragger-20171106
(c) University of Michigan
Peptide index read in 328ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 4959.14MB
386688044 fragments to be searched in 1 slices (2.88GB total)
Operating on slice 1 of 1:
10361ms
b1906_293T_proteinID_01A_QE3_122212.mzXML
5054ms
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 547/41820 (1.31%) - 106.59 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 1084/41820 (2.59%) - 104.62 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 1596/41820 (3.82%) - 101.93 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 2117/41820 (5.06%) - 101.52 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 2638/41820 (6.31%) - 101.50 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 3137/41820 (7.50%) - 99.03 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 3664/41820 (8.76%) - 104.27 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 4186/41820 (10.01%) - 102.31 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 4710/41820 (11.26%) - 103.05 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 5233/41820 (12.51%) - 102.21 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 5754/41820 (13.76%) - 103.07 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 6266/41820 (14.98%) - 100.06 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 6786/41820 (16.23%) - 103.83 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 7299/41820 (17.45%) - 99.96 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 7811/41820 (18.68%) - 102.24 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 8303/41820 (19.85%) - 97.35 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 8809/41820 (21.06%) - 100.10 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 9335/41820 (22.32%) - 102.49 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 9867/41820 (23.59%) - 105.24 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 10410/41820 (24.89%) - 106.76 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 10913/41820 (26.10%) - 99.21 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 11399/41820 (27.26%) - 94.98 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 11877/41820 (28.40%) - 93.41 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 12360/41820 (29.56%) - 95.85 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 12843/41820 (30.71%) - 95.57 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 13333/41820 (31.88%) - 97.24 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 13819/41820 (33.04%) - 97.04 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 14288/41820 (34.17%) - 93.63 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 14786/41820 (35.36%) - 97.92 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 15266/41820 (36.50%) - 94.38 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 15745/41820 (37.65%) - 95.06 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 16205/41820 (38.75%) - 91.85 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 16663/41820 (39.84%) - 91.18 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 17130/41820 (40.96%) - 91.55 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 17593/41820 (42.07%) - 91.88 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 18066/41820 (43.20%) - 92.44 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 18541/41820 (44.34%) - 93.97 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 19017/41820 (45.47%) - 94.46 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 19485/41820 (46.59%) - 91.73 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 19948/41820 (47.70%) - 92.47 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 20409/41820 (48.80%) - 90.64 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 20870/41820 (49.90%) - 91.78 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 21347/41820 (51.04%) - 94.36 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 21827/41820 (52.19%) - 95.26 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 22314/41820 (53.36%) - 95.47 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 22819/41820 (54.56%) - 99.29 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 23294/41820 (55.70%) - 94.57 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 23768/41820 (56.83%) - 92.90 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 24242/41820 (57.97%) - 92.36 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 24719/41820 (59.11%) - 94.96 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 25205/41820 (60.27%) - 95.03 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 25657/41820 (61.35%) - 88.30 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 26131/41820 (62.48%) - 93.07 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 26601/41820 (63.61%) - 91.67 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 27067/41820 (64.72%) - 91.39 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 27546/41820 (65.87%) - 93.65 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 28018/41820 (67.00%) - 92.28 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 28504/41820 (68.16%) - 96.16 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 28971/41820 (69.28%) - 91.55 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 29457/41820 (70.44%) - 95.28 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 29932/41820 (71.57%) - 93.69 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 30409/41820 (72.71%) - 94.66 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 30882/41820 (73.85%) - 94.17 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 31360/41820 (74.99%) - 95.14 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 31832/41820 (76.12%) - 93.10 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 32322/41820 (77.29%) - 96.34 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 32782/41820 (78.39%) - 91.00 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 33262/41820 (79.54%) - 94.10 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 33752/41820 (80.71%) - 97.55 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 34244/41820 (81.88%) - 96.74 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 34726/41820 (83.04%) - 94.77 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 35205/41820 (84.18%) - 94.20 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 35668/41820 (85.29%) - 92.45 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 36137/41820 (86.41%) - 92.80 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 36613/41820 (87.55%) - 95.05 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 37108/41820 (88.73%) - 98.55 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 37607/41820 (89.93%) - 97.52 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 38109/41820 (91.13%) - 99.92 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 38612/41820 (92.33%) - 99.82 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 39122/41820 (93.55%) - 99.98 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 39634/41820 (94.77%) - 100.37 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 40144/41820 (95.99%) - 100.28 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 40655/41820 (97.21%) - 101.41 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 41166/41820 (98.44%) - 100.79 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 41702/41820 (99.72%) - 107.03 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 41818/41820 (100.00%) - 23.09 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 5054ms [progress: 41820/41820 (100.00%) - 9.17 spectra/s]
- completed 436525ms
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
Process started
WARN[13:54:48] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases
INFO[13:54:48] Creating workspace
INFO[13:54:48] Done
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel 2 --database D:\ProjectMQMSFRAG\Philosopher\2018-01-22-td-UP000005640.fas D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\b1906_293T_proteinID_01A_QE3_122212.pepXML
Process started
INFO[13:54:48] Executing PeptideProphet
file 1: D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\b1906_293T_proteinID_01A_QE3_122212.pepXML
processed altogether 39966 results
INFO: Results written to file: D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
- D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
'mv' is not recognized as an internal or external command,
operable program or batch file.
command "mv -f "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a05492" "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml"" failed: Operation not permitted
failed to update D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml from temp file D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a05492, error 2 "No such file or directory"
'mv' is not recognized as an internal or external command,
operable program or batch file.
'mv' is not recognized as an internal or external command,
operable program or batch file.
error: no RefreshParser data written to file D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
command "mv -f "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a05492" "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml"" failed: Operation not permitted
failed to update D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml from temp file D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a05492, error 2 "No such file or directory"
command "mv -f "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a05492" "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml"" failed: Operation not permitted
failed to update D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml from temp file D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a05492, error 2 "No such file or directory"Using Decoy Label "rev".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
init with X! Tandem trypsin
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 22441 2+, 13533 3+, 3484 4+, 394 5+, 103 6+, and 4 7+ spectra.
Found 5599 Decoys, and 34360 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
'mv' is not recognized as an internal or external command,
operable program or batch file.
'mv' is not recognized as an internal or external command,
operable program or batch file.
'mv' is not recognized as an internal or external command,
operable program or batch file.
