DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
Compiled on Dec  1 2022 14:47:06
Current date and time: Fri Jun 14 11:25:03 2024
Logical CPU cores: 128
/usr/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --threads 64 --qvalue 0.01 --matrices --predictor --met-excision --cut K*,R* --min-pep-len 6 --max-pep-len 30 --smart-profiling --fasta-search --fasta /misc/fasta/p34486_Proteobench_TripleProteome_20240614.fasta --var-mods 1 --var-mod UniMod:35,15.994915,M --min-pr-charge 2 --max-pr-charge 3 --min-pr-mz 400 --max-pr-mz 1500 --min-fr-mz 200 --max-fr-mz 1800 --use-quant --verbose 1 --unimod4 --missed-cleavages 1 --mass-acc 20 --mass-acc-ms1 15 --reanalyse --relaxed-prot-inf --no-norm --f /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.mzML --f /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.mzML --f /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.mzML --f /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.mzML --f /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.mzML --f /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.mzML --out-lib /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-lib.tsv --out-lib-copy --temp /scratch/DIANN_A314/WU304578/temp-2024-06-14/ --out /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report.tsv 

Thread number set to 64
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
Deep learning will be used to generate a new in silico spectral library from peptides provided
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Min peptide length set to 6
Max peptide length set to 30
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Library-free search enabled
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Min precursor charge set to 2
Max precursor charge set to 3
Min precursor m/z set to 400
Max precursor m/z set to 1500
Min fragment m/z set to 200
Max fragment m/z set to 1800
Existing .quant files will be used
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of missed cleavages set to 1
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
Highly heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers; use with caution for anything else
Normalisation disabled
Copies of the spectral library and the FASTA database will be saved along with the final report
Mass accuracy will be fixed to 2e-05 (MS2) and 1.5e-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

6 files will be processed
[0:00] Loading FASTA /misc/fasta/p34486_Proteobench_TripleProteome_20240614.fasta
[0:04] Processing FASTA
[0:13] Assembling elution groups
[0:18] 3992300 precursors generated
[0:18] Protein names missing for some isoforms
[0:18] Gene names missing for some isoforms
[0:18] Library contains 31679 proteins, and 0 genes
[0:21] [0:28] [5:46] [6:35] [8:13] [8:15] Saving the library to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-lib.predicted.speclib
[8:18] Initialising library

[8:23] First pass: generating a spectral library from DIA data
[8:23] File #1/6
[8:23] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.mzML
[9:19] 3143698 library precursors are potentially detectable
[9:20] Processing...
[10:08] RT window set to 10.3781
[10:08] Peak width: 6.316
[10:08] Scan window radius set to 13
[10:08] Recommended MS1 mass accuracy setting: 8.61252 ppm
[12:40] Removing low confidence identifications
[12:40] Removing interfering precursors
[12:45] Training neural networks: 112736 targets, 95437 decoys
[12:50] Number of IDs at 0.01 FDR: 68279
[12:51] Calculating protein q-values
[12:51] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[12:51] Quantification
[12:52] Quantification information saved to /scratch/DIANN_A314/WU304578/temp-2024-06-14/_scratch_DIANN_A314_WU304578_LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01_mzML.quant.

[12:53] File #2/6
[12:53] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.mzML
[13:54] 3143698 library precursors are potentially detectable
[13:54] Processing...
[14:42] RT window set to 11.3678
[14:43] Recommended MS1 mass accuracy setting: 9.83736 ppm
[17:30] Removing low confidence identifications
[17:31] Removing interfering precursors
[17:37] Training neural networks: 128159 targets, 108355 decoys
[17:42] Number of IDs at 0.01 FDR: 77680
[17:43] Calculating protein q-values
[17:43] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[17:43] Quantification
[17:45] Quantification information saved to /scratch/DIANN_A314/WU304578/temp-2024-06-14/_scratch_DIANN_A314_WU304578_LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01_mzML.quant.

[17:46] File #3/6
[17:46] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.mzML
[18:47] 3143698 library precursors are potentially detectable
[18:47] Processing...
[19:32] RT window set to 9.51254
[19:32] Recommended MS1 mass accuracy setting: 9.12688 ppm
[21:30] Removing low confidence identifications
[21:30] Removing interfering precursors
[21:35] Training neural networks: 111739 targets, 88548 decoys
[21:39] Number of IDs at 0.01 FDR: 64773
[21:40] Calculating protein q-values
[21:40] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[21:40] Quantification
[21:41] Quantification information saved to /scratch/DIANN_A314/WU304578/temp-2024-06-14/_scratch_DIANN_A314_WU304578_LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03_mzML.quant.

