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Nesvilab / philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
https://philosopher.nesvilab.org
GNU General Public License v3.0
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Filtering step fails #29

Closed glnegri closed 5 years ago

glnegri commented 5 years ago

I tried running philosopher (20181128) on a sample but it fails at the filtering step.

./philosopher_linux_amd64 workspace --clean ./philosopher_linux_amd64 workspace --init ./philosopher_linux_amd64 comet --param comet.params TMT1_1.mzML ./philosopher_linux_amd64 peptideprophet --database 2019-01-08-td-UP000005640.fas --accmass --decoy rev_ --decoyprobs --nonparam TMT1_1.pep.xml ./philosopher_linux_amd64 proteinprophet interact-TMT1_1.pep.xml ./philosopher_linux_amd64 filter --pepxml interact-TMT1_1.pep.xml ./philosopher_linux_amd64 filter --pepxml interact-TMT1_1.pep.xml INFO[10:18:51] Executing Filter 20181128 INFO[10:18:51] Processing peptide identification files INFO[10:18:54] 1+ Charge profile decoy=0 target=0 INFO[10:18:54] 2+ Charge profile decoy=540 target=7375 INFO[10:18:54] 3+ Charge profile decoy=710 target=8356 INFO[10:18:54] 4+ Charge profile decoy=177 target=2261 INFO[10:18:54] 5+ Charge profile decoy=0 target=0 INFO[10:18:54] 6+ Charge profile decoy=0 target=0 INFO[10:18:54] Database search results ions=8208 peptides=6996 psms=19419 INFO[10:18:54] Converged to 1.00 % FDR with 16116 PSMs decoy=162 threshold=0.7821 total=16278 INFO[10:18:54] Converged to 0.99 % FDR with 4944 Peptides decoy=49 threshold=0.9156 total=4993 INFO[10:18:54] Converged to 0.99 % FDR with 6038 Ions decoy=60 threshold=0.8988 total=6098 FATA[10:18:54] Database data not available, interrupting processing

prvst commented 5 years ago

it seems that you forgot to run the database command before running the filter. Please take a look at the tutorial examples to see how its done.

https://prvst.github.io/philosopher/tutorial.html

glnegri commented 5 years ago

I did run the database command before but I just tried again and I get the same error.

`-bash-4.2$ ./philosopher_linux_amd64 workspace --clean INFO[13:04:22] Executing Workspace 20181128 WARN[13:04:23] GitHub unreachable for the moment, can't check for versions right now. INFO[13:04:23] Removing workspace INFO[13:04:23] Done -bash-4.2$ ./philosopher_linux_amd64 workspace --init INFO[13:04:23] Executing Workspace 20181128 WARN[13:04:23] GitHub unreachable for the moment, can't check for versions right now. INFO[13:04:23] Creating workspace INFO[13:04:23] Done -bash-4.2$ ./philosopher_linux_amd64 database --id UP000005640 --contam --reviewed INFO[13:04:23] Executing Database 20181128 INFO[13:04:23] Fetching database INFO[13:04:34] Processing decoys INFO[13:04:35] Creating file INFO[13:04:36] Done -bash-4.2$ ./philosopher_linux_amd64 comet --param comet.params TMT1_1.mzML INFO[13:04:36] Executing Comet 20181128 INFO[13:04:36] Indexing spectra: please wait, this can take a few minutes INFO[13:04:36] Indexing TMT1_1.mzML Comet version "2017.01 rev. 2"

Search start: 01/09/2019, 01:05:59 PM

INFO[13:06:44] Done -bash-4.2$ ./philosopher_linuxamd64 peptideprophet --database 2019-01-09-td-UP000005640.fas --accmass --decoy rev --decoyprobs --nonparam TMT1_1.pep.xml INFO[13:06:45] Executing PeptideProphet 20181128 file 1: /projects/ptx_analysis/gnegri/philosopher/TMT1_1.pep.xml processed altogether 39069 results INFO: Results written to file: /projects/ptx_analysis/gnegri/philosopher/interact-TMT1_1.pep.xml