error: no peptideprophet data written to file D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
command "mv -f "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a01332" "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml"" failed: Operation not permitted
failed to update D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml from temp file D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a01332, error 2 "No such file or directory"
command "mv -f "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a01332" "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml"" failed: Operation not permitted
failed to update D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml from temp file D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a01332, error 2 "No such file or directory"
command "mv -f "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a01332" "D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml"" failed: Operation not permitted
failed to update D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml from temp file D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml.tmp.a01332, error 2 "No such file or directory"
INFO[13:55:26] Done
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
Process started
WARN[13:55:27] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases
INFO[13:55:27] Removing workspace
INFO[13:55:27] Done
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
Process started
WARN[13:55:28] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases
INFO[13:55:28] Creating workspace
INFO[13:55:28] Done
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe proteinprophet --output interact --maxppmdiff 20 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
Process started
INFO[13:55:28] 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:/ProjectMQMSFRAG/Data/OutputData_MSFRAG/HEK293_Test/interact-b1906_293T_proteinID_01A_QE3_122212.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
WARNING: no data - output file will be empty
INFO[13:55:31] Done
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
Process started
WARN[13:55:32] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases
INFO[13:55:32] Removing workspace
INFO[13:55:32] Done
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --init
Process started
WARN[13:55:33] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases
INFO[13:55:33] Creating workspace
INFO[13:55:33] Done
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe database --annotate D:\ProjectMQMSFRAG\Philosopher\2018-01-22-td-UP000005640.fas
Process started
INFO[13:55:34] Processing database
INFO[13:56:11] Done
Process finished, exit value: 0
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe filter --sequential --mapmods --pepxml D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test --protxml D:\ProjectMQMSFRAG\Data\OutputData_MSFRAG\HEK293_Test\interact.prot.xml
Process started
INFO[13:56:11] Executing filter
INFO[13:56:11] Processing peptide identification files
INFO[13:56:13] 1+ Charge profile decoy=0 target=0
INFO[13:56:13] 2+ Charge profile decoy=3038 target=19403
INFO[13:56:13] 3+ Charge profile decoy=1877 target=11656
INFO[13:56:13] 4+ Charge profile decoy=562 target=2922
INFO[13:56:13] 5+ Charge profile decoy=80 target=314
INFO[13:56:13] 6+ Charge profile decoy=40 target=63
INFO[13:56:13] Database search results ions=26985 peptides=22674 psms=39966
INFO[13:56:13] Converged to 0.00 % FDR with 0 PSMs decoy=0 threshold=10 total=0
INFO[13:56:13] Converged to 0.00 % FDR with 0 Peptides decoy=0 threshold=10 total=0
INFO[13:56:14] Converged to 0.00 % FDR with 0 Ions decoy=0 threshold=10 total=0
FATA[13:56:14] No Protein groups detected, check your file and try again
Process finished, exit value: 1
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe report
Process started
INFO[13:56:14] Executing report
FATA[13:56:14] cannot restore serialized data structures: invalid argument
Process finished, exit value: 1
Executing command:
$> D:\ProjectMQMSFRAG\Philosopher\philosopher_windows_386.exe workspace --clean
Process started
WARN[13:56:15] There is a new version of Philosopher available for download: https://github.com/prvst/philosopher/releases
INFO[13:56:15] Removing workspace
INFO[13:56:15] Done
Process finished, exit value: 0
=========================
===
=== Done
===
=========================
Hi there,
I have been working on using the non-GUI version of msFragger on a phospho-enriched sample. The search completes and I end up getting a pepXML output, however when I attempt to open the file via TPP or other parsing tools I end up getting a parsing error. For TPP, I receive the following error:
unable to read pepxml file: error parsing pepxml file: XML parsing error: not well-formed (invalid token), at xml file line 20, column 333.
Would you happen to know what could be causing the error?
Best,
Ian
1 2 3 test
Hi Dmitry,
I have downloaded the new version (v4.3) for windows. Unfortunately it doesn't start after running the .exe file or the jar file. I didn't have this problem with v4.2. Any help is greatly appreciated.
Thanks
Selecting a value from dropdown should fill in the appropriate fields.
There should be at least Trypsin and Non-specific digest.
Many people seem to set output type to tsv instead of pepxml while still using peptideprophet, so it all breaks. Check the value of that setting before a run and fix the value upon user confirmation.
Hi,
We are currently trying to run a file and it is failing and displaying the following errors:
Executing command:
$> C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\philosopher-source_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\rSP_Hu_Mix1_090716.fasta C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output\ID22689_04_E749_4234_031116.pepXML
Process started
Failed to open input file 'C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output/ID22689_04_E749_4234_031116.mzXML'.
WARNING: cannot open data file C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output/ID22689_04_E749_4234_031116.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output/ID22689_04_E749_4234_031116.mzML'.
WARNING: CANNOT correct data file C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output/ID22689_04_E749_4234_031116.mzML in msms_run_summary tag...
Failed to open input file 'C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output/ID22689_04_E749_4234_031116.mzXML'.
WARNING: cannot open data file C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output/ID22689_04_E749_4234_031116.mzXML in msms_run_summary tag... trying .mzML ...
Failed to open input file 'C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output/ID22689_04_E749_4234_031116.mzML'.
WARNING: CANNOT correct data file C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\output/ID22689_04_E749_4234_031116.mzML in msms_run_summary tag...
Is there something wrong with the input we are giving MSFragger?
Thanks,
Austin
Hi,
I wanted to search some .mgf files using your software. Running MSfragger alone (i.e. without Peptide/ProteinProphet and Philosopher) using MSfraggerGUI, it fails with the following errors:
Will execute 1 commands:
java -jar D:\Data\Lasse\NitroLaminin\Lam_ONOOH_DDA_3\test5\MSFragger.jar D:\Data\Lasse\NitroLaminin\Lam_ONOOH_DDA_3\test5\fragger.params D:\Data\Lasse\NitroLaminin\Lam_ONOOH_DDA_3\test5\100X_A_RA5_01_941.mgf
~~~~~~~~~~~~~~~~~~~~~~
Executing command:
$> java -jar D:\Data\Lasse\NitroLaminin\Lam_ONOOH_DDA_3\test5\MSFragger.jar D:\Data\Lasse\NitroLaminin\Lam_ONOOH_DDA_3\test5\fragger.params D:\Data\Lasse\NitroLaminin\Lam_ONOOH_DDA_3\test5\100X_A_RA5_01_941.mgf
Process started
Peptide index read in 317ms
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 1995.85MB
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.io.EOFException
at java.io.RandomAccessFile.readInt(Unknown Source)
at m.a(Unknown Source)
at MSFragger.main(Unknown Source)
... 5 more
871218620 fragments to be searched in 4 slices (6.49GB total)
Process finished, exit value: 1
=========================
===
=== Done
===
=========================
I have previously searched this mgf file with X!tandem with no issues, so the file should not be corrupted.
I hope you can help solve this issue, as I would really like to use this software.
Thank you in advance,
Lasse
Hi,
I am running a closed search using a set of mgf files. I am interesting in adding a peptide N terminal pyro-glu modifcation to my analysis. But MSFragger freezes after starting the process. There are no error messages given. Could you please guide me as to what may be the problem?
Here is how I define the modification: 'variable_mod_04 = -17.02650 nQ'. Alternatively, I also tested another N terminal peptide modification facing the same problem: 'variable_mod_05 = -17.0106 nE'.
Thanks in advance,
AR
fragger.params file has the following parameters for specifying fixed modifications that are currently not shown in the GUI. We need to add them:
add_Cterm_peptide = 0.0
add_Nterm_peptide = 0.0
add_Cterm_protein = 0.0
add_Nterm_protein = 0.0
Alexey
Hi, I tried searching a file (*.mzML) and got the error below. What is the problem here?
Thanks,
Yishai
Will execute 13 commands:
java -jar D:\MSFragger-GUI_v3.0\MSFragger_20170103_v2\MSFragger_20170103\MSFragger.jar D:\Temp\fragger.params P:\Projects\Instrument_benchmarking\prot_repo\old\HF1_pierce_hela_120717_01.mzML
java -cp D:\MSFragger-GUI_v3.0\MSFragger-GUI.jar umich.msfragger.util.FileMove P:\Projects\Instrument_benchmarking\prot_repo\old\HF1_pierce_hela_120717_01.pepXML D:\Temp\HF1_pierce_hela_120717_01.pepXML
philosopher_windows_amd64.exe workspace --init
philosopher_windows_amd64.exe peptideprophet --decoy rev --decoyprobs --ppm --accmass --nonparam --expectscore --database P:\Databases\2017_08_Working_DBs\Human\Human_SP_2017_Aug_crap.fasta D:\Temp\HF1_pierce_hela_120717_01.pepXML
philosopher_windows_amd64.exe workspace --clean
philosopher_windows_amd64.exe workspace --init
philosopher_windows_amd64.exe proteinprophet --output interact interact-HF1_pierce_hela_120717_01.pep.xml
philosopher_windows_amd64.exe workspace --clean
philosopher_windows_amd64.exe workspace --init
philosopher_windows_amd64.exe database --annotate P:\Databases\2017_08_Working_DBs\Human\Human_SP_2017_Aug_crap.fasta
philosopher_windows_amd64.exe filter --sequential --mapmods --pepxml D:\Temp --protxml D:\Temp\interact.prot.xml
philosopher_windows_amd64.exe report
philosopher_windows_amd64.exe workspace --clean
~~~~~~~~~~~~~~~~~~~~~~
Executing command:
$> java -jar D:\MSFragger-GUI_v3.0\MSFragger_20170103_v2\MSFragger_20170103\MSFragger.jar D:\Temp\fragger.params P:\Projects\Instrument_benchmarking\prot_repo\old\HF1_pierce_hela_120717_01.mzML
Process started
Peptide index read in 170ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 23710.23MB
171344664 fragments to be searched in 1 slices (1.28GB total)
Operating on slice 1 of 1:
Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NoClassDefFoundError: umich/ms/fileio/filetypes/LCMSDataSource
at m.d(Unknown Source)
at m.a(Unknown Source)
at MSFragger.main(Unknown Source)
... 5 more
Caused by: java.lang.ClassNotFoundException: umich.ms.fileio.filetypes.LCMSDataSource
at java.base/java.net.URLClassLoader.findClass(Unknown Source)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
... 8 more
4686ms
HF1_pierce_hela_120717_01.mzML
Process finished, exit value: 1
Executing command:
$> java -cp D:\MSFragger-GUI_v3.0\MSFragger-GUI.jar umich.msfragger.util.FileMove P:\Projects\Instrument_benchmarking\prot_repo\old\HF1_pierce_hela_120717_01.pepXML D:\Temp\HF1_pierce_hela_120717_01.pepXML
Process started
File does not exist: P:\Projects\Instrument_benchmarking\prot_repo\old\HF1_pierce_hela_120717_01.pepXML
Process finished, exit value: 1
Executing command:
$> philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:29:04] Creating workspace
WARN[09:29:04] existing workspace detected, will not overwrite
INFO[09:29:04] Done
Process finished, exit value: 0
Executing command:
$> philosopher_windows_amd64.exe peptideprophet --decoy rev --decoyprobs --ppm --accmass --nonparam --expectscore --database P:\Databases\2017_08_Working_DBs\Human\Human_SP_2017_Aug_crap.fasta D:\Temp\HF1_pierce_hela_120717_01.pepXML
Process started
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure[abi:cxx11]> >'
what(): failed opening file: The system cannot find the file specified.
