DIA-NN 1.9.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Jul 15 2024 09:42:01
Current date and time: Wed Apr 22 15:25:30 2026
Logical CPU cores: 128
/home/robbe/bin/diann-1.9.1/diann-linux --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d --fasta /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta --out /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.1/report.tsv --threads 32 --missed-cleavages 2 --min-pep-len 7 --max-pep-len 30 --mass-acc 20 --mass-acc-ms1 20 --qvalue 0.01 --protein-qvalue 0.01 --min-pr-charge 2 --max-pr-charge 4 --min-pr-mz 400 --max-pr-mz 1200 --min-fr-mz 200 --max-fr-mz 2000 --unimod4 --var-mod UniMod:35,15.994915,M --gen-spec-lib --fasta-search 

Thread number set to 32
Maximum number of missed cleavages set to 2
Min peptide length set to 7
Max peptide length set to 30
Output will be filtered at 0.01 FDR
Output will be filtered at 0.01 protein-level FDR
Min precursor charge set to 2
Max precursor charge set to 4
Min precursor m/z set to 400
Max precursor m/z set to 1200
Min fragment m/z set to 200
Max fragment m/z set to 2000
Cysteine carbamidomethylation enabled as a fixed modification
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
A spectral library will be generated
DIA-NN will carry out FASTA digest for in silico lib generation
Mass accuracy will be fixed to 2e-05 (MS2) and 2e-05 (MS1)
WARNING: FASTA digest mode enabled and raw data are provided, turning on deep learning spectra/RT/IM prediction
WARNING: it is strongly recommended to first generate an in silico-predicted library in a separate pipeline step and then use it to process the raw data, now without activating FASTA digest
WARNING: peptidoform scoring enabled because variable modifications have been declared; to disable, use --no-peptidoforms
The following variable modifications will be scored: UniMod:35 

6 files will be processed
[0:00] Loading FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:06] Processing FASTA
[0:14] Assembling elution groups
[0:24] 8103720 precursors generated
[0:24] Protein names missing for some isoforms
[0:24] Gene names missing for some isoforms
[0:24] Library contains 31680 proteins, and 0 genes
[0:30] [0:45] [6:14] [6:57] [7:00] [7:03] Saving the library to report-lib.predicted.speclib
[7:26] Initialising library
[7:41] Loading spectral library report-lib.predicted.speclib
[7:48] Library annotated with sequence database(s): /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[7:50] Spectral library loaded: 31832 protein isoforms, 43199 protein groups and 8103720 precursors in 3825450 elution groups.
[7:50] Loading protein annotations from FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[7:50] Annotating library proteins with information from the FASTA database
[7:50] Protein names missing for some isoforms
[7:50] Gene names missing for some isoforms
[7:50] Library contains 31680 proteins, and 0 genes
[7:58] [8:10] [13:43] [14:26] [14:29] [14:33] Saving the library to report-lib.predicted.speclib
[14:56] Initialising library

[15:11] File #1/6
[15:11] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
WARNING: for most Slice/DIA-PASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to values in the range 10-15 ppm
[15:30] 7127359 library precursors are potentially detectable
[15:31] Processing...
[16:59] RT window set to 1.98876
[16:59] Ion mobility window set to 0.0409563
[16:59] Peak width: 3.94
[16:59] Scan window radius set to 8
[16:59] Recommended MS1 mass accuracy setting: 14.8689 ppm
[29:31] Removing low confidence identifications
[35:31] Precursors at 1% peptidoform FDR: 67387
[35:33] Removing interfering precursors
[35:38] Training neural networks: 140607 targets, 88601 decoys
[35:43] Number of IDs at 0.01 FDR: 103263
[35:50] Precursors at 1% peptidoform FDR: 69002
[35:51] Calculating protein q-values
[35:51] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[35:51] Quantification
[35:52] Precursors with monitored PTMs at 1% FDR: 256 out of 35902 considered
[35:52] Unmodified precursors with monitored PTM sites at 1% FDR: 12274
[35:52] Precursors with PTMs localised (when required) with > 90% confidence: 249 out of 256
[35:54] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d.quant

[35:54] File #2/6
[35:54] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
[36:14] 7127359 library precursors are potentially detectable
[36:15] Processing...
[37:51] RT window set to 2.12532
[37:51] Ion mobility window set to 0.0397778
[37:52] Recommended MS1 mass accuracy setting: 15.1789 ppm
[51:02] Removing low confidence identifications
[57:22] Precursors at 1% peptidoform FDR: 69199
[57:24] Removing interfering precursors
[57:29] Training neural networks: 145026 targets, 91561 decoys
[57:34] Number of IDs at 0.01 FDR: 105837
[57:41] Precursors at 1% peptidoform FDR: 69484
[57:42] Calculating protein q-values
[57:43] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[57:43] Quantification
[57:43] Precursors with monitored PTMs at 1% FDR: 346 out of 36625 considered
[57:43] Unmodified precursors with monitored PTM sites at 1% FDR: 12188
[57:43] Precursors with PTMs localised (when required) with > 90% confidence: 338 out of 346
[57:45] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d.quant