using Accurate Mass Bins Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (Comet) adding ACCMASS mixture distribution init with Comet 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+, 12529 2+, 16050 3+, 5645 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 10611 Decoys, and 23613 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[13:07:29] Done -bash-4.2$ ./philosopher_linux_amd64 proteinprophet interact-TMT1_1.pep.xml INFO[13:07:29] Executing ProteinProphet 20181128 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705221614-exported (Linux-x86_64)) (no FPKM) (using degen pep info) Reading in /projects/ptx_analysis/gnegri/philosopher/interact-TMT1_1.pep.xml... ...read in 0 1+, 7665 2+, 8742 3+, 2344 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 7722 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database /projects/ptx_analysis/gnegri/philosopher/2019-01-09-td-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000 .........:......WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG ...:.........:.........:.........:.........:.........:.........:.........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000 .........:.........:......WARNING: Found the following zero-mass residues in protein entry sp|Q86VQ6|TRXR3_HUMAN : U MERSPPQSPGPGKAGDAPNRRSGHVRGARVLSPPGRRARLSSPGPSRSSEAREELRRHLVGLIERSRVVIFSKSYCPHSTRVKELFSSLGVECNVLELDQVDDGARVQEVLSEITNQKTVPNIFVNKVHVGGCDQTFQAYQSGLLQKLLQEDLAYDYDLIIIGGGSGGLSCAKEAAILGKKVMVLDFVVPSPQGTSWGLGGTCVNVGCIPKKLMHQAALLGQALCDSRKFGWEYNQQVRHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIKATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITSDDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVMVQQLEKGSPGKLKVLAKSTEGTETIEGVYNTVLLAIGRDSCTRKIGLEKIGVKINEKSGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEKCDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLEIYHTLFWPLEWTVAGRENNTCYAKIICNKFDHDRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGEVFTTLEITKSSGLDITQKGCUG ...:.........:.........:.........:.........:.........:.........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........:......... Total: 40894 Computing degenerate peptides for 3907 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 4066 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 4066 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 4066 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 4066 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 4066 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 3646 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating sensitivity...and error tables... Computing MU for 4066 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% INFO: mu=2.2265e-05, db_size=45483563

Finished INFO[13:07:35] Done -bash-4.2$ ./philosopher_linux_amd64 filter --pepxml interact-TMT1_1.pep.xml INFO[13:07:35] Executing Filter 20181128 INFO[13:07:35] Processing peptide identification files INFO[13:07:38] 1+ Charge profile decoy=0 target=0 INFO[13:07:38] 2+ Charge profile decoy=540 target=7375 INFO[13:07:38] 3+ Charge profile decoy=711 target=8356 INFO[13:07:38] 4+ Charge profile decoy=177 target=2261 INFO[13:07:38] 5+ Charge profile decoy=0 target=0 INFO[13:07:38] 6+ Charge profile decoy=0 target=0 INFO[13:07:38] Database search results ions=8208 peptides=6996 psms=19420 INFO[13:07:38] Converged to 1.00 % FDR with 16116 PSMs decoy=162 threshold=0.7821 total=16278 INFO[13:07:38] Converged to 0.99 % FDR with 4944 Peptides decoy=49 threshold=0.9156 total=4993 INFO[13:07:39] Converged to 0.99 % FDR with 6038 Ions decoy=60 threshold=0.8988 total=6098 FATA[13:07:39] Database data not available, interrupting processing `

prvst commented 5 years ago

are you running it through FragPipe ?

glnegri commented 5 years ago

No, just following the example on github.

prvst commented 5 years ago

are you using the latest version ? If not I suggest trying the latest release

glnegri commented 5 years ago

Yes I'm using the 20181128 version.

HYTang69 commented 5 years ago

Hi, I also have the same problem with philosopher 20190116, i.e. fatal error "Database data not available, interrupting processing" during filtering. I also ran the database command, and not using FragPipe.

D:\Users\tangh\Desktop\Philosopher\Test>philosopher filter --pepxml interact-alt ierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml INFO[20:45:38] Executing Filter 20190116 INFO[20:45:38] Processing peptide identification files INFO[20:45:39] 1+ Charge profile decoy=0 target=0 INFO[20:45:39] 2+ Charge profile decoy=798 target=67 93 INFO[20:45:39] 3+ Charge profile decoy=443 target=41 32 INFO[20:45:39] 4+ Charge profile decoy=43 target=644

INFO[20:45:39] 5+ Charge profile decoy=7 target=137 INFO[20:45:39] 6+ Charge profile decoy=10 target=78 INFO[20:45:39] Database search results ions=7850 peptides= 6703 psms=13085 INFO[20:45:39] Converged to 1.00 % FDR with 9549 PSMs decoy=96 threshold= 0.8366 total=9645 INFO[20:45:39] Converged to 0.99 % FDR with 3911 Peptides decoy=39 threshold= 0.917 total=3950 INFO[20:45:39] Converged to 1.00 % FDR with 4888 Ions decoy=49 threshold= 0.9052 total=4937 FATA[20:45:40] Database data not available, interrupting processing

prvst commented 5 years ago

@HYTang69 , did you ran the database command before ? If so, can you paste your command here ?

HYTang69 commented 5 years ago

Here is the database command: D:\Users\tangh\Desktop\Philosopher\Test>philosopher database --id UP000005640 -- contam --reviewed INFO[17:11:41] Executing Database 20190116 INFO[17:11:41] Fetching database INFO[17:12:00] Processing decoys INFO[17:12:01] Creating file INFO[17:12:02] Done

HYTang69 commented 5 years ago

Here is the entire command and response.

