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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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DIA-NN exited just after loading timsTOF-pro *.d data #162

Closed animesh closed 3 years ago

animesh commented 3 years ago

Probably the setup is the issue?

image

It says it is creating a report though:

[0:26] Processing FASTA
DIA-NN exited
diann.exe --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_57.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_58.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_59.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_60.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_61.d
" --lib "" --threads 12 --verbose 1 --out "C:\DIA-NN\1.8\report.tsv" --qvalue 0.01 --matrices  --out-lib "C:\DIA-NN\1.8\report-lib.tsv" --gen-spec-lib --predictor --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --reanalyse --smart-profiling 
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Mon Aug 16 15:37:41 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 24
Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Deep learning will be used to generate a new in silico spectral library from peptides provided
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
The following variable modifications will be scored: UniMod:1 

6 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
[0:17] Processing FASTA
[0:33] Assembling elution groups
[0:59] 7125376 precursors generated
[0:59] Gene names missing for some isoforms
[0:59] Library contains 77708 proteins, and 20476 genes
[1:00] Encoding peptides for spectra and RTs prediction
[1:17] Predicting spectra and IMs
DIA-NN exited
DIA-NN-plotter.exe "C:\DIA-NN\1.8\report.stats.tsv" "C:\DIA-NN\1.8\report.tsv" "C:\DIA-NN\1.8\report.pdf"
PDF report will be generated in the background

diann.exe --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_57.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_58.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_59.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_60.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_61.d
" --lib "" --threads 12 --verbose 1 --out "C:\DIA-NN\1.8\report.tsv" --qvalue 0.01 --matrices  --out-lib "C:\DIA-NN\1.8\report-lib.tsv" --gen-spec-lib --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --reanalyse --smart-profiling 
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Mon Aug 16 15:41:41 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 24
Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
The following variable modifications will be scored: UniMod:1 
WARNING: it's strongly recommended to use deep learning spectra/RTs prediction. If impossible because some unsupported modifications need to be searched, consider using either (i) the --strip-unknown-mods command or (ii) a 'training library' specified with the --learn-lib command. A training library might facilitate about 1.5x more IDs, deep learning - about 2x-3x more IDs.

6 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
[0:18] Processing FASTA
[0:35] Assembling elution groups
[1:01] 7125376 precursors generated
[1:01] Gene names missing for some isoforms
[1:01] Library contains 77708 proteins, and 20476 genes
[1:06] Initialising library

[1:10] First pass: generating a spectral library from DIA data
[1:10] File #1/6
[1:10] Loading run C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to 10 ppm.

DIA-NN exited
DIA-NN-plotter.exe "C:\DIA-NN\1.8\report.stats.tsv" "C:\DIA-NN\1.8\report.tsv" "C:\DIA-NN\1.8\report.pdf"
PDF report will be generated in the background

diann.exe --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_57.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_58.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_59.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_60.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_61.d
" --lib "" --threads 12 --verbose 1 --out "C:\DIA-NN\1.8\report.tsv" --qvalue 0.01 --matrices  --out-lib "C:\DIA-NN\1.8\report-lib.tsv" --gen-spec-lib --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --mass-acc 10 --mass-acc-ms1 10.0 --reanalyse --smart-profiling 
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Mon Aug 16 15:44:52 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 24
Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1)
The following variable modifications will be scored: UniMod:1 
WARNING: it's strongly recommended to use deep learning spectra/RTs prediction. If impossible because some unsupported modifications need to be searched, consider using either (i) the --strip-unknown-mods command or (ii) a 'training library' specified with the --learn-lib command. A training library might facilitate about 1.5x more IDs, deep learning - about 2x-3x more IDs.