[57:45] File #3/6
[57:45] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
[58:06] 7127359 library precursors are potentially detectable
[58:07] Processing...
[60:03] RT window set to 2.0149
[60:03] Ion mobility window set to 0.0403412
[60:04] Recommended MS1 mass accuracy setting: 14.7568 ppm
[73:20] Removing low confidence identifications
[79:27] Precursors at 1% peptidoform FDR: 69425
[79:29] Removing interfering precursors
[79:34] Training neural networks: 144683 targets, 91899 decoys
[79:38] Number of IDs at 0.01 FDR: 107335
[79:46] Precursors at 1% peptidoform FDR: 71006
[79:47] Calculating protein q-values
[79:47] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[79:47] Quantification
[79:48] Precursors with monitored PTMs at 1% FDR: 327 out of 37571 considered
[79:48] Unmodified precursors with monitored PTM sites at 1% FDR: 12502
[79:48] Precursors with PTMs localised (when required) with > 90% confidence: 319 out of 327
[79:49] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d.quant

[79:49] File #4/6
[79:49] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
[80:09] 7127359 library precursors are potentially detectable
[80:10] Processing...
[81:48] RT window set to 2.13015
[81:48] Ion mobility window set to 0.0394325
[81:48] Recommended MS1 mass accuracy setting: 14.899 ppm
[94:49] Removing low confidence identifications
[100:59] Precursors at 1% peptidoform FDR: 67554
[101:01] Removing interfering precursors
[101:06] Training neural networks: 139231 targets, 88397 decoys
[101:11] Number of IDs at 0.01 FDR: 104426
[101:18] Precursors at 1% peptidoform FDR: 70526
[101:18] Calculating protein q-values
[101:19] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[101:19] Quantification
[101:19] Precursors with monitored PTMs at 1% FDR: 440 out of 36506 considered
[101:19] Unmodified precursors with monitored PTM sites at 1% FDR: 12639
[101:20] Precursors with PTMs localised (when required) with > 90% confidence: 428 out of 440
[101:21] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d.quant

[101:21] File #5/6
[101:21] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
[101:40] 7127359 library precursors are potentially detectable
[101:41] Processing...
[103:18] RT window set to 2.00429
[103:18] Ion mobility window set to 0.0420096
[103:18] Recommended MS1 mass accuracy setting: 13.719 ppm
[115:48] Removing low confidence identifications
[121:44] Precursors at 1% peptidoform FDR: 68667
[121:45] Removing interfering precursors
[121:50] Training neural networks: 141421 targets, 89821 decoys
[121:55] Number of IDs at 0.01 FDR: 104774
[122:03] Precursors at 1% peptidoform FDR: 71299
[122:03] Calculating protein q-values
[122:04] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[122:04] Quantification
[122:05] Precursors with monitored PTMs at 1% FDR: 574 out of 36314 considered
[122:05] Unmodified precursors with monitored PTM sites at 1% FDR: 12905
[122:05] Precursors with PTMs localised (when required) with > 90% confidence: 566 out of 574
[122:06] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d.quant

[122:06] File #6/6
[122:06] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
[122:26] 7127359 library precursors are potentially detectable
[122:27] Processing...
[124:06] RT window set to 2.19242
[124:06] Ion mobility window set to 0.0418804
[124:06] Recommended MS1 mass accuracy setting: 15.3738 ppm
[137:35] Removing low confidence identifications
[143:55] Precursors at 1% peptidoform FDR: 68828
[143:57] Removing interfering precursors
[144:02] Training neural networks: 141732 targets, 91223 decoys
[144:07] Number of IDs at 0.01 FDR: 106141
[144:14] Precursors at 1% peptidoform FDR: 71950
[144:15] Calculating protein q-values
[144:16] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[144:16] Quantification
[144:16] Precursors with monitored PTMs at 1% FDR: 393 out of 36852 considered
[144:16] Unmodified precursors with monitored PTM sites at 1% FDR: 12919
[144:16] Precursors with PTMs localised (when required) with > 90% confidence: 385 out of 393
[144:18] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d.quant

[144:18] Cross-run analysis
[144:18] Reading quantification information: 6 files
[144:25] Quantifying peptides
[145:29] Quantification parameters: 0.323847, 0.00155639, 0.00324421, 0.0773976, 0.137593, 0.132574, 0.269821, 0.0134523, 0.013851, 0.120274, 0.0947079, 0.106962, 0.166513, 0.0848316, 0.0804264, 0.0120454
[145:35] Assembling protein groups
[145:37] Quantifying proteins
[145:38] Calculating q-values for protein and gene groups
[145:40] Calculating global q-values for protein and gene groups
[145:40] Protein groups with global q-value <= 0.01: 27938
[145:43] Compressed report saved to /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.1/report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[145:43] Writing report
[145:50] Report saved to /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.1/report.tsv.
[145:50] Stats report saved to /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.1/report.stats.tsv
[145:50] Generating spectral library:
[145:53] 187200 target and 1530 decoy precursors saved
WARNING: 3352 precursors without any fragments annotated were skipped
[145:53] Spectral library saved to report-lib.parquet

