DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 15 2022 08:45:18
Current date and time: Wed Aug  5 12:26:58 2026
Logical CPU cores: 128
/usr/diann/1.8.1/diann --f /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_01_uncalibrated.mzML --f /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_02_uncalibrated.mzML --f /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_03_uncalibrated.mzML --fasta /public/local/ProteoBench/fastas/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta --out /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1/report.tsv --temp /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1 --threads 100 --missed-cleavages 1 --min-pep-len 6 --max-pep-len 40 --qvalue 0.01 --protein-qvalue 0.01 --min-pr-charge 1 --max-pr-charge 5 --min-pr-mz 380 --max-pr-mz 980 --min-fr-mz 150 --max-fr-mz 2000 --cut  --gen-spec-lib --predictor --mass-acc 20 --mass-acc-ms1 20 --unimod4 --var-mods 0 --gen-spec-lib --fasta-search --reanalyse --dg-keep-cterm 2 --dg-min-shuffle 2.0 --dg-min-mut 7.0 --dg-max-mut 25.0 

Thread number set to 100
Maximum number of missed cleavages set to 1
Min peptide length set to 6
Max peptide length set to 40
Output will be filtered at 0.01 FDR
Output will be filtered at 0.01 protein-level FDR
Min precursor charge set to 1
Max precursor charge set to 5
Min precursor m/z set to 380
Max precursor m/z set to 980
Min fragment m/z set to 150
Max fragment m/z set to 2000
A spectral library will be generated
Deep learning will be used to generate a new in silico spectral library from peptides provided
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 0
A spectral library will be generated
Library-free search enabled
A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step
WARNING: unrecognised option [--dg-keep-cterm 2]
WARNING: unrecognised option [--dg-min-shuffle 2.0]
WARNING: unrecognised option [--dg-min-mut 7.0]
WARNING: unrecognised option [--dg-max-mut 25.0]
Mass accuracy will be fixed to 2e-05 (MS2) and 2e-05 (MS1)
Exclusion of fragments shared between heavy and light peptides from quantification is not supported in FASTA digest mode - disabled; to enable, generate an in silico predicted spectral library and analyse with this library

3 files will be processed
[0:00] Loading FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta
[0:24] Processing FASTA
[0:32] Assembling elution groups
[0:50] 5521496 precursors generated
[0:52] Gene names missing for some isoforms
[0:52] Library contains 2841736 proteins, and 0 genes
[0:59] [1:07] [8:53] [9:57] [10:02] [10:11] Saving the library to lib.predicted.speclib
Could not save lib.predicted.speclib
[10:11] Initialising library

[10:24] First pass: generating a spectral library from DIA data
[10:24] File #1/3
[10:24] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_01_uncalibrated.mzML
[12:51] 5517054 library precursors are potentially detectable
[12:52] Processing...
[14:23] RT window set to 1.1358
[14:23] Peak width: 2.812
[14:23] Scan window radius set to 6
[14:24] Recommended MS1 mass accuracy setting: 2.22037 ppm
[16:03] Removing low confidence identifications
[16:03] Removing interfering precursors
[16:10] Training neural networks: 163856 targets, 137696 decoys
[16:14] Number of IDs at 0.01 FDR: 73566
[16:14] Calculating protein q-values
[16:15] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[16:15] Quantification
[16:16] Quantification information saved to /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1/_public_local_ProteoBench_Entrapment_DIA_LFQ_Astral_DIA_15min_50ng_Human_01_uncalibrated_mzML.quant.

[16:17] File #2/3
[16:17] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_02_uncalibrated.mzML
[17:57] 5517054 library precursors are potentially detectable
[17:58] Processing...
[18:33] RT window set to 1.21186
[18:33] Recommended MS1 mass accuracy setting: 2.29196 ppm
[19:33] Removing low confidence identifications
[19:33] Removing interfering precursors
[19:39] Training neural networks: 150008 targets, 132192 decoys
[19:43] Number of IDs at 0.01 FDR: 72643
[19:43] Calculating protein q-values
[19:44] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[19:44] Quantification
[19:45] Quantification information saved to /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1/_public_local_ProteoBench_Entrapment_DIA_LFQ_Astral_DIA_15min_50ng_Human_02_uncalibrated_mzML.quant.