Microsoft Windows [Version 6.1.7601] Copyright (c) 2009 Microsoft Corporation. All rights reserved.

C:\Users\tangh>d:

D:>cd D:\Users\tangh\Desktop\Philosopher\Test

D:\Users\tangh\Desktop\Philosopher\Test>philosopher workspace --init INFO[17:10:04] Executing Workspace 20190116 INFO[17:10:04] Creating workspace INFO[17:10:04] Done

D:\Users\tangh\Desktop\Philosopher\Test>philosopher database --id UP000005640 -- contam --reviewed INFO[17:11:41] Executing Database 20190116 INFO[17:11:41] Fetching database INFO[17:12:00] Processing decoys INFO[17:12:01] Creating file INFO[17:12:02] Done

D:\Users\tangh\Desktop\Philosopher\Test>philosopher comet --print INFO[17:12:26] Executing Comet 20190116 INFO[17:12:26] Printing parameter file INFO[17:12:27] Done

D:\Users\tangh\Desktop\Philosopher\Test>philosopher comet --param comet.params A ltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.mzXML INFO[17:17:32] Executing Comet 20190116 FATA[17:17:33] open D:\Users\tangh\Desktop\Philosopher\Test\comet.params: The sy stem cannot find the file specified.

D:\Users\tangh\Desktop\Philosopher\Test>philosopher comet --param comet.params A ltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.mzXML INFO[17:17:48] Executing Comet 20190116 INFO[17:17:48] mz file format not supported for indexing, skipping the indexing

Comet version "2017.01 rev. 2"

Search start: 01/29/2019, 05:17:48 PM

INFO[17:20:03] Done

D:\Users\tangh\Desktop\Philosopher\Test>philosopher peptideprophet --database 20 19-01-29-td-UP000005640.fas --accmass --decoy rev_ --decoyprobs --nonparam Altie riD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.pep.xml INFO[20:33:13] Executing PeptideProphet 20190116 file 1: D:\Users\tangh\Desktop\Philosopher\Test\AltieriD-17-G129-LonP1-Normoxia -Trypsin4ul-HF.pep.xml processed altogether 36424 results INFO: Results written to file: D:\Users\tangh\Desktop\Philosopher\Test\interact- AltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.pep.xml

using Accurate Mass Bins Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (Comet) adding ACCMASS mixture distribution init with Comet stricttrypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, Ionizati on: 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+, 14352 2+, 12821 3+, 4745 4+, 1613 5+, 555 6+, and 0 7+ spectra. Initialising statistical models ... Found 11544 Decoys, and 22542 Non-Decoys Iterations: .........10.........20....... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (7+). model complete after 28 iterations INFO[20:34:14] Done

D:\Users\tangh\Desktop\Philosopher\Test>philosopher proteinprophet interact-alti erid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml INFO[20:42:03] Executing ProteinProphet 20190116 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Pe rl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_N T-x86_64)) (no FPKM) (using degen pep info) Reading in D:/Users/tangh/Desktop/Philosopher/Test/interact-altierid-17-g129-lon p1-normoxia-trypsin4ul-hf.pep.xml... ...read in 0 1+, 7590 2+, 4575 3+, 686 4+, 144 5+, 88 6+, 0 7+ spectra with min prob 0.05

Initializing 7871 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%. ..80%...90%...100% Calculating protein lengths and molecular weights from database d:/Users/tangh/D esktop/Philosopher/Test/2019-01-29-td-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........: .........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........: .........:........WARNING: Found the following zero-mass residues in protein ent ry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGA CFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYL GEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQ CTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTAR MVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLE LGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARL MEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQ AYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEAT EADGADGRQRSYSSKPPLWAAELCVTUSS .37000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........: ......... Total: 40896 Computing degenerate peptides for 3057 proteins: 0%...10%...20%...30%...40%...50 %...60%...70%...80%...90%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 2795 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80 %...90%...100% Calculating sensitivity...and error tables... Computing MU for 3208 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...8 0%...90%...100% INFO: mu=4.1656e-005, db_size=45481909

Finished INFO[20:42:08] Done

D:\Users\tangh\Desktop\Philosopher\Test>philosopher filter --pepxml interact-alt ierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml --protxml interact.prot.xml INFO[20:44:08] Executing Filter 20190116 INFO[20:44:08] Processing peptide identification files INFO[20:44:09] 1+ Charge profile decoy=0 target=0 INFO[20:44:09] 2+ Charge profile decoy=798 target=67 93 INFO[20:44:09] 3+ Charge profile decoy=443 target=41 32 INFO[20:44:09] 4+ Charge profile decoy=43 target=644