: iostream error
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure[abi:cxx11]> >'
what(): failed opening file: The system cannot find the file specified.
: iostream error
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure[abi:cxx11]> >'
what(): failed opening file: The system cannot find the file specified.
: iostream error
- D:\Temp\interact-HF1_pierce_hela_120717_01.pep.xml
using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Using non-parametric distributions
INFO[09:29:05] Done
Process finished, exit value: 0
Executing command:
$> philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:29:05] Removing workspace
WARN[09:29:05] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:29:05] Done
Process finished, exit value: 0
Executing command:
$> philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:29:05] Creating workspace
WARN[09:29:05] existing workspace detected, will not overwrite
INFO[09:29:05] Done
Process finished, exit value: 0
Executing command:
$> philosopher_windows_amd64.exe proteinprophet --output interact interact-HF1_pierce_hela_120717_01.pep.xml
Process started
2017/11/05 09:29:06 open C:\Users\bsyishai\AppData\Local\Temp\1\fea1b2d5-3247-432e-9a3d-9d13835f5b1e\interact.prot.xml: The system cannot find the file specified.
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))
Error! Input file not found: D:/Temp/interact-HF1_pierce_hela_120717_01.pep.xml
Exiting
Process finished, exit value: 1
Executing command:
$> philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:29:06] Removing workspace
WARN[09:29:06] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:29:06] Done
Process finished, exit value: 0
Executing command:
$> philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:29:06] Creating workspace
WARN[09:29:06] existing workspace detected, will not overwrite
INFO[09:29:06] Done
Process finished, exit value: 0
Executing command:
$> philosopher_windows_amd64.exe database --annotate P:\Databases\2017_08_Working_DBs\Human\Human_SP_2017_Aug_crap.fasta
Process started
INFO[09:29:06] Processing database
panic: runtime error: index out of range
goroutine 1 [running]:
github.com/prvst/cmsl/db.ProcessUniProtKB(0xc0421cab81, 0x9, 0xc0421d3c60, 0x16, 0xad4e7e, 0x4, 0x0, 0x0, 0x0, 0x0, ...)
/home/felipevl/go/src/github.com/prvst/cmsl/db/db.go:132 +0xbe5
github.com/prvst/philosopher/lib/data.(*Base).ProcessDB(0xc04203ca80, 0xc042010140, 0x43, 0xad4e7e, 0x4, 0xad4c4a)
/home/felipevl/go/src/github.com/prvst/philosopher/lib/data/data.go:78 +0x6a1
github.com/prvst/philosopher/cmd.glob..func4(0x2c8ed80, 0xc0421ba960, 0x0, 0x2)
/home/felipevl/go/src/github.com/prvst/philosopher/cmd/database.go:33 +0x48a
github.com/spf13/cobra.(*Command).execute(0x2c8ed80, 0xc0421ba940, 0x2, 0x2, 0x2c8ed80, 0xc0421ba940)
/home/felipevl/go/src/github.com/spf13/cobra/command.go:653 +0x2a9
github.com/spf13/cobra.(*Command).ExecuteC(0x2c901c0, 0xc04207df70, 0x4044ab, 0xc04205e058)
/home/felipevl/go/src/github.com/spf13/cobra/command.go:728 +0x305
github.com/spf13/cobra.(*Command).Execute(0x2c901c0, 0x49, 0x2c90400)
/home/felipevl/go/src/github.com/spf13/cobra/command.go:687 +0x32
github.com/prvst/philosopher/cmd.Execute()
/home/felipevl/go/src/github.com/prvst/philosopher/cmd/root.go:31 +0x34
main.main()
/home/felipevl/go/src/github.com/prvst/philosopher/main.go:6 +0x27
Process finished, exit value: 2
Executing command:
$> philosopher_windows_amd64.exe filter --sequential --mapmods --pepxml D:\Temp --protxml D:\Temp\interact.prot.xml
Process started
INFO[09:29:08] Processing peptide identification files
FATA[09:29:08] No pepXML files found, check your files and try again
Process finished, exit value: 1
Executing command:
$> philosopher_windows_amd64.exe report
Process started
FATA[09:29:08] cannot restore serialized data structures: invalid argument
Process finished, exit value: 1
Executing command:
$> philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:29:09] Removing workspace
WARN[09:29:09] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:29:09] Done
Process finished, exit value: 0
=========================
===
=== Done
===
=========================
unless I'm looking at the wrong place?
Thanks!
David.
Dear developers,
when i try to run the msfraggerGUI.exe i double click the *.exe and then nothing happens. When I try to run the java executable i'll get the following error:
\MSFragger-GUI_v4.1>java -jar MSFragger-GUI.jar
Exception in thread "AWT-EventQueue-0" java.lang.IllegalStateException: Can't interpret variable mod from properties as delta mass and sites
at umich.msfragger.params.fragger.MsfraggerParams.getVariableMods(MsfraggerParams.java:661)
at umich.msfragger.gui.FraggerPanel.fillFormFromParams(FraggerPanel.java:224)
at umich.msfragger.gui.FraggerPanel.initMore(FraggerPanel.java:115)
at umich.msfragger.gui.FraggerPanel.(FraggerPanel.java:85)
at umich.msfragger.gui.MsfraggerGuiFrame.initMore(MsfraggerGuiFrame.java:145)
at umich.msfragger.gui.MsfraggerGuiFrame.(MsfraggerGuiFrame.java:128)
at umich.msfragger.gui.MsfraggerGuiFrame$54.run(MsfraggerGuiFrame.java:3936)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Do you know, what this means?
I have a windows 10 system with java 8 161 with german language settings.
Best
Roman
Hi
I get the following error for the last command in the GUI:
Executing command:
$> /home/compomics/Downloads/philosopher_linux_amd64 database --annotate /home/compomics/Downloads/MSFragger_20170103/all.revCat.fasta
Process started
time="15:16:15" level=info msg="Processing database"
panic: runtime error: index out of range
goroutine 1 [running]:
github.com/prvst/cmsl/db.ProcessUniProtKB(0xc4201b1a79, 0x5, 0xc4201c5680, 0x235, 0xadf157, 0x4, 0x0, 0x0, 0x0, 0x0, ...)