[21:42] File #4/6
[21:42] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.mzML
[22:45] 3143698 library precursors are potentially detectable
[22:45] Processing...
[23:44] RT window set to 9.53246
[23:45] Recommended MS1 mass accuracy setting: 9.10201 ppm
[26:35] Removing low confidence identifications
[26:35] Removing interfering precursors
[26:41] Training neural networks: 128822 targets, 100212 decoys
[26:46] Number of IDs at 0.01 FDR: 72951
[26:46] Calculating protein q-values
[26:47] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[26:47] Quantification
[26:48] Quantification information saved to /scratch/DIANN_A314/WU304578/temp-2024-06-14/_scratch_DIANN_A314_WU304578_LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03_mzML.quant.

[26:49] File #5/6
[26:49] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.mzML
[27:53] 3143698 library precursors are potentially detectable
[27:53] Processing...
[28:54] RT window set to 9.32302
[28:54] Recommended MS1 mass accuracy setting: 8.95223 ppm
[32:00] Removing low confidence identifications
[32:00] Removing interfering precursors
[32:05] Training neural networks: 129207 targets, 100059 decoys
[32:10] Number of IDs at 0.01 FDR: 71472
[32:11] Calculating protein q-values
[32:11] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[32:11] Quantification
[32:13] Quantification information saved to /scratch/DIANN_A314/WU304578/temp-2024-06-14/_scratch_DIANN_A314_WU304578_LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02_mzML.quant.

[32:13] File #6/6
[32:13] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.mzML
[33:16] 3143698 library precursors are potentially detectable
[33:16] Processing...
[34:16] RT window set to 8.93734
[34:16] Recommended MS1 mass accuracy setting: 9.23167 ppm
[37:11] Removing low confidence identifications
[37:11] Removing interfering precursors
[37:17] Training neural networks: 139678 targets, 109409 decoys
[37:22] Number of IDs at 0.01 FDR: 81145
[37:23] Calculating protein q-values
[37:23] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[37:23] Quantification
[37:25] Quantification information saved to /scratch/DIANN_A314/WU304578/temp-2024-06-14/_scratch_DIANN_A314_WU304578_LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02_mzML.quant.

[37:25] Cross-run analysis
[37:25] Reading quantification information: 6 files
[37:26] Quantifying peptides
[37:27] Assembling protein groups
[37:29] Quantifying proteins
[37:29] Calculating q-values for protein and gene groups
[37:29] Calculating global q-values for protein and gene groups
[37:29] Writing report
[37:42] Report saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-first-pass.tsv.
[37:42] Saving precursor levels matrix
[37:43] Precursor levels matrix (1% precursor and protein group FDR) saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-first-pass.pr_matrix.tsv.
[37:43] Saving protein group levels matrix
[37:43] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-first-pass.pg_matrix.tsv.
[37:43] Saving gene group levels matrix
[37:43] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-first-pass.gg_matrix.tsv.
[37:43] Saving unique genes levels matrix
[37:43] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-first-pass.unique_genes_matrix.tsv.
[37:43] Stats report saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-first-pass.stats.tsv
[37:43] Generating spectral library:
[37:43] 101736 precursors passing the FDR threshold are to be extracted
[37:43] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.mzML
[38:42] 3143698 library precursors are potentially detectable
[38:44] 9772 spectra added to the library
[38:44] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.mzML
[39:47] 3143698 library precursors are potentially detectable
[39:50] 21917 spectra added to the library
[39:50] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.mzML
[40:55] 3143698 library precursors are potentially detectable
[40:56] 8314 spectra added to the library
[40:56] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.mzML
[42:02] 3143698 library precursors are potentially detectable
[42:02] 4518 spectra added to the library
[42:02] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.mzML
[43:08] 3143698 library precursors are potentially detectable
[43:10] 13996 spectra added to the library
[43:10] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.mzML
[44:18] 3143698 library precursors are potentially detectable
[44:21] 21914 spectra added to the library
[44:21] Saving spectral library to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-lib.tsv
[44:27] 101736 precursors saved
[44:27] Loading the generated library and saving it in the .speclib format
[44:27] Loading spectral library /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-lib.tsv
[44:29] Spectral library loaded: 11825 protein isoforms, 12239 protein groups and 101736 precursors in 91584 elution groups.
[44:29] Loading protein annotations from FASTA /misc/fasta/p34486_Proteobench_TripleProteome_20240614.fasta
[44:29] Protein names missing for some isoforms
[44:29] Gene names missing for some isoforms
[44:29] Library contains 11773 proteins, and 0 genes
[44:29] Saving the library to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report-lib.tsv.speclib

