The execution of the Philosopher was unexpectedly stuck. #541
Description
Describe the bug
Windows system: when using Fragpipe (version 20.0) to perform a database search with DDA data.
the program proceeds normally until it reaches the Philosopher module, where it appears to be stuck without generating an error message (After waiting for about 5-12 hours, there was no further progress).
The process becomes stuck at a certain step for an extended period.
To Reproduce
When restart program, the files causing the delay vary, suggesting that the issue is not attributable to any specific raw mass spectrometry file. Furthermore, files that had previously undergone successful searches are also unable to complete the full processing workflow (default workflow).
Various attempts were made to resolve the issue, including switching the version of Philosopher (tested versions v5.1.0 and v5.0.0), as well as using different types of data (both Bruker and Thermo formats), but none of these measures resolved the problem. Same or different files were also failed in different computer.
LogFile
There are three logsfile.
the log file of dealing raw files generated by timsTOF
Computing degenerate peptides for 18017 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 18358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 18358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 18358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 18358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 18358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 18358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 18358 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
Computing MU for 18358 proteins: 0%...10%...20%INFO: mu=0.000100163, db_size=45707758
...30%...40%...50%...60%...70%...80%...90%...100%
INFO[10:44:08] Done
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: E:\HCX\TOF\Res\TOF1_DDA_20240308_293T_100ng_60min_column0305_QC_RA8_1_6211]
C:\Software\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate E:\HCX\2025-08-26-decoys-contam-250625_uniprote_human_reviewed_IRT_20432.fasta.fas --prefix rev_
INFO[10:44:08] Executing Database v5.1.0
INFO[10:44:08] Annotating the database
INFO[10:44:08] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: E:\HCX\TOF\Res\TOF1_DDA_20240308_293T_100ng_60min_column0305_QC_RA8_1_6211]
C:\Software\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\HCX\TOF\Res\TOF1_DDA_20240308_293T_100ng_60min_column0305_QC_RA8_1_6211 --protxml E:\HCX\TOF\Res\combined.prot.xml --razor
INFO[10:44:08] Executing Filter v5.1.0
INFO[10:44:08] Processing peptide identification files
INFO[10:44:08] Parsing E:\HCX\TOF\Res\TOF1_DDA_20240308_293T_100ng_60min_column0305_QC_RA8_1_6211\interact-TOF1_DDA_20240308_293T_100ng_60min_column0305_QC_RA8_1_6211.pep.xml
### the log file of dealing raw files generated by E480
PhilosopherFilter [Work dir: E:\HCX\4801\Res\QC_E4801_240702]
C:\Software\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\HCX\4801\Res\QC_E4801_240702 --protxml E:\HCX\4801\Res\combined.prot.xml --razor
INFO[17:40:24] Executing Filter v5.1.0
INFO[17:40:24] Processing peptide identification files
INFO[17:40:24] Parsing E:\HCX\4801\Res\QC_E4801_240702\interact-QC_E4801_240702_DDA_293T_500ng_120min_R1.pep.xml
INFO[17:40:30] 1+ Charge profile decoy=0 target=0
INFO[17:40:30] 2+ Charge profile decoy=594 target=57752
INFO[17:40:30] 3+ Charge profile decoy=162 target=30640
INFO[17:40:30] 4+ Charge profile decoy=16 target=3319
INFO[17:40:30] 5+ Charge profile decoy=4 target=365
INFO[17:40:30] 6+ Charge profile decoy=1 target=33
INFO[17:40:30] Database search results ions=78234 peptides=72344 psms=92886
INFO[17:40:30] Converged to 0.84 % FDR with 92109 PSMs decoy=777 threshold=0.500003 total=92886
INFO[17:40:30] Converged to 1.00 % FDR with 71536 Peptides decoy=715 threshold=0.521573 total=72251
INFO[17:40:30] Converged to 0.98 % FDR with 77474 Ions decoy=760 threshold=0.500003 total=78234
INFO[17:40:30] Protein inference results decoy=3615 target=10993
INFO[17:40:30] Converged to 0.99 % FDR with 8480 Proteins decoy=84 threshold=0.9839 total=8564
INFO[17:40:31] Applying sequential FDR estimation ions=77120 peptides=71231 psms=91753
INFO[17:40:31] Converged to 0.04 % FDR with 91717 PSMs decoy=36 threshold=0.500776 total=91753
INFO[17:40:31] Converged to 0.05 % FDR with 71197 Peptides decoy=34 threshold=0.500776 total=71231
INFO[17:40:31] Converged to 0.04 % FDR with 77086 Ions decoy=34 threshold=0.500776 total=77120
INFO[17:40:31] Post processing identifications
INFO[17:40:32] Assigning protein identifications to layers
INFO[17:40:46] Processing protein inference
INFO[17:40:46] Synchronizing PSMs and proteins
INFO[17:40:47] Final report numbers after FDR filtering, and post-processing ions=77086 peptides=71197 proteins=7583 psms=91717
INFO[17:40:47] Saving
INFO[17:40:48] Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherFilter [Work dir: E:\HCX\4801\Res\QC_E4801_240705]
C:\Software\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml E:\HCX\4801\Res\QC_E4801_240705 --protxml E:\HCX\4801\Res\combined.prot.xml --probin E:\HCX\4801\Res\QC_E4801_240702 --razor
INFO[17:40:48] Executing Filter v5.1.0
INFO[17:40:48] Fetching protein inference from E:\HCX\4801\Res\QC_E4801_240702
INFO[17:40:48] Processing peptide identification files
INFO[17:40:48] Parsing E:\HCX\4801\Res\QC_E4801_240705\interact-QC_E4801_240705_DDA_293T_500ng_120min_R1.pep.xml
the log file of dealing raw files generated by E480(different computer)
java -cp D:\softwares\Fragpipe-20.0\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete E:\HCX\E4801\Result_MS\QC_E4801_240702_DDA_293T_500ng_120min_R1\QC_E4801_240702_DDA_293T_500ng_120min_R1_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: E:\HCX\E4801\Result_MS\QC_E4801_240705_DDA_293T_500ng_120min_R1]
java -cp D:\softwares\Fragpipe-20.0\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QC_E4801_240705_DDA_293T_500ng_120min_R1.pin QC_E4801_240705_DDA_293T_500ng_120min_R1 QC_E4801_240705_DDA_293T_500ng_120min_R1_percolator_target_psms.tsv QC_E4801_240705_DDA_293T_500ng_120min_R1_percolator_decoy_psms.tsv interact-QC_E4801_240705_DDA_293T_500ng_120min_R1 DDA 0.5 E:\HCX\E4801\QC_E4801_240705_DDA_293T_500ng_120min_R1_uncalibrated.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
java -cp D:\softwares\Fragpipe-20.0\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete E:\HCX\E4801\Result_MS\QC_E4801_240705_DDA_293T_500ng_120min_R1\QC_E4801_240705_DDA_293T_500ng_120min_R1_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
java -cp D:\softwares\Fragpipe-20.0\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete E:\HCX\E4801\Result_MS\QC_E4801_240705_DDA_293T_500ng_120min_R1\QC_E4801_240705_DDA_293T_500ng_120min_R1_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: E:\HCX\E4801\Result_MS]
D:\softwares\philosopher_v5.0.0_windows_amd64_3\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined E:\HCX\E4801\Result_MS\filelist_proteinprophet.txt
INFO[15:35:48] Executing ProteinProphet v5.0.0
Please complete the following information:
- OS: [Windows]
- Fragpipe [20.0]
- MsFragger [3.8]
- philosopher [v5.1.0 and v5.0.0)]