/home/felipevl/go/src/github.com/prvst/cmsl/db/db.go:132 +0xbc9
github.com/prvst/philosopher/lib/data.(*Base).ProcessDB(0xc4201d0000, 0x7fff410b061d, 0x3d, 0xadf157, 0x4, 0xddf560)
/home/felipevl/go/src/github.com/prvst/philosopher/lib/data/data.go:78 +0x673
github.com/prvst/philosopher/cmd.glob..func4(0x2c5d840, 0xc4201bd0c0, 0x0, 0x2)
/home/felipevl/go/src/github.com/prvst/philosopher/cmd/database.go:33 +0x5ff
github.com/spf13/cobra.(*Command).execute(0x2c5d840, 0xc4201bd080, 0x2, 0x2, 0x2c5d840, 0xc4201bd080)
/home/felipevl/go/src/github.com/spf13/cobra/command.go:653 +0x299
github.com/spf13/cobra.(*Command).ExecuteC(0x2c5ec80, 0x1, 0x0, 0x0)
/home/felipevl/go/src/github.com/spf13/cobra/command.go:728 +0x339
github.com/spf13/cobra.(*Command).Execute(0x2c5ec80, 0x0, 0x2c5eec0)
/home/felipevl/go/src/github.com/spf13/cobra/command.go:687 +0x2b
github.com/prvst/philosopher/cmd.Execute()
/home/felipevl/go/src/github.com/prvst/philosopher/cmd/root.go:31 +0x2d
main.main()
/home/felipevl/go/src/github.com/prvst/philosopher/main.go:6 +0x20
Process finished, exit value: 2
Not sure what I do wrong...
Hi,
I'm trying out this software on a dataset with a lot of chemically induced modifications, with the majority being +45. Identification of peptides with these mass shits have already been confirmed with other search engines, i.e. MS-GF+ and X!tandem.
Although MSFragger does identify peptides with these mass shifts in closed mode, it fails to do so in the open search (default parameters). However, by setting +45 as an expected modification in the open search (all other parameters being equal), the peptides are again identified.
I hope you can help me find out what is wrong here.
Hi Dmitry,
I am trying to get MSFragger-GUI to work. It generates the PeptideProphet and ProteinProphet files. The problem occurs when Philosopher is trying to generate the reports. The fatal error is "Cannot identify the database type " and "Database data not available, interrupting processing". What do you think the problem is? I have attached my log file for your review. The files are also available if you are interested to check them.
Thanks
H
Msfragger_log_20170620.txt
Dear developers,
i have now the first dataset analysed with MSFragger. My primary aim for using MSFragger was the open search option. There were a lot of modifcations assigned/observed. My first question is for the difference between them. Am i right, that the assigned modifications are those I've selected to search for and the observed ones are the ones coming from the open search?
Whe I look into the modifications.tsv and i compare the mass bins between assigned and observed and there are for Oxidation (15.9926) i get ~ 1400 for assigned and 170 for observed. Does this mean that the main modification is as selected a Methionin oxidation and 170 modifications are non methionin oxidations? How do i see the residues in an overview that are observed for oxdidation modification?
I assume that for IAA modifications it's similar?
modifications.zip
Is there a quantified overview of the observed modifications including the modified residues? Or can i calculate them somehow from the protein.fas or peptide.tsv?
proteins.zip
psm.zip
Actually, i want to use the enlighted "dark" modifications by MSFragger to enhance the PSM in Crosslink-PSM programms like Kojak.
Thank you in advance
Best
Roman
I am running MSFragger from the command line and have my output set to tsv. MSFragger runs successfully, and I can see the expected peptides in my tsv file. However, there are no headers in the columns of my tsv file, the first few rows of which are attached.
Are there supposed to be headers? If so, any ideas why they aren't included in my files? Would someone be able to tell me what the headers should be, so I can continue working with this data file?
Thanks very much.
tsvoutput.xlsx
HI,
could anyone please share a instruction for running the MSFragger GUI 3.0
I have installed but could not get the MSFragger.jar file and thus could not run the GUI to test.
THanks,
Trayambak.
Hi,
right now i am trying to recreate the results of MSFragger + Philosopher as in the Paper.
Are the default parameters for open searching in MSFragger-GUI taken from the manual of MSFragger ? They seem to be pretty much the same.
However i am not sure how to set the parameters for Philosopher according to the paper.
I also wanted to mention that there's a small bug with the report tables: The psm.tsv from open search has a typo in the column header. 'Oberved modifications' is created instead of 'Observed modifications'
Thanks,
tom
Hi,
Does MSFragger support ETD fragmentation? And if so, where can I select the ion type in the search?
Hello,
I'm wondering whether or not you'd recommend against using a large precursor mass tolerance (i.e. 2000 Da) in an open search. I've tried using this parameter across several datasets that used HCD mediated fragmentation, and when I try downstream analysis with philosopher (i.e. philosopher's peptideprophet and proteinprophet), I have been unable to get any confident protein identifications. Thanks for any input.
Dear all,
I am trying to try the MSFragger sw, with a mzXML file (converted from RAW using msconvert)
java -jar MSFragger.jar fragger_open.params 00523_A10_P003818_B0A_A00_R1.mzXML
and it gives the following error
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NumberFormatException: For input string: "0,000000"
at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
at sun.misc.FloatingDecimal.parseDouble(Unknown Source)
at java.lang.Double.parseDouble(Unknown Source)
at ad.a(Unknown Source)
at ad.a(Unknown Source)
at ad.<init>(Unknown Source)
at MSFragger.main(Unknown Source)
... 5 more
What's wrong?
Thanks in advance.
Alba.
Fragger should print the current Fragger version and the JVM version. Also, probably, the max possible heap .size
Hello,
I'm currently trying to use MSFragger (not the GUI) with a human proteome dataset with ITRAQ modifications. I know that MSFragger has an option to exclude spectra within a 0-150 Mz Range, but I'm wondering how MSFragger handles ITRAQ modifications (specified as variable or fixed) in generating a database. More specifically, ITRAQ tags are lost upon CID, and I don't know if MSFragger takes this into account when generating a fragment index.
If you have any recommendations as to how to deal with this sort of problem, that would be greatly appreciated.
Thanks!
Hi,
When searching multiple LC-MS files at once, let's say, a set of AP-MS experiments, it would be really interesting to get information relative to spectral counting for each proteins in separated columns in report.tsv file.
Completely made up example :
Protein ID Total Spectral Count FILE A Spectral count FILE B Spectral count
A 75 70 5
B 12 6 6
D 33 3 30
This would be pretty useful to extract quantitative information (spectral counting) for further processing like AP-MS enrichment analysis (SAINT/Perseus/etc.) or differentially expressed proteins in different samples in total cells/tissues extracts (treated/untreated /// healthy/mutant).
Best regards,
Vivian
I'm submitting a:
My MSFragger use case:
** put your general problem description here **
Fragger not analyzing my data
You can find that printed on the Config tab.
e.g. "TMT, Human, full cell lysate with Trypsin" , "AP-MS pulldowns, mouse,
liver tissue"
...