6 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
[0:17] Processing FASTA
[0:34] Assembling elution groups
[0:59] 7125376 precursors generated
[0:59] Gene names missing for some isoforms
[0:59] Library contains 77708 proteins, and 20476 genes
[1:05] Initialising library

[1:09] First pass: generating a spectral library from DIA data
[1:09] File #1/6
[1:09] Loading run C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d

DIA-NN exited
DIA-NN-plotter.exe "C:\DIA-NN\1.8\report.stats.tsv" "C:\DIA-NN\1.8\report.tsv" "C:\DIA-NN\1.8\report.pdf"
PDF report will be generated in the background

diann.exe --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_57.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_58.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_59.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_60.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_61.d
" --lib "" --threads 12 --verbose 1 --out "C:\DIA-NN\1.8\report.tsv" --qvalue 0.01 --matrices  --out-lib "C:\DIA-NN\1.8\report-lib.tsv" --gen-spec-lib --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --mass-acc 10 --mass-acc-ms1 10.0 --reanalyse --smart-profiling 
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Mon Aug 16 16:09:07 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 24
Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1)
The following variable modifications will be scored: UniMod:1 
WARNING: it's strongly recommended to use deep learning spectra/RTs prediction. If impossible because some unsupported modifications need to be searched, consider using either (i) the --strip-unknown-mods command or (ii) a 'training library' specified with the --learn-lib command. A training library might facilitate about 1.5x more IDs, deep learning - about 2x-3x more IDs.

6 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
[0:29] Processing FASTA
[0:58] Assembling elution groups
[1:38] 7125376 precursors generated
[1:38] Gene names missing for some isoforms
[1:38] Library contains 77708 proteins, and 20476 genes
[1:46] Initialising library

[1:51] First pass: generating a spectral library from DIA data
[1:51] File #1/6
[1:51] Loading run C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d

DIA-NN exited
DIA-NN-plotter.exe "C:\DIA-NN\1.8\report.stats.tsv" "C:\DIA-NN\1.8\report.tsv" "C:\DIA-NN\1.8\report.pdf"
PDF report will be generated in the background

diann.exe --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_57.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_58.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_59.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_60.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_61.d
" --lib "" --threads 12 --verbose 1 --out "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.tsv" --qvalue 0.01 --matrices  --out-lib "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\pdf.tsv" --gen-spec-lib --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --mass-acc 10 --mass-acc-ms1 10.0 --reanalyse --smart-profiling 
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Mon Aug 16 16:13:26 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 24
Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1)
The following variable modifications will be scored: UniMod:1 
WARNING: it's strongly recommended to use deep learning spectra/RTs prediction. If impossible because some unsupported modifications need to be searched, consider using either (i) the --strip-unknown-mods command or (ii) a 'training library' specified with the --learn-lib command. A training library might facilitate about 1.5x more IDs, deep learning - about 2x-3x more IDs.

6 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
DIA-NN exited
diann.exe --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_57.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_58.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_59.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_60.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_61.d
" --lib "" --threads 12 --verbose 1 --out "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.tsv" --qvalue 0.01 --matrices  --out-lib "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\pdf.tsv" --gen-spec-lib --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --mass-acc 10 --mass-acc-ms1 10.0 --reanalyse --smart-profiling 
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Mon Aug 16 16:13:45 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 24
Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1)
The following variable modifications will be scored: UniMod:1 
WARNING: it's strongly recommended to use deep learning spectra/RTs prediction. If impossible because some unsupported modifications need to be searched, consider using either (i) the --strip-unknown-mods command or (ii) a 'training library' specified with the --learn-lib command. A training library might facilitate about 1.5x more IDs, deep learning - about 2x-3x more IDs.

6 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
[0:28] Processing FASTA
[0:55] Assembling elution groups
[1:37] 7125376 precursors generated
[1:38] Gene names missing for some isoforms
[1:38] Library contains 77708 proteins, and 20476 genes
[1:46] Initialising library

[1:51] First pass: generating a spectral library from DIA data
[1:51] File #1/6
[1:51] Loading run C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d

DIA-NN exited
DIA-NN-plotter.exe "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.stats.tsv" "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.tsv" "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.pdf"
PDF report will be generated in the background

diann.exe --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_57.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_58.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_59.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_60.d
" --f "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_61.d
" --lib "" --threads 6 --verbose 1 --out "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.tsv" --qvalue 0.01 --matrices  --out-lib "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\pdf.tsv" --gen-spec-lib --predictor --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --mass-acc 10 --mass-acc-ms1 10.0 --reanalyse --smart-profiling 
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Tue Aug 17 14:33:48 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 24
Thread number set to 6
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Deep learning will be used to generate a new in silico spectral library from peptides provided
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1)
The following variable modifications will be scored: UniMod:1 