INFO[20:44:09] 5+ Charge profile decoy=7 target=137 INFO[20:44:09] 6+ Charge profile decoy=10 target=78 INFO[20:44:09] Database search results ions=7850 peptides= 6703 psms=13085 INFO[20:44:09] Converged to 1.00 % FDR with 9549 PSMs decoy=96 threshold= 0.8366 total=9645 INFO[20:44:09] Converged to 0.99 % FDR with 3911 Peptides decoy=39 threshold= 0.917 total=3950 INFO[20:44:09] Converged to 1.00 % FDR with 4888 Ions decoy=49 threshold= 0.9052 total=4937 INFO[20:44:10] Protein inference results decoy=1112 target=1 683 INFO[20:44:10] Converged to 1.05 % FDR with 381 Proteins decoy=4 threshold=0 .9869 total=385 INFO[20:44:10] 2D FDR estimation: Protein mirror image decoy=381 target=38 1 INFO[20:44:10] Second filtering results ions=5479 peptides= 4377 psms=10395 INFO[20:44:10] Converged to 0.61 % FDR with 10332 PSMs decoy=63 threshold= 0.0518 total=10395 INFO[20:44:10] Converged to 1.00 % FDR with 4286 Peptides decoy=43 threshold= 0.106 total=4329 INFO[20:44:11] Converged to 0.97 % FDR with 5423 Ions decoy=53 threshold= 0.0532 total=5476 FATA[20:44:11] Database data not available, interrupting processing

D:\Users\tangh\Desktop\Philosopher\Test>philosopher filter --pepxml interact-alt ierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml INFO[20:45:38] Executing Filter 20190116 INFO[20:45:38] Processing peptide identification files INFO[20:45:39] 1+ Charge profile decoy=0 target=0 INFO[20:45:39] 2+ Charge profile decoy=798 target=67 93 INFO[20:45:39] 3+ Charge profile decoy=443 target=41 32 INFO[20:45:39] 4+ Charge profile decoy=43 target=644

INFO[20:45:39] 5+ Charge profile decoy=7 target=137 INFO[20:45:39] 6+ Charge profile decoy=10 target=78 INFO[20:45:39] Database search results ions=7850 peptides= 6703 psms=13085 INFO[20:45:39] Converged to 1.00 % FDR with 9549 PSMs decoy=96 threshold= 0.8366 total=9645 INFO[20:45:39] Converged to 0.99 % FDR with 3911 Peptides decoy=39 threshold= 0.917 total=3950 INFO[20:45:39] Converged to 1.00 % FDR with 4888 Ions decoy=49 threshold= 0.9052 total=4937 FATA[20:45:40] Database data not available, interrupting processing

D:\Users\tangh\Desktop\Philosopher\Test>

prvst commented 5 years ago

@HYTang69 @5utr I just released an updated version with a fix to this problem, please try it and let me know.

Thanks for reporting.

HYTang69 commented 5 years ago

Unfortunately, the updated version did not fix the problem. Still get the same error.

Microsoft Windows [Version 6.1.7601] Copyright (c) 2009 Microsoft Corporation. All rights reserved.

C:\Users\tangh>d:

D:>cd D:\Users\tangh\Desktop\Philosopher\Test2

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher workspace --init INFO[12:03:48] Executing Workspace 20190204 INFO[12:03:49] Creating workspace INFO[12:03:49] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher database --id UP000005640 - -contam --reviewed INFO[12:04:04] Executing Database 20190204 INFO[12:04:04] Fetching database INFO[12:04:17] Processing decoys INFO[12:04:17] Creating file INFO[12:04:18] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher comet --print INFO[12:04:49] Executing Comet 20190204 INFO[12:04:50] Printing parameter file INFO[12:04:50] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher comet --param comet.params AltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.mzXML INFO[12:06:55] Executing Comet 20190204 INFO[12:06:55] mz file format not supported for indexing, skipping the indexing

Comet version "2017.01 rev. 2"

Search start: 02/05/2019, 12:06:56 PM

INFO[12:09:16] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher peptideprophet --database 2 019-02-05-td-UP000005640.fas --accmass --decoy rev_ --decoyprobs --nonparam Alti eriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.pep.xml INFO[12:09:41] Executing PeptideProphet 20190204 file 1: D:\Users\tangh\Desktop\Philosopher\Test2\AltieriD-17-G129-LonP1-Normoxi a-Trypsin4ul-HF.pep.xml processed altogether 36424 results INFO: Results written to file: D:\Users\tangh\Desktop\Philosopher\Test2\interact -AltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.pep.xml

using Accurate Mass Bins Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (Comet) adding ACCMASS mixture distribution init with Comet stricttrypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, Ionizati on: 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+, 14352 2+, 12821 3+, 4745 4+, 1613 5+, 555 6+, and 0 7+ spectra. Initialising statistical models ... Found 11544 Decoys, and 22542 Non-Decoys Iterations: .........10.........20....... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (7+). model complete after 28 iterations INFO[12:10:49] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher proteinprophet interact-alt ierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml INFO[12:11:13] Executing ProteinProphet 20190204 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Pe rl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_N T-x86_64)) (no FPKM) (using degen pep info) Reading in D:/Users/tangh/Desktop/Philosopher/Test2/interact-altierid-17-g129-lo np1-normoxia-trypsin4ul-hf.pep.xml... ...read in 0 1+, 7590 2+, 4575 3+, 686 4+, 144 5+, 88 6+, 0 7+ spectra with min prob 0.05