** e.g. "fractionated HeLa, 5 samples, 3 bio replicates, 2 technical replicates" or "ten 3 hour LC gradients, full cell lysate, fruit fly" or
or at least "5 mzml files 1.5Gb each" **
** your response here, preferably a link or at least name, organism etc. **
** Size of the either in proteins or in megabytes **
** You can find it in the output directory you specified for analysis. **
num_threads = 0 # 0=poll CPU to set num threads; else specify num threads directly (max 64)
precursor_mass_tolerance = 500.00
precursor_mass_lower = -500 # Overrides the lower bound of the window set by precursor_mass_tolerance
precursor_mass_upper = 500 # Overrides the upper bound of the window set by precursor_mass_tolerance
precursor_mass_units = 0 # 0=Daltons, 1=ppm
precursor_true_tolerance = 20
precursor_true_units = 1 # 0=Daltons, 1=ppm
fragment_mass_tolerance = 20
fragment_mass_units = 1 # 0=Daltons, 1=ppm
isotope_error = 0 # 0=off, -1/0/1/2/3 (standard C13 error)
mass_offsets = 0 # allow for additional precursor mass window shifts. Multiplexed with isotope_error. mass_offsets = 0/79.966 can be used as a restricted รขโฌหopenรขโฌโข search that looks for unmodified and phosphorylated peptides (on any residue)
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2 # 2 for enzymatic, 1 for semi-enzymatic, 0 for nonspecific digestion
allowed_missed_cleavage = 1 # maximum value is 5
clip_nTerm_M = 1
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
# variable_mod_03 = 79.96633 STY
# variable_mod_04 = -17.02650 nQnC
# variable_mod_05 = -18.01060 nE
allow_multiple_variable_mods_on_residue = 1 # static mods are not considered
max_variable_mods_per_mod = 3 # maximum of 5
max_variable_mods_combinations = 5000 # maximum of 65534, limits number of modified peptides generated from sequence
output_file_extension = pepXML
output_format = pepXML
output_report_topN = 1
output_max_expect = 50.0
precursor_charge = 0 0 # precursor charge range to analyze; does not override any existing charge; 0 as 1st entry ignores parameter
override_charge = 0 # 0=no, 1=yes to override existing precursor charge states with precursor_charge parameter
digest_min_length = 7
digest_max_length = 50
digest_mass_range = 500.0 5000.0 # MH+ peptide mass range to analyze
max_fragment_charge = 2 # set maximum fragment charge state to analyze (allowed max 5)
track_zero_topN = 0 # in addition to topN results, keep track of top results in zero bin
zero_bin_accept_expect = 0 # boost top zero bin entry to top if it has expect under 0.01 - set to 0 to disable
zero_bin_mult_expect = 1 # disabled if above passes - multiply expect of zero bin for ordering purposes (does not affect reported expect)
add_topN_complementary = 0
minimum_peaks = 15 # required minimum number of peaks in spectrum to search (default 10)
use_topN_peaks = 100
min_fragments_modelling = 3
min_matched_fragments = 6
minimum_ratio = 0.01 # filter peaks below this fraction of strongest peak
clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range
add_Cterm_peptide = 0.000000
add_Nterm_peptide = 0.000000
add_Cterm_protein = 0.000000
add_Nterm_protein = 0.000000
add_G_glycine = 0.000000
add_A_alanine = 0.000000
add_S_serine = 0.000000
add_P_proline = 0.000000
add_V_valine = 0.000000
add_T_threonine = 0.000000
add_C_cysteine = 57.021464
add_L_leucine = 0.000000
add_I_isoleucine = 0.000000
add_N_asparagine = 0.000000
add_D_aspartic_acid = 0.000000
add_Q_glutamine = 0.000000
add_K_lysine = 0.000000
add_E_glutamic_acid = 0.000000
add_M_methionine = 0.000000
add_H_histidine = 0.000000
add_F_phenylalanine = 0.000000
add_R_arginine = 0.000000
add_Y_tyrosine = 0.000000
add_W_tryptophan = 0.000000
add_B_user_amino_acid = 0.000000
add_J_user_amino_acid = 0.000000
add_O_user_amino_acid = 0.000000
add_U_user_amino_acid = 0.000000
add_X_user_amino_acid = 0.000000
add_Z_user_amino_acid = 0.000000
database_name = Z:\Protein Databases\cRAP_from_UNIPROT_append_to_all_DBs.fasta
System info:
System OS: Windows 7, Architecture: AMD64
Java Info: 1.8.0_161, Java HotSpot(TM) Client VM, Oracle Corporation
Version info:
MSFragger-GUI version 6.0
MSFragger version 20180316
Philosopher version 20180323 (build 201803231722)
Will execute 9 commands:
java -jar -Xmx2G E:\MSFragger\MSFragger-20180316.jar E:\MSFragger_Results\BSA_TEST\fragger.params Z:\VELOS\170609\170609_0636_096_BSA_Lo_Ag.mzML
java -cp E:\MSFragger\MSFragger-GUI.jar umich.msfragger.util.FileMove Z:\VELOS\170609\170609_0636_096_BSA_Lo_Ag.pepXML E:\MSFragger_Results\BSA_TEST\170609_0636_096_BSA_Lo_Ag.pepXML
philosopher_windows_amd64.exe workspace --clean
philosopher_windows_amd64.exe workspace --init
philosopher_windows_amd64.exe peptideprophet --decoy rev_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database Z:\Protein Databases\cRAP_from_UNIPROT_append_to_all_DBs.fasta E:\MSFragger_Results\BSA_TEST\170609_0636_096_BSA_Lo_Ag.pepXML
philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20 interact-170609_0636_096_BSA_Lo_Ag.pep.xml
philosopher_windows_amd64.exe database --annotate Z:\Protein Databases\cRAP_from_UNIPROT_append_to_all_DBs.fasta --prefix rev_
philosopher_windows_amd64.exe filter --sequential --mapmods --tag rev_ --pepxml E:\MSFragger_Results\BSA_TEST --protxml E:\MSFragger_Results\BSA_TEST\interact.prot.xml
philosopher_windows_amd64.exe report
~~~~~~~~~~~~~~~~~~~~~~
Executing command:
$> java -jar -Xmx2G E:\MSFragger\MSFragger-20180316.jar E:\MSFragger_Results\BSA_TEST\fragger.params Z:\VELOS\170609\170609_0636_096_BSA_Lo_Ag.mzML
Process started
Error occurred during initialization of VM
Could not reserve enough space for 2097152KB object heap
Process finished, exit value: 1
Previous process returned exit code [1], cancelling further processing..
Cancelled execution of:
java -cp E:\MSFragger\MSFragger-GUI.jar umich.msfragger.util.FileMove Z:\VELOS\170609\170609_0636_096_BSA_Lo_Ag.pepXML E:\MSFragger_Results\BSA_TEST\170609_0636_096_BSA_Lo_Ag.pepXML
Cancelled execution of:
philosopher_windows_amd64.exe workspace --clean
Cancelled execution of:
philosopher_windows_amd64.exe workspace --init
Cancelled execution of:
philosopher_windows_amd64.exe peptideprophet --decoy rev_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database Z:\Protein Databases\cRAP_from_UNIPROT_append_to_all_DBs.fasta E:\MSFragger_Results\BSA_TEST\170609_0636_096_BSA_Lo_Ag.pepXML
Cancelled execution of:
philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20 interact-170609_0636_096_BSA_Lo_Ag.pep.xml
Cancelled execution of:
philosopher_windows_amd64.exe database --annotate Z:\Protein Databases\cRAP_from_UNIPROT_append_to_all_DBs.fasta --prefix rev_
Cancelled execution of:
philosopher_windows_amd64.exe filter --sequential --mapmods --tag rev_ --pepxml E:\MSFragger_Results\BSA_TEST --protxml E:\MSFragger_Results\BSA_TEST\interact.prot.xml
Cancelled execution of:
philosopher_windows_amd64.exe report
=========================
===
=== Done
===
=========================
I have previously signed the license agreement to download the then-current 20170103 version of MSFragger. I saw now that a version 11282017 seems to be available, presumably with some bug fixes and/or improvements (although a changelog seems to be missing).
However, when I try to download this latest MSFragger version the Nouvant system (correctly) reports that I have already signed the license agreement in the past and I'm directed to their site to download again. Unfortunately the link there still refers to the older version I originally downloaded and I can't see any options to change the version.
How can I still updated my MSFragger to the latest version?
Hi,
I tried running an mgf file, none specific digestion and got the error below.
I set the memory to 80GB, since the machine has 130GB RAM.
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
at java.util.concurrent.FutureTask.report(Unknown Source)
at java.util.concurrent.FutureTask.get(Unknown Source)
at x.a(Unknown Source)
at v.a(Unknown Source)
at e.a(Unknown Source)
at MSFragger.main(Unknown Source)
... 5 more
Caused by: java.lang.OutOfMemoryError: Java heap space
Any idea how to fix this?
MSFragger parameters file has a 'mass_offsets' parameter. It implements the same functionality as the Comet's option with the same name.
Mass_offsets in MSFragger creates multiple precursor tolerance windows with
specified mass offsets. These values are multiplexed with the isotope error option. For example,
mass_offsets = 0/79.966 can be used as a restricted โopenโ search that looks for unmodified and
phosphorylated peptides (on any residue). Setting isotope_error to 0/1/2 in combination with this example will create search windows around (0,1,2,79.966, 80.966, 81.966).