6 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
[0:24] Processing FASTA
[0:48] Assembling elution groups
[1:23] 7125376 precursors generated
[1:24] Gene names missing for some isoforms
[1:24] Library contains 77708 proteins, and 20476 genes
[1:25] Encoding peptides for spectra and RTs prediction
[1:49] Predicting spectra and IMs
[56:39] Predicting RTs
[65:47] Decoding predicted spectra and IMs
[66:17] Decoding RTs
[66:24] Saving the library to C:\Users\animeshs\Desktop\Documents\DDA_PASEF\pdf.predicted.speclib
[66:45] Initialising library

[66:49] First pass: generating a spectral library from DIA data
[66:49] File #1/6
[66:49] Loading run C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d

DIA-NN exited
DIA-NN-plotter.exe "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.stats.tsv" "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.tsv" "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\tsv.pdf"
PDF report will be generated in the background

any ideas what going on @vdemichev ?

vdemichev commented 3 years ago

Also, what's the amount of RAM in the system and how large the tdf_bin file in that .d folder is?

vdemichev commented 3 years ago

Any update?

Koehlermc commented 3 years ago

Hi @vdemichev,

I am having the same problem @animesh described (outputs the same as they've posted).

diann.exe --f "W:\F49\TIMTOF\Stella\Proteomics_SR\DDA44_K645_100ng_S2-A10_1_257.d " --f "W:\F49\TIMTOF\Stella\Seer-Test\ok\Hela-150ng-DIA44-py8-1_S1-A1_1_2.d " --lib "R:\R\RITORTO.Stella\library_hela_evosep_semi.tsv" --threads 16 --verbose 1 --out "C:\Users\FRG-TSLAB-ANALYZE\Desktop\Koehler\Seer\timsTOF test\timsTOF_Test1.tsv" --qvalue 0.01 --matrices --temp "C:\Users\FRG-TSLAB-ANALYZE\Desktop\Koehler\timsTOF Test" --reannotate --fasta "C:\Users\FRG-TSLAB-ANALYZE\Desktop\Stella\FASTA\uniprot-human-filtered-reviewed_yes.fasta" --met-excision --cut K,R --missed-cleavages 2 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 2 --max-pr-charge 4 --unimod4 --var-mods 3 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,n --monitor-mod UniMod:1 --mass-acc 10 --mass-acc-ms1 10 --double-search --reanalyse --smart-profiling --peak-center DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks) Compiled on Jun 28 2021 14:55:31 Current date and time: Tue Sep 14 08:57:27 2021 CPU: GenuineIntel Intel(R) Xeon(R) CPU E7- 2830 @ 2.13GHz SIMD instructions: SSE4.1 SSE4.2 Logical CPU cores: 16 Thread number set to 16 Output will be filtered at 0.01 FDR Precursor/protein x samples expression level matrices will be saved along with the main report Library precursors will be reannotated using the FASTA database N-terminal methionine excision enabled In silico digest will involve cuts at K,R Maximum number of missed cleavages set to 2 Min peptide length set to 7 Max peptide length set to 30 Min precursor m/z set to 300 Max precursor m/z set to 1800 Min precursor charge set to 2 Max precursor charge set to 4 Cysteine carbamidomethylation enabled as a fixed modification Maximum number of variable modifications set to 3 Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable Modification UniMod:1 with mass delta 42.0106 at n will be considered as variable Neural networks will be used for peak selection 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 When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones Fixed-width center of each elution peak will be used for quantification Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1) The following variable modifications will be scored: UniMod:1 WARNING: double-pass mode is incompatible with PTM scoring, turned off