Initializing 7871 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%. ..80%...90%...100% Calculating protein lengths and molecular weights from database d:/Users/tangh/D esktop/Philosopher/Test2/2019-02-05-td-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........: .........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........: .........:........WARNING: Found the following zero-mass residues in protein ent ry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGA CFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYL GEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQ CTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTAR MVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLE LGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARL MEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQ AYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEAT EADGADGRQRSYSSKPPLWAAELCVTUSS .37000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........: ......... Total: 40896 Computing degenerate peptides for 3057 proteins: 0%...10%...20%...30%...40%...50 %...60%...70%...80%...90%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 2795 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80 %...90%...100% Calculating sensitivity...and error tables... Computing MU for 3208 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...8 0%...90%...100% INFO: mu=4.1656e-005, db_size=45481909

Finished INFO[12:11:18] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher filter --pepxml interact-al tierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml --protxml interact.prot.xml INFO[12:11:49] Executing Filter 20190204 INFO[12:11:49] Processing peptide identification files INFO[12:11:50] 1+ Charge profile decoy=0 target=0 INFO[12:11:50] 2+ Charge profile decoy=798 target=67 93 INFO[12:11:50] 3+ Charge profile decoy=443 target=41 32 INFO[12:11:50] 4+ Charge profile decoy=43 target=644

INFO[12:11:50] 5+ Charge profile decoy=7 target=137 INFO[12:11:50] 6+ Charge profile decoy=10 target=78 INFO[12:11:50] Database search results ions=7850 peptides= 6703 psms=13085 INFO[12:11:50] Converged to 1.00 % FDR with 9549 PSMs decoy=96 threshold= 0.8366 total=9645 INFO[12:11:50] Converged to 0.99 % FDR with 3911 Peptides decoy=39 threshold= 0.917 total=3950 INFO[12:11:50] Converged to 1.00 % FDR with 4888 Ions decoy=49 threshold= 0.9052 total=4937 INFO[12:11:51] Protein inference results decoy=1112 target=1 683 INFO[12:11:51] Converged to 1.05 % FDR with 381 Proteins decoy=4 threshold=0 .9869 total=385 INFO[12:11:51] 2D FDR estimation: Protein mirror image decoy=381 target=38 1 INFO[12:11:51] Second filtering results ions=5479 peptides= 4377 psms=10395 INFO[12:11:51] Converged to 0.61 % FDR with 10332 PSMs decoy=63 threshold= 0.0518 total=10395 INFO[12:11:51] Converged to 1.00 % FDR with 4286 Peptides decoy=43 threshold= 0.106 total=4329 INFO[12:11:51] Converged to 0.97 % FDR with 5423 Ions decoy=53 threshold= 0.0532 total=5476 FATA[12:11:52] Database data not available, interrupting processing

D:\Users\tangh\Desktop\Philosopher\Test2>

From: Felipe Leprevost notifications@github.com Sent: Monday, February 4, 2019 1:48 PM To: Nesvilab/philosopher Cc: HYTang69; Mention Subject: Re: [Nesvilab/philosopher] Filtering step fails (#29)

@HYTang69https://github.com/HYTang69 @5utrhttps://github.com/5utr I just released an updated version with a fix to this problem, please try it and let me know.

Thanks for reporting.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/philosopher/issues/29#issuecomment-460365054, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AhXZXB8Qim3aPdEZ1iyzaO9SQ1LSPujvks5vKICVgaJpZM4Z4Ce8.

HYTang69 commented 5 years ago

Unfortunately the new version still gives the same error:

Microsoft Windows [Version 6.1.7601] Copyright (c) 2009 Microsoft Corporation. All rights reserved.