It is currently missing in the GUI interface.
Alexey
Hi,
I am running MSFragger on Linux using default open search parameters. The reverse decoy database were generated using DecoyDatabaseBuilder_dist_1.5.47. Decoy label "REV_" were added to the decoy database entries and then concatenated to the original database. The results showed almost half hits from decoy databases. Thus no protein or peptide were identified at 1% FDRs.
Here is an example output of peptide prophet from one of the runs
Using Decoy Label "REV".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
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+, 134 2+, 313 3+, 33 4+, 2 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 207 Decoys, and 275 Non-Decoys
Iterations: .........10.........20.....
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (2+).
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 26 iterations
Running MSFragger on Linux using default close search parameters has reduced the proportion of decoy hits. However there are still no protein or peptide were identified by 1% FDRs.
While i have tried to run maxQuant using parameters to comparable close search, 4K+ protein groups were identified. It seems that the MS data is ok in terms of quality.
The PSM scoring algorithms seems to be quite similar between X! Tandem and Andrometa.
Any suggestions on what might be possible reasons that i could not achieve any peptide ids using MSFragger?
if you need any information for forensics, please let me know.
Thank you very much!
Best regards,
Runxuan
For a peptidomics experiment with a nonspecific search, MSFragger is generating too many peptides. It appears that 2^31 - 1 is the maximum number allowed. Are there any planned updates to expand this, or any practical workarounds you can suggest? I am running on a cluster with 1.5 TB RAM and 20 cores, so system resources shouldn't be an issue for me.
Hi
Is there a way to queue and sequentially analyse multiple mzXML files in MSfragger + Philosopher without combining resulting pep / prot.xml files?
E.g. I want to end up with modification and pep / prot.xml files for every single mzXML file.
Many thanks and all the best
Hello,
I believe I have an issue/might need help with peptide prophet.
I'm on Linux and try to run the latest version of MSFraggerGUI and I get that kind of error when I try to analyze an MZML file:
"Executing command:
$> java -cp /mnt/users/benoitk/MSFragger/MSFragger-GUI.jar umich.msfragger.util.FileMove /mnt/users/benoitk/Proteomics/MZML_PW/T7C_11.tsv /mnt/users/benoitk/MSFragger/output/T7C_11.tsv
Process started
Process finished, exit value: 0Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 workspace --init
Process started
time="17:54:47" level=info msg="Creating workspace"
time="17:54:47" level=info msg=DoneProcess finished, exit value: 0
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel 2 --database /mnt/users/benoitk/Moda/moda_v1.51/Database/Prokka_contigs500_Concat_Decoy.fa /mnt/users/benoitk/MSFragger/output/T7C_11.tsv
Process started
time="17:54:47" level=info msg="Executing PeptideProphet"terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure >'
what(): failed opening file: No such file or directory
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure >'
what(): failed opening file: No such file or directory
time="17:54:49" level=info msg=Done
- /mnt/users/benoitk/MSFragger/output/interact-T7C_11.pep.xml
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Using non-parametric distributionsProcess finished, exit value: 0
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 workspace --clean
Process started
time="17:54:50" level=info msg="Removing workspace"
time="17:54:50" level=info msg=DoneProcess finished, exit value: 0
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 workspace --init
Process started
time="17:54:51" level=info msg="Creating workspace"time="17:54:51" level=info msg=Done
Process finished, exit value: 0
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 proteinprophet --output interact --maxppmdiff 20 interact-T7C_11.pep.xml
Process started
time="17:54:51" level=info msg="Executing ProteinProphet"
2018/02/19 17:54:51 open /tmp/91e605bd-01e5-4338-ae94-8a0b867c8753/interact.prot.xml: no such file or directoryProteinProphet (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))
Error! Input file not found: /mnt/users/benoitk/MSFragger/output/interact-T7C_11.pep.xml
ExitingProcess finished, exit value: 1
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 workspace --clean
Process started
time="17:54:52" level=info msg="Removing workspace"
time="17:54:52" level=info msg=DoneProcess finished, exit value: 0
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 workspace --init
Process started
time="17:54:54" level=info msg="Creating workspace"
time="17:54:54" level=info msg=DoneProcess finished, exit value: 0
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 database --annotate /mnt/users/benoitk/Moda/moda_v1.51/Database/Prokka_contigs500_Concat_Decoy.fa
Process started
time="17:54:54" level=info msg="Processing database"time="17:54:58" level=info msg=Done
Process finished, exit value: 0
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 filter --sequential --mapmods --pepxml /mnt/users/benoitk/MSFragger/output --protxml /mnt/users/benoitk/MSFragger/output/interact.prot.xml
Process started
time="17:54:58" level=info msg="Executing filter"
time="17:54:58" level=info msg="Processing peptide identification files"
time="17:54:58" level=fatal msg="No pepXML files found, check your files and try again"Process finished, exit value: 1
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 report
Process started
time="17:54:58" level=info msg="Executing report"
time="17:54:58" level=fatal msg="cannot restore serialized data structures: invalid argument"Process finished, exit value: 1
Executing command:
$> /mnt/users/benoitk/MSFragger/MSFragger-20171106/philosopher_linux_amd64 workspace --clean
Process started
time="17:55:00" level=info msg="Removing workspace"
time="17:55:00" level=info msg=DoneProcess finished, exit value: 0
=========================
=== Done"
I start wandering if the issue is not due to Philosopher as I have also issue when I try to analyze MGF files from ProteoWizard.
I've downloaded philosopher_linux_amd64, and I could put the path to it in MSFragger, but still it doesn't seem to use it.
Do you guys have any idea of what I'm missing?
Thanks a lot for your help!
Best,
Benoit
@chhh @andytyk ,
i'm getting error as
"Invalid Maximum Heap Size:XmxBG
Error:Could not create java virtual machine
Error: A fatal exception has occured .
Program will Exit."
I'm using default params file .
my system configuration is 8GB RAM , i7 processor.
please help
emailid :[email protected]
Hello,
I am having an issue using Philosopher to analyze the results of MSFragger. Here is the command line output of running the program:
Will execute 12 commands:
java -jar -Xmx8G C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\MSFragger-Jar\MSFragger.jar C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\fragger.params C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.mzXML
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData --protxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact.prot.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Executing command:
$> java -jar -Xmx8G C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\MSFragger-Jar\MSFragger.jar C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\fragger.params C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.mzXML
Process started
Peptide index read in 219ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 4981.53MB
205026136 fragments to be searched in 1 slices (1.53GB total)
Operating on slice 1 of 1:
6415ms
b1906_293T_proteinID_01A_QE3_122212.mzXML
95173ms
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 1535/41820 (3.67%) - 303.66 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 3103/41820 (7.42%) - 310.25 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 4708/41820 (11.26%) - 313.66 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 6267/41820 (14.99%) - 310.25 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 7847/41820 (18.76%) - 313.74 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 9405/41820 (22.49%) - 310.17 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 11017/41820 (26.34%) - 318.89 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 12561/41820 (30.04%) - 303.64 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 14120/41820 (33.76%) - 306.53 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 15691/41820 (37.52%) - 307.74 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 17216/41820 (41.17%) - 303.48 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 18757/41820 (44.85%) - 302.04 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 20296/41820 (48.53%) - 304.51 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 21853/41820 (52.25%) - 310.90 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 23449/41820 (56.07%) - 315.79 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 25014/41820 (59.81%) - 311.44 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 26569/41820 (63.53%) - 308.35 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 28138/41820 (67.28%) - 308.49 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 29743/41820 (71.12%) - 312.68 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 31368/41820 (75.01%) - 317.57 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 32957/41820 (78.81%) - 316.34 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 34589/41820 (82.71%) - 321.77 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 36193/41820 (86.54%) - 313.34 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 37875/41820 (90.57%) - 327.62 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 39645/41820 (94.80%) - 345.77 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 41399/41820 (98.99%) - 350.24 spectra/s]
b1906_293T_proteinID_01A_QE3_122212.mzXML 95173ms [progress: 41820/41820 (100.00%) - 214.25 spectra/s]
- completed 134540ms
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[08:47:04] Creating workspace
WARN[08:47:04] existing workspace detected, will not overwrite
INFO[08:47:04] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
Process started
file 1: C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1906_293T_proteinID_01A_QE3_122212.pepXML
processed altogether 34084 results
INFO: Results written to file: C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
- C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
- Building Commentz-Walter keyword tree...