[44:32] Second pass: using the newly created spectral library to reanalyse the data
[44:32] File #1/6
[44:32] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.mzML
[45:32] 101736 library precursors are potentially detectable
[45:32] Processing...
[45:33] RT window set to 2.63932
[45:33] Recommended MS1 mass accuracy setting: 7.45919 ppm
[45:36] Removing low confidence identifications
[45:36] Removing interfering precursors
[45:38] Training neural networks: 89287 targets, 58079 decoys
[45:41] Number of IDs at 0.01 FDR: 79343
[45:42] Calculating protein q-values
[45:42] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[45:42] Quantification

[45:42] File #2/6
[45:42] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.mzML
[46:42] 101736 library precursors are potentially detectable
[46:42] Processing...
[46:43] RT window set to 2.63052
[46:43] Recommended MS1 mass accuracy setting: 7.87782 ppm
[46:46] Removing low confidence identifications
[46:46] Removing interfering precursors
[46:49] Training neural networks: 95885 targets, 59701 decoys
[46:52] Number of IDs at 0.01 FDR: 91317
[46:53] Calculating protein q-values
[46:53] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[46:53] Quantification

[46:54] File #3/6
[46:54] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.mzML
[47:53] 101736 library precursors are potentially detectable
[47:53] Processing...
[47:54] RT window set to 2.60418
[47:54] Recommended MS1 mass accuracy setting: 8.39598 ppm
[47:56] Removing low confidence identifications
[47:56] Removing interfering precursors
[47:58] Training neural networks: 87383 targets, 53319 decoys
[48:01] Number of IDs at 0.01 FDR: 77564
[48:02] Calculating protein q-values
[48:02] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[48:02] Quantification

[48:03] File #4/6
[48:03] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.mzML
[49:06] 101736 library precursors are potentially detectable
[49:06] Processing...
[49:06] RT window set to 2.52606
[49:06] Recommended MS1 mass accuracy setting: 9.5013 ppm
[49:09] Removing low confidence identifications
[49:09] Removing interfering precursors
[49:12] Training neural networks: 92588 targets, 54029 decoys
[49:14] Number of IDs at 0.01 FDR: 87714
[49:15] Calculating protein q-values
[49:15] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[49:15] Quantification

[49:16] File #5/6
[49:16] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.mzML
[50:19] 101736 library precursors are potentially detectable
[50:19] Processing...
[50:21] RT window set to 2.54783
[50:21] Recommended MS1 mass accuracy setting: 9.10326 ppm
[50:25] Removing low confidence identifications
[50:25] Removing interfering precursors
[50:27] Training neural networks: 90850 targets, 62445 decoys
[50:31] Number of IDs at 0.01 FDR: 81395
[50:31] Calculating protein q-values
[50:31] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[50:31] Quantification

[50:32] File #6/6
[50:32] Loading run /scratch/DIANN_A314/WU304578/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.mzML
[51:35] 101736 library precursors are potentially detectable
[51:35] Processing...
[51:36] RT window set to 2.52978
[51:36] Recommended MS1 mass accuracy setting: 8.76527 ppm
[51:40] Removing low confidence identifications
[51:40] Removing interfering precursors
[51:42] Training neural networks: 96813 targets, 63654 decoys
[51:46] Number of IDs at 0.01 FDR: 92321
[51:47] Calculating protein q-values
[51:47] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[51:47] Quantification

[51:48] Cross-run analysis
[51:48] Reading quantification information: 6 files
[51:48] Quantifying peptides
[51:49] Quantifying proteins
[51:50] Calculating q-values for protein and gene groups
[51:50] Calculating global q-values for protein and gene groups
[51:50] Writing report
[52:04] Report saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report.tsv.
[52:04] Saving precursor levels matrix
[52:04] Precursor levels matrix (1% precursor and protein group FDR) saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report.pr_matrix.tsv.
[52:04] Saving protein group levels matrix
[52:04] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report.pg_matrix.tsv.
[52:04] Saving gene group levels matrix
[52:04] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report.gg_matrix.tsv.
[52:04] Saving unique genes levels matrix
[52:04] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report.unique_genes_matrix.tsv.
[52:04] Stats report saved to /scratch/DIANN_A314/WU304578/out-2024-06-14//WU304578_report.stats.tsv

Finished