2 files will be processed [0:00] Loading spectral library R:\R\RITORTO.Stella\library_hela_evosep_semi.tsv [0:28] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [0:29] Spectral library loaded: 8248 protein isoforms, 8248 protein groups and 149188 precursors in 122233 elution groups. [0:29] Loading FASTA C:\Users\FRG-TSLAB-ANALYZE\Desktop\Stella\FASTA\uniprot-human-filtered-reviewed_yes.fasta [3:53] Reannotating library precursors with information from the FASTA database [3:54] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [3:54] 149188 precursors generated [3:54] Gene names missing for some isoforms [3:54] Library contains 11902 proteins, and 10986 genes [3:57] Initialising library [3:57] Saving the library to R:\R\RITORTO.Stella\library_hela_evosep_semi.tsv.speclib Could not save R:\R\RITORTO.Stella\library_hela_evosep_semi.tsv.speclib

[3:57] First pass: generating a spectral library from DIA data [3:57] File #1/2 [3:57] Loading run W:\F49\TIMTOF\Stella\Proteomics_SR\DDA44_K645_100ng_S2-A10_1_257.d

DIA-NN exited DIA-NN-plotter.exe "C:\Users\FRG-TSLAB-ANALYZE\Desktop\Koehler\Seer\timsTOF test\timsTOF_Test1.stats.tsv" "C:\Users\FRG-TSLAB-ANALYZE\Desktop\Koehler\Seer\timsTOF test\timsTOF_Test1.tsv" "C:\Users\FRG-TSLAB-ANALYZE\Desktop\Koehler\Seer\timsTOF test\timsTOF_Test1.pdf" PDF report will be generated in the background

Here is what happens when I run the command you suggested:

PS C:\DIA-NN\1.8> .\diann.exe --f CW:\F49\TIMTOF\Stella\S-Test\ok\Hela-150ng-DIA44-py8-1_S1-A1_1_2.d --convert DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks) Compiled on Jun 28 2021 14:55:31 Current date and time: Mon Sep 13 15:56:59 2021 CPU: GenuineIntel Intel(R) Xeon(R) CPU E7- 2830 @ 2.13GHz SIMD instructions: SSE4.1 SSE4.2 Logical CPU cores: 16 MS data files will be converted to .dia format

1 files will be processed [0:00] Loading run CW:\F49\TIMTOF\Stella\S-Test\ok\Hela-150ng-DIA44-py8-1_S1-A1_1_2.d For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to 10 ppm. ERROR: cannot open the raw data folder CW:/F49/TIMTOF/Stella/S-Test/ok/Hela-150ng-DIA44-py8-1_S1-A1_1_2.d ERROR: cannot write to CW:\F49\TIMTOF\Stella\S-Test\ok\Hela-150ng-DIA44-py8-1_S1-A1_1_2.d.dia. Check if the destination folder is write-protected or the file is in use Finished

We normally designate a different temp/.dia directory because we cannot write in the directory the data is stored, so I'm not sure the "cannot write" error should apply. I don't know why it cannot open the raw data folder.

System RAM - 120GB Example tdf_bin size - 5GB

Any insight would be greatly appreciated! Thanks!

vdemichev commented 3 years ago

Looks like either corrupted file or no access right to that location, for a particular user. Does running diann.exe as an Administrator solve the problem?

Apologies for the lack of detail error information printed by DIA-NN, in the future we will add detail error reporting, so that it will then be immediately clear what the problem is, if something does not work.

Best, Vadim

Koehlermc commented 3 years ago

Running diann as an administrator seems to have solved the problem. Thanks for your help, I appreciate it!

Best, Matt

animesh commented 3 years ago

Sorry @vdemichev i just got back to this issue. I tried running your command-line as admin and i am not getting any error but nothing seems to be happening either?

(base) c:\DIA-NN\1.8>diann.exe --f C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d --convert
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Wed Sep 15 13:05:27 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2
Logical CPU cores: 24
MS data files will be converted to .dia format

1 files will be processed
[0:00] Loading run C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d
For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to 10 ppm.