- Searching the tree...
- Linking duplicate entries...
- Printing results...
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
init with X! Tandem trypsin
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 18190 2+, 12391 3+, 3101 4+, 324 5+, 73 6+, and 3 7+ spectra.
Found 0 Decoys, and 34082 Non-Decoys
WARNING: No decoys with label rev were found in this dataset. reverting to fully unsupervised method.
negmean = 0.0533258
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
INFO: Processing standard MixtureModel ...
Initialising statistical models ...
INFO[08:48:17] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[08:48:17] Removing workspace
WARN[08:48:17] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[08:48:17] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[08:48:17] Creating workspace
WARN[08:48:17] existing workspace detected, will not overwrite
INFO[08:48:17] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1906_293T_proteinID_01A_QE3_122212.pep.xml
Process started
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 C:/Users/acadigan/Desktop/AlexStuff/MSFragger/TestData/interact-b1906_293T_proteinID_01A_QE3_122212.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
WARNING: no data - output file will be empty
INFO[08:48:19] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[08:48:20] Removing workspace
WARN[08:48:20] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[08:48:20] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[08:48:20] Creating workspace
WARN[08:48:20] existing workspace detected, will not overwrite
INFO[08:48:20] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta
Process started
INFO[08:48:20] Processing database
INFO[08:48:34] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData --protxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact.prot.xml
Process started
INFO[08:48:34] Processing peptide identification files
INFO[08:48:37] 1+ Charge profile decoy=0 target=0
INFO[08:48:37] 2+ Charge profile decoy=0 target=18190
INFO[08:48:37] 3+ Charge profile decoy=0 target=12391
INFO[08:48:37] 4+ Charge profile decoy=0 target=3101
INFO[08:48:37] 5+ Charge profile decoy=0 target=324
INFO[08:48:37] 6+ Charge profile decoy=0 target=73
INFO[08:48:37] Database search results ions=24050 peptides=20473 psms=34084
INFO[08:48:37] Converged to 0.00 % FDR with 34084 PSMs decoy=0 threshold=0 total=34084
INFO[08:48:38] Converged to 0.00 % FDR with 20473 Peptides decoy=0 threshold=0 total=20473
INFO[08:48:38] Converged to 0.00 % FDR with 24050 Ions decoy=0 threshold=0 total=24050
FATA[08:48:38] No Protein groups detected, check your file and try again
Process finished, exit value: 1
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
Process started
INFO[08:48:38] Creating PSM report
INFO[08:48:38] Creating peptide Ion report
INFO[08:48:38] Creating peptide report
INFO[08:48:38] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[08:48:38] Removing workspace
WARN[08:48:38] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[08:48:38] Done
Process finished, exit value: 0
=========================
===
=== Done
===
=========================
Here is another run using a different mzXML file:
Will execute 12 commands:
java -jar -Xmx14G C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\MSFragger-Jar\MSFragger.jar C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\fragger.params C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.mzXML
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.pepXML
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1922_293T_proteinID_02A_QE3_122212.pep.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData --protxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact.prot.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Executing command:
$> java -jar -Xmx14G C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\MSFragger-Jar\MSFragger.jar C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\fragger.params C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.mzXML
Process started
Peptide index read in 203ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 9350.73MB
205026136 fragments to be searched in 1 slices (1.53GB total)
Operating on slice 1 of 1:
6426ms
b1922_293T_proteinID_02A_QE3_122212.mzXML
147102ms
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 1221/46856 (2.61%) - 240.07 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 2682/46856 (5.72%) - 291.79 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 4167/46856 (8.89%) - 293.77 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 5615/46856 (11.98%) - 283.87 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 7069/46856 (15.09%) - 285.04 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 8494/46856 (18.13%) - 279.36 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 9875/46856 (21.08%) - 274.06 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 11288/46856 (24.09%) - 280.30 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 12729/46856 (27.17%) - 285.97 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 14184/46856 (30.27%) - 283.35 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 15607/46856 (33.31%) - 282.40 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 17022/46856 (36.33%) - 277.40 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 18461/46856 (39.40%) - 285.57 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 19909/46856 (42.49%) - 285.49 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 21353/46856 (45.57%) - 287.36 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 22801/46856 (48.66%) - 288.16 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 24272/46856 (51.80%) - 292.68 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 25758/46856 (54.97%) - 291.32 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 27261/46856 (58.18%) - 292.87 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 28720/46856 (61.29%) - 291.22 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 30186/46856 (64.42%) - 291.74 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 31671/46856 (67.59%) - 294.70 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 33136/46856 (70.72%) - 292.59 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 34644/46856 (73.94%) - 295.51 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 36177/46856 (77.21%) - 306.11 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 37713/46856 (80.49%) - 299.18 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 39250/46856 (83.77%) - 300.25 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 40773/46856 (87.02%) - 304.11 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 42394/46856 (90.48%) - 319.60 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 44034/46856 (93.98%) - 326.37 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 45652/46856 (97.43%) - 323.08 spectra/s]
b1922_293T_proteinID_02A_QE3_122212.mzXML 147102ms [progress: 46856/46856 (100.00%) - 248.09 spectra/s]
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:17:45] Creating workspace
WARN[09:17:45] existing workspace detected, will not overwrite
INFO[09:17:45] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe peptideprophet --nonparam --expectscore --decoy rev --decoyprobs --masswidth 1000.0 --clevel -2 --database C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.pepXML
Process started
file 1: C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\b1922_293T_proteinID_02A_QE3_122212.pepXML
processed altogether 38597 results
INFO: Results written to file: C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact-b1922_293T_proteinID_02A_QE3_122212.pep.xml
C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact-b1922_293T_proteinID_02A_QE3_122212.pep.xml
Building Commentz-Walter keyword tree...
Searching the tree...
Linking duplicate entries...
Printing results...
Using Decoy Label "rev".
Decoy Probabilities will be reported.
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
init with X! Tandem trypsin
PeptideProphet (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 21822 2+, 13646 3+, 2786 4+, 259 5+, 80 6+, and 1 7+ spectra.
Found 0 Decoys, and 38594 Non-Decoys
WARNING: No decoys with label rev were found in this dataset. reverting to fully unsupervised method.
negmean = 0.0533258
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
INFO: Processing standard MixtureModel ...
Initialising statistical models ...
INFO[09:19:15] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:19:15] Removing workspace
WARN[09:19:15] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:19:15] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:19:16] Creating workspace
WARN[09:19:16] existing workspace detected, will not overwrite
INFO[09:19:16] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe proteinprophet --output interact --maxppmdiff 20.0 interact-b1922_293T_proteinID_02A_QE3_122212.pep.xml
Process started
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 C:/Users/acadigan/Desktop/AlexStuff/MSFragger/TestData/interact-b1922_293T_proteinID_02A_QE3_122212.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
WARNING: no data - output file will be empty
INFO[09:19:18] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:19:18] Removing workspace
WARN[09:19:18] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:19:18] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --init
Process started
INFO[09:19:18] Creating workspace
WARN[09:19:18] existing workspace detected, will not overwrite
INFO[09:19:18] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe database --annotate C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\CompleteHumanProteome.fasta
Process started
INFO[09:19:18] Processing database
INFO[09:19:32] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe filter --sequential --pepxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData --protxml C:\Users\acadigan\Desktop\AlexStuff\MSFragger\TestData\interact.prot.xml
Process started
INFO[09:19:32] Processing peptide identification files
INFO[09:19:43] 1+ Charge profile decoy=0 target=0
INFO[09:19:43] 2+ Charge profile decoy=0 target=40012
INFO[09:19:43] 3+ Charge profile decoy=0 target=26037
INFO[09:19:43] 4+ Charge profile decoy=0 target=5887
INFO[09:19:43] 5+ Charge profile decoy=0 target=583
INFO[09:19:43] 6+ Charge profile decoy=0 target=153
INFO[09:19:43] Database search results ions=49651 peptides=41576 psms=72681
INFO[09:19:43] Converged to 0.00 % FDR with 72681 PSMs decoy=0 threshold=0 total=72681
INFO[09:19:44] Converged to 0.00 % FDR with 41576 Peptides decoy=0 threshold=0 total=41576
INFO[09:19:44] Converged to 0.00 % FDR with 49651 Ions decoy=0 threshold=0 total=49651
FATA[09:19:44] No Protein groups detected, check your file and try again
Process finished, exit value: 1
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe report
Process started
INFO[09:19:44] Creating PSM report
INFO[09:19:44] Creating peptide Ion report
INFO[09:19:44] Creating peptide report
INFO[09:19:44] Done
Process finished, exit value: 0
Executing command:
$> C:\Users\acadigan\Desktop\AlexStuff\MSFragger\MSFraggerApp\philosopher_windows_amd64.exe workspace --clean
Process started
INFO[09:19:44] Removing workspace
WARN[09:19:44] cannot remove the meta data: remove .meta\meta.bin: The process cannot access the file because it is being used by another process.