[19:45] File #3/3
[19:45] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_03_uncalibrated.mzML
[21:27] 5517054 library precursors are potentially detectable
[21:27] Processing...
[22:02] RT window set to 1.18056
[22:02] Recommended MS1 mass accuracy setting: 2.35343 ppm
[23:09] Removing low confidence identifications
[23:09] Removing interfering precursors
[23:15] Training neural networks: 148797 targets, 131286 decoys
[23:19] Number of IDs at 0.01 FDR: 71126
[23:20] Calculating protein q-values
[23:21] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[23:21] Quantification
[23:22] Quantification information saved to /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1/_public_local_ProteoBench_Entrapment_DIA_LFQ_Astral_DIA_15min_50ng_Human_03_uncalibrated_mzML.quant.

[23:22] Cross-run analysis
[23:22] Reading quantification information: 3 files
[23:23] Quantifying peptides
[23:27] Assembling protein groups
[23:33] Quantifying proteins
[23:34] Calculating q-values for protein and gene groups
[23:35] Calculating global q-values for protein and gene groups
[23:35] Writing report
[23:39] Report saved to /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1/report-first-pass.tsv.
[23:39] Stats report saved to /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1/report-first-pass.stats.tsv
[23:39] Generating spectral library:
[23:39] 84818 precursors passing the FDR threshold are to be extracted
[23:39] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_01_uncalibrated.mzML
[24:27] 5517054 library precursors are potentially detectable
[24:29] 22598 spectra added to the library
[24:29] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_02_uncalibrated.mzML
[25:17] 5517054 library precursors are potentially detectable
[25:19] 26715 spectra added to the library
[25:19] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_03_uncalibrated.mzML
[26:11] 5517054 library precursors are potentially detectable
[26:13] 27320 spectra added to the library
[26:13] Saving spectral library to lib.tsv
ERROR: cannot write to lib.tsv. Check if the destination folder is write-protected or the file is in use
[26:13] Loading the generated library and saving it in the .speclib format
[26:13] Loading spectral library lib.tsv
cannot read the file
[26:13] Loading protein annotations from FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta
[26:29] Library contains 0 proteins, and 0 genes
[26:29] Saving the library to lib.tsv.speclib
Could not save lib.tsv.speclib

[26:32] Second pass: using the newly created spectral library to reanalyse the data
[26:32] File #1/3
[26:33] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_01_uncalibrated.mzML
[27:22] 77436 library precursors are potentially detectable
[27:22] Processing...
[27:22] RT window set to 0.425412
[27:22] Recommended MS1 mass accuracy setting: 2.19951 ppm
[27:23] Removing low confidence identifications
[27:23] Removing interfering precursors
[27:24] Training neural networks: 75016 targets, 54592 decoys
[27:26] Number of IDs at 0.01 FDR: 72504
[27:27] Calculating protein q-values
[27:27] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[27:27] Quantification

[27:27] File #2/3
[27:27] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_02_uncalibrated.mzML
[28:14] 77436 library precursors are potentially detectable
[28:14] Processing...
[28:15] RT window set to 0.442739
[28:15] Recommended MS1 mass accuracy setting: 2.38269 ppm
[28:15] Removing low confidence identifications
[28:15] Removing interfering precursors
[28:17] Training neural networks: 74907 targets, 55783 decoys
[28:18] Number of IDs at 0.01 FDR: 72291
[28:19] Calculating protein q-values
[28:19] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[28:19] Quantification

[28:20] File #3/3
[28:20] Loading run /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_03_uncalibrated.mzML
[29:13] 77436 library precursors are potentially detectable
[29:13] Processing...
[29:13] RT window set to 0.407964
[29:13] Recommended MS1 mass accuracy setting: 2.35048 ppm
[29:14] Removing low confidence identifications
[29:14] Removing interfering precursors
[29:16] Training neural networks: 74537 targets, 53638 decoys
[29:17] Number of IDs at 0.01 FDR: 71757
[29:18] Calculating protein q-values
[29:18] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[29:18] Quantification

[29:18] Cross-run analysis
[29:18] Reading quantification information: 3 files
[29:18] Quantifying peptides
[29:22] Quantifying proteins
[29:23] Calculating q-values for protein and gene groups
[29:24] Calculating global q-values for protein and gene groups
[29:24] Writing report
[29:27] Report saved to /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1/report.tsv.
[29:27] Stats report saved to /home/robbe/PB_output/results/Entrapment_trying_bad/Entrapment_DIA/diann_v1.8.1/report.stats.tsv

Finished