C:\Users\tangh>d:

D:>cd D:\Users\tangh\Desktop\Philosopher\Test2

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher workspace --init INFO[12:03:48] Executing Workspace 20190204 INFO[12:03:49] Creating workspace INFO[12:03:49] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher database --id UP000005640 - -contam --reviewed INFO[12:04:04] Executing Database 20190204 INFO[12:04:04] Fetching database INFO[12:04:17] Processing decoys INFO[12:04:17] Creating file INFO[12:04:18] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher comet --print INFO[12:04:49] Executing Comet 20190204 INFO[12:04:50] Printing parameter file INFO[12:04:50] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher comet --param comet.params AltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.mzXML INFO[12:06:55] Executing Comet 20190204 INFO[12:06:55] mz file format not supported for indexing, skipping the indexing

Comet version "2017.01 rev. 2"

Search start: 02/05/2019, 12:06:56 PM

INFO[12:09:16] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher peptideprophet --database 2 019-02-05-td-UP000005640.fas --accmass --decoy rev_ --decoyprobs --nonparam Alti eriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.pep.xml INFO[12:09:41] Executing PeptideProphet 20190204 file 1: D:\Users\tangh\Desktop\Philosopher\Test2\AltieriD-17-G129-LonP1-Normoxi a-Trypsin4ul-HF.pep.xml processed altogether 36424 results INFO: Results written to file: D:\Users\tangh\Desktop\Philosopher\Test2\interact -AltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.pep.xml

using Accurate Mass Bins Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (Comet) adding ACCMASS mixture distribution init with Comet stricttrypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, Ionizati on: 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+, 14352 2+, 12821 3+, 4745 4+, 1613 5+, 555 6+, and 0 7+ spectra. Initialising statistical models ... Found 11544 Decoys, and 22542 Non-Decoys Iterations: .........10.........20....... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (7+). model complete after 28 iterations INFO[12:10:49] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher proteinprophet interact-alt ierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml INFO[12:11:13] Executing ProteinProphet 20190204 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Pe rl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_N T-x86_64)) (no FPKM) (using degen pep info) Reading in D:/Users/tangh/Desktop/Philosopher/Test2/interact-altierid-17-g129-lo np1-normoxia-trypsin4ul-hf.pep.xml... ...read in 0 1+, 7590 2+, 4575 3+, 686 4+, 144 5+, 88 6+, 0 7+ spectra with min prob 0.05

Initializing 7871 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%. ..80%...90%...100% Calculating protein lengths and molecular weights from database d:/Users/tangh/D esktop/Philosopher/Test2/2019-02-05-td-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........: .........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........: .........:........WARNING: Found the following zero-mass residues in protein ent ry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGA CFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYL GEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQ CTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTAR MVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLE LGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARL MEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQ AYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEAT EADGADGRQRSYSSKPPLWAAELCVTUSS .37000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........: ......... Total: 40896 Computing degenerate peptides for 3057 proteins: 0%...10%...20%...30%...40%...50 %...60%...70%...80%...90%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 2795 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80 %...90%...100% Calculating sensitivity...and error tables... Computing MU for 3208 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...8 0%...90%...100% INFO: mu=4.1656e-005, db_size=45481909

Finished INFO[12:11:18] Done

D:\Users\tangh\Desktop\Philosopher\Test2>philosopher filter --pepxml interact-al tierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml --protxml interact.prot.xml INFO[12:11:49] Executing Filter 20190204 INFO[12:11:49] Processing peptide identification files INFO[12:11:50] 1+ Charge profile decoy=0 target=0 INFO[12:11:50] 2+ Charge profile decoy=798 target=67 93 INFO[12:11:50] 3+ Charge profile decoy=443 target=41 32 INFO[12:11:50] 4+ Charge profile decoy=43 target=644

INFO[12:11:50] 5+ Charge profile decoy=7 target=137 INFO[12:11:50] 6+ Charge profile decoy=10 target=78 INFO[12:11:50] Database search results ions=7850 peptides= 6703 psms=13085 INFO[12:11:50] Converged to 1.00 % FDR with 9549 PSMs decoy=96 threshold= 0.8366 total=9645 INFO[12:11:50] Converged to 0.99 % FDR with 3911 Peptides decoy=39 threshold= 0.917 total=3950 INFO[12:11:50] Converged to 1.00 % FDR with 4888 Ions decoy=49 threshold= 0.9052 total=4937 INFO[12:11:51] Protein inference results decoy=1112 target=1 683 INFO[12:11:51] Converged to 1.05 % FDR with 381 Proteins decoy=4 threshold=0 .9869 total=385 INFO[12:11:51] 2D FDR estimation: Protein mirror image decoy=381 target=38 1 INFO[12:11:51] Second filtering results ions=5479 peptides= 4377 psms=10395 INFO[12:11:51] Converged to 0.61 % FDR with 10332 PSMs decoy=63 threshold= 0.0518 total=10395 INFO[12:11:51] Converged to 1.00 % FDR with 4286 Peptides decoy=43 threshold= 0.106 total=4329 INFO[12:11:51] Converged to 0.97 % FDR with 5423 Ions decoy=53 threshold= 0.0532 total=5476 FATA[12:11:52] Database data not available, interrupting processing

D:\Users\tangh\Desktop\Philosopher\Test2>

prvst commented 5 years ago

@HYTang69 I got the wrong binaries uploaded by mistake, I replaced them last night, they have the same name and version. Could you download Philosopher and try again ?