INFO[09:19:44] Done
Process finished, exit value: 0
=========================
I believe that MSFragger is running properly, but Philosopher is just producing output files with no results in them. I am using two different mzXML files I downloaded from this link: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/06/PXD001468. I have also attached a zip file of the protein data set I was using: CompleteHumanProteome.zip. Any advice on what I'm doing wrong and how to fix the issue would be greatly appreciated!
Thanks so much!
-Alex
it would be wonderful if you could provide sample .mzml, .fasta and .params file to test open search with the gui. This would help establishing that the installation was successful and to separate out troubles associated with the format of other files.
Suppose I have a fasta protein with header
sp|A0A075B6H9|LV469_HUMAN Immunoglobulin lambda variable 4-69 OS=Homo sapiens GN=IGLV4-69 PE=1 SV=1
How do I format the decoy version of this protein in the fasta file? Where do I add a prefix? I don't get it to work.
Thanks
Trying the new version of MSFragger (V4.3) with updated version of Philosopher (philosopher_windows_386) on win7 (the log file is attached). I believe the philosopher is not compatible with windows. Any thoughts? This is similar error to the issue that I had with DIA-umpire GUI. Hope there is a fix. Thank you for doing such a great work.
Cleaning the philosopher work space and MSFragger cache doesn't fix the problem for me.
MSFragger_error.txt
Hi,
I'm trying to run MSFragger-GUI on Windows, and am getting a "java.lang.NullPointerException" error:
`Executing command:
$> java -jar C:\xxxx\yyyy\zzzz\MSFragger-20171106.jar C:\xxxx\yyyy\zzzz\run1\fragger.params C:\xxxx\yyyy\zzzz\mgf\QE05561-LUMOS.mzML C:\xxxx\yyyy\zzzz\mgf\QE05562-LUMOS.mzML C:\xxxx\yyyy\zzzz\mgf\QE05563-LUMOS.mzML C:\xxxx\yyyy\zzzz\mgf\QE05564-LUMOS.mzML
Process started
MSFragger version MSFragger-20171106
(c) University of Michigan
Sequence database filtered and tagged in 5ms
Digestion completed in 26ms
Merged digestion results in 2ms
Sorting digested sequences...
of length 7: 34
of length 8: 43
of length 9: 42
of length 10: 30
of length 11: 40
of length 12: 36
of length 13: 41
of length 14: 33
of length 15: 38
of length 16: 45
of length 17: 33
of length 18: 51
of length 19: 32
of length 20: 22
of length 21: 26
of length 22: 31
of length 23: 46
of length 24: 29
of length 25: 27
of length 26: 24
of length 27: 20
of length 28: 27
of length 29: 16
of length 30: 16
of length 31: 27
of length 32: 14
of length 33: 26
of length 34: 14
of length 35: 18
of length 36: 16
of length 37: 14
of length 38: 16
of length 39: 19
of length 40: 6
of length 41: 15
of length 42: 20
of length 43: 13
of length 44: 15
of length 45: 17
of length 46: 21
of length 47: 14
of length 48: 3
of length 49: 3
of length 50: 1
DONE
Removing duplicates and compacting...
Reduced to 1052 peptides in 105ms
Generating modified peptides...DONE in 28ms
Generated 1439 modified peptides
Merging peptide pools from threads... DONE in 2ms
Sorting modified peptides by mass...DONE in 2ms
Peptide index written in 87ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 1312.79MB
136340 fragments to be searched in 1 slices (0.00GB total)
Operating on slice 1 of 1:
299ms
QE05561-LUMOS.mzML
java.lang.NullPointerException
at o.b(Unknown Source)
at n.d(Unknown Source)
at n.a(Unknown Source)
at MSFragger.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Error parsing: QE05561-LUMOS.mzML5388ms
QE05562-LUMOS.mzML
java.lang.NullPointerException
at o.b(Unknown Source)
at n.d(Unknown Source)
at n.a(Unknown Source)
at MSFragger.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Error parsing: QE05562-LUMOS.mzML2009ms
QE05563-LUMOS.mzML
java.lang.NullPointerException
at o.b(Unknown Source)
at n.d(Unknown Source)
at n.a(Unknown Source)
at MSFragger.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Error parsing: QE05563-LUMOS.mzML1614ms
QE05564-LUMOS.mzML
java.lang.NullPointerException
at o.b(Unknown Source)
at n.d(Unknown Source)
at n.a(Unknown Source)
at MSFragger.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Error parsing: QE05564-LUMOS.mzML2196ms
Process finished, exit value: 0`
All subsequent steps fail because no pepXML files are written due to the java error.
Any ideas?
Java Info:
java.version: 1.8.0_161
java.vm.specification.version: 1.8
java.vm.specification.vendor: Oracle Corporation
java.vm.specification.name: Java Virtual Machine Specification
java.vm.version: 25.161-b12
java.vm.vendor: Oracle Corporation
java.vm.name: Java HotSpot(TM) 64-Bit Server VM
java.specification.version: 1.8
java.specification.vendor: Oracle Corporation
java.specification.name: Java Platform API Specification
Add a button on the Run tab for export
For --maxppmdiff, the argument only accepts integers so the ProteinProphet component of Philosopher errors out when given 20.0 (the default parameters in the GUI). This should be changed to 20.
Process started
Error: invalid argument "20.0" for "--maxppmdiff" flag: strconv.ParseUint: parsing "20.0": invalid syntax
Usage:
Hey,
Gave a try to MSFragger GUI with std configuration with open search + philosopher. Everything is fine until grouping.
I am using a concatenated target/decoy from uniprot (canonical + isof : swiss + trembl- 03/2017) and my decoys are flagged with the "rev_" tag.
Is there something to change to the FASTA ?
INFO[21:01:10] Processing peptide identification files
INFO[21:01:13] 1+ Charge profile decoy=0 target=0
INFO[21:01:13] 2+ Charge profile decoy=2019 target=18584
INFO[21:01:13] 3+ Charge profile decoy=2386 target=15240
INFO[21:01:13] 4+ Charge profile decoy=815 target=4289
INFO[21:01:13] 5+ Charge profile decoy=188 target=950
INFO[21:01:13] 6+ Charge profile decoy=94 target=348
INFO[21:01:13] Database search results ions=31664 peptides=29682 psms=45464
INFO[21:01:14] Converged to 0.00 % FDR with 45464 PSMs decoy=0 threshold=0 total=45464
INFO[21:01:14] Converged to 0.00 % FDR with 29682 Peptides decoy=0 threshold=0 total=29682
INFO[21:01:14] Converged to 0.00 % FDR with 31664 Ions decoy=0 threshold=0 total=31664
FATA[21:01:14] No Protein groups detected, check your file and try again
Process finished, exit value: 1
Cheers,
Vivian
you need to specify the decoy tag when running the philosopher database command, like this:
philosopher database --annotate db.fasta --tag DECOY_
Some users are having problems with their analysis because Philosopher uses rev_ as the default value for all tag definition, but they are using a different one.
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