HYTang69 commented 5 years ago

Just downloaded the new version, but it still failed at the same place.

Microsoft Windows [Version 6.1.7601] Copyright (c) 2009 Microsoft Corporation. All rights reserved.

C:\Users\tangh>d:

D:>cd D:\Users\tangh\Desktop\Philosopher\Test3

D:\Users\tangh\Desktop\Philosopher\Test3>philosopher workspace --init INFO[22:11:34] Executing Workspace 20190204 INFO[22:11:34] Creating workspace INFO[22:11:34] Done

D:\Users\tangh\Desktop\Philosopher\Test3>philosopher database --id UP000005640 - -contam --reviewed INFO[22:12:09] Executing Database 20190204 INFO[22:12:09] Fetching database INFO[22:12:20] Processing decoys INFO[22:12:20] Creating file INFO[22:12:21] Done

D:\Users\tangh\Desktop\Philosopher\Test3>philosopher comet --param comet.params AltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.mzXML INFO[22:13:18] Executing Comet 20190204 INFO[22:13:18] mz file format not supported for indexing, skipping the indexing

Comet version "2017.01 rev. 2"

Search start: 02/05/2019, 10:13:18 PM

INFO[22:15:57] Done

D:\Users\tangh\Desktop\Philosopher\Test3>philosopher peptideprophet --database 2 019-02-05-td-UP000005640.fas --accmass --decoy rev_ --decoyprobs --nonparam Alti eriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.pep.xml INFO[22:16:07] Executing PeptideProphet 20190204 file 1: D:\Users\tangh\Desktop\Philosopher\Test3\AltieriD-17-G129-LonP1-Normoxi a-Trypsin4ul-HF.pep.xml processed altogether 36424 results INFO: Results written to file: D:\Users\tangh\Desktop\Philosopher\Test3\interact -AltieriD-17-G129-LonP1-Normoxia-Trypsin4ul-HF.pep.xml

using Accurate Mass Bins Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (Comet) adding ACCMASS mixture distribution init with Comet stricttrypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: Q Exactive, Ionizati on: 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+, 14352 2+, 12821 3+, 4745 4+, 1613 5+, 555 6+, and 0 7+ spectra. Initialising statistical models ... Found 11544 Decoys, and 22542 Non-Decoys Iterations: .........10.........20....... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (7+). model complete after 28 iterations INFO[22:17:02] Done

D:\Users\tangh\Desktop\Philosopher\Test3>philosopher proteinprophet interact-alt ierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml INFO[22:17:13] Executing ProteinProphet 20190204 ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Pe rl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705191533-7588 (Windows_N T-x86_64)) (no FPKM) (using degen pep info) Reading in D:/Users/tangh/Desktop/Philosopher/Test3/interact-altierid-17-g129-lo np1-normoxia-trypsin4ul-hf.pep.xml... ...read in 0 1+, 7590 2+, 4575 3+, 686 4+, 144 5+, 88 6+, 0 7+ spectra with min prob 0.05

Initializing 7871 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%. ..80%...90%...100% Calculating protein lengths and molecular weights from database d:/Users/tangh/D esktop/Philosopher/Test3/2019-02-05-td-UP000005640.fas .........:.........:.........:.........:.........:.........:.........:.........: .........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........7000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........8000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........9000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........10000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........11000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........12000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........13000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........14000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........15000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........16000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........17000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........18000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........19000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........20000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........21000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........22000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........23000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........24000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........25000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........26000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........27000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........28000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........29000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........30000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........31000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........32000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........33000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........34000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........35000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........36000 .........:.........:.........:.........:.........:.........:.........:.........: .........:........WARNING: Found the following zero-mass residues in protein ent ry sp|Q9BVL4|SELO_HUMAN : U MAVYRAALGASLAAARLLPLGRCSPSPAPRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGA CFTRVQPTPLRQPRLVALSEPALALLGLGAPPAREAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYL GEVCTATGERWELQLKGAGPTPFSRQADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQ CTVVLRVASTFIRFGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFREVTRRTAR MVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDRYDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLE LGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTGADFTNTFYLLSSFPVELESPGLAEFLARL MEQCASLEELRLAFRPQMDPRQLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQ AYRARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEVRRVLKLLETPYHCEAGAATDAEAT EADGADGRQRSYSSKPPLWAAELCVTUSS .37000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........38000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........39000 .........:.........:.........:.........:.........:.........:.........:.........: .........:.........40000 .........:.........:.........:.........:.........:.........:.........:.........: ......... Total: 40896 Computing degenerate peptides for 3057 proteins: 0%...10%...20%...30%...40%...50 %...60%...70%...80%...90%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 3208 proteins. Loop 1: 0%...20%...40%...60%...80%.. .100% Loop 2: 0%...20%...40%...60%...80%...100% Computing 2795 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80 %...90%...100% Calculating sensitivity...and error tables... Computing MU for 3208 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...8 0%...90%...100% INFO: mu=4.1656e-005, db_size=45481909

Finished INFO[22:17:20] Done

D:\Users\tangh\Desktop\Philosopher\Test3>philosopher filter --pepxml interact-al tierid-17-g129-lonp1-normoxia-trypsin4ul-hf.pep.xml --protxml interact.prot.xml INFO[22:17:42] Executing Filter 20190204 INFO[22:17:42] Processing peptide identification files INFO[22:17:44] 1+ Charge profile decoy=0 target=0 INFO[22:17:44] 2+ Charge profile decoy=798 target=67 93 INFO[22:17:44] 3+ Charge profile decoy=443 target=41 32 INFO[22:17:44] 4+ Charge profile decoy=43 target=644

INFO[22:17:44] 5+ Charge profile decoy=7 target=137 INFO[22:17:44] 6+ Charge profile decoy=10 target=78 INFO[22:17:44] Database search results ions=7850 peptides= 6703 psms=13085 INFO[22:17:44] Converged to 1.00 % FDR with 9549 PSMs decoy=96 threshold= 0.8366 total=9645 INFO[22:17:44] Converged to 0.99 % FDR with 3911 Peptides decoy=39 threshold= 0.917 total=3950 INFO[22:17:44] Converged to 1.00 % FDR with 4888 Ions decoy=49 threshold= 0.9052 total=4937 INFO[22:17:45] Protein inference results decoy=1112 target=1 683 INFO[22:17:45] Converged to 1.05 % FDR with 381 Proteins decoy=4 threshold=0 .9869 total=385 INFO[22:17:45] 2D FDR estimation: Protein mirror image decoy=381 target=38 1 INFO[22:17:45] Second filtering results ions=5479 peptides= 4377 psms=10395 INFO[22:17:45] Converged to 0.61 % FDR with 10332 PSMs decoy=63 threshold= 0.0518 total=10395 INFO[22:17:45] Converged to 1.00 % FDR with 4286 Peptides decoy=43 threshold= 0.106 total=4329 INFO[22:17:45] Converged to 0.97 % FDR with 5423 Ions decoy=53 threshold= 0.0532 total=5476 FATA[22:17:46] Database data not available, interrupting processing

D:\Users\tangh\Desktop\Philosopher\Test3>

prvst commented 5 years ago

I believe to have fixed the issue with the release from today, please give it a try and let me know. Thanks for reporting the issue.

glnegri commented 5 years ago

Still getting the same error with today's release:

-bash-4.1$ ./philosopher_linux_amd64 filter --pepxml interact-TMT1_1.pep.xml INFO[10:55:42] Executing Filter 20190206 INFO[10:55:42] Processing peptide identification files INFO[10:55:45] 1+ Charge profile decoy=0 target=0 INFO[10:55:45] 2+ Charge profile decoy=540 target=7375 INFO[10:55:45] 3+ Charge profile decoy=711 target=8356 INFO[10:55:45] 4+ Charge profile decoy=177 target=2261 INFO[10:55:45] 5+ Charge profile decoy=0 target=0 INFO[10:55:45] 6+ Charge profile decoy=0 target=0 INFO[10:55:45] Database search results ions=8208 peptides=6996 psms=19420 INFO[10:55:45] Converged to 1.00 % FDR with 16116 PSMs decoy=162 threshold=0.7821 total=16278 INFO[10:55:45] Converged to 0.99 % FDR with 4944 Peptides decoy=49 threshold=0.9156 total=4993 INFO[10:55:45] Converged to 0.99 % FDR with 6038 Ions decoy=60 threshold=0.8988 total=6098 FATA[10:55:45] Database data not available, interrupting processing

prvst commented 5 years ago

did you removed the folder and started from the beginning?

glnegri commented 5 years ago

Yes started from scratch with the new release.

HYTang69 commented 5 years ago

Ok. Today's version works for me. No more "Database data not available, interrupting processing" error. Thanks. Would like to continue with the tutorial but the link (https://github.com/Nesvilab/philosopher/blob/master/tutorial.md) is broken.

glnegri commented 5 years ago

It works for me too. In the last try I didn't regenerate the database after --init. Does it mean the same reference proteome cannot be use for multiple analysis but it has to be generate every time?

prvst commented 5 years ago

No, the reference proteome can be used for multiple analysis. The reason I asked you to run those commands again is because the bug you found was in that function. Normally, the database creation / annotation needs to be executed only once.