(base) c:\DIA-NN\1.8>diann.exe --f C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d --convert
vdemichev commented 3 years ago

A .dia file is being created in the same folder. If it's created successfully, then all works fine. So once you launch the GUI as an Administrator (or enable access to the raw files for regular users in Windows settings), all should work

animesh commented 3 years ago

don't see a *.dia file there

(base) c:\DIA-NN\1.8>dir C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d\*.dia
 Volume in drive C is Windows
 Volume Serial Number is 24A5-040B

 Directory of C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d

File Not Found

13-Sep-21  10:19 PM    <DIR>          .
13-Sep-21  10:19 PM    <DIR>          ..
13-Sep-21  10:20 PM    <DIR>          2021-08-15_19-05-33_One-column-separation
13-Sep-21  10:20 PM    <DIR>          2021-08-15_19-05-33_Waiting-for-Oven-Temperature,-open-context-menu-to-stop-waiting
15-Aug-21  09:38 PM               223 4f954600-6711-41a7-b8cd-9a6cd63c5e82_1.mcf
15-Aug-21  09:38 PM            26,624 4f954600-6711-41a7-b8cd-9a6cd63c5e82_1.mcf_idx
13-Sep-21  10:20 PM    <DIR>          56.m
15-Aug-21  09:30 PM             9,892 analysis.0.DataAnalysis.method
15-Aug-21  09:30 PM        17,799,071 analysis.0.result_c
15-Aug-21  09:30 PM               104 analysis.content
15-Aug-21  09:22 PM       258,625,536 analysis.tdf
15-Aug-21  09:22 PM     4,641,734,656 analysis.tdf_bin
15-Aug-21  09:37 PM        24,143,745 BackgroundLinePos.ami
15-Aug-21  07:22 PM           120,832 chromatography-data-pre.sqlite
15-Aug-21  09:22 PM         2,571,264 chromatography-data.sqlite
15-Aug-21  09:22 PM                 0 chromatography-data.sqlite-journal
15-Aug-21  09:28 PM        28,550,821 DensViewPos.ami
15-Aug-21  09:28 PM                 0 HeLa_200ng_Slot1-1_1_56.d
15-Aug-21  09:38 PM       636,529,313 HeLa_200ng_Slot1-1_1_56_5.3.342.mgf
15-Aug-21  09:30 PM           198,647 HeLa_200ng_Slot1-1_1_56_BPC 350.0000-2200.0000 +All MS.xy
15-Aug-21  09:30 PM           212,077 HeLa_200ng_Slot1-1_1_56_TIC +All MS FullScan.xy
15-Aug-21  09:30 PM         1,110,237 HeLa_200ng_Slot1-1_1_56_TIC +All MSn.xy
16-Aug-21  11:11 AM                56 LockInfo
16-Aug-21  11:11 AM                 0 ProjectCreationHelper
15-Aug-21  07:22 PM             5,344 SampleInfo.xml
15-Aug-21  09:30 PM            24,576 Storage.mcf_idx
16-Aug-21  11:11 AM                 0 SyncHelper
              22 File(s)  5,611,663,018 bytes
               5 Dir(s)  278,035,505,152 bytes free

running the GUI as admin doesn't seem to create the report either

diann.exe --f "C:\Users\animeshs\Desktop\210902_sudhl5_tot_2_Slot1-29_1_180.d
" --lib "" --threads 12 --verbose 1 --out "C:\DIA-NN\1.8\report.tsv" --qvalue 0.01 --matrices  --out-lib "C:\DIA-NN\1.8\report-lib.tsv" --gen-spec-lib --predictor --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --reanalyse --smart-profiling 
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Wed Sep 15 12:29:14 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 24
Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Deep learning will be used to generate a new in silico spectral library from peptides provided
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
WARNING: MBR turned off, two or more raw files are required

1 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
[0:14] Processing FASTA
[0:24] Assembling elution groups
[0:42] 5158764 precursors generated
[0:43] Gene names missing for some isoforms
[0:43] Library contains 77708 proteins, and 20476 genes
[0:43] Encoding peptides for spectra and RTs prediction
[0:53] Predicting spectra and IMs
[25:47] Predicting RTs
[30:41] Decoding predicted spectra and IMs
[30:54] Decoding RTs
[30:58] Saving the library to C:\DIA-NN\1.8\report-lib.predicted.speclib
[31:08] Initialising library

[31:11] File #1/1
[31:11] Loading run C:\Users\animeshs\Desktop\210902_sudhl5_tot_2_Slot1-29_1_180.d
For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to 10 ppm.

DIA-NN exited
DIA-NN-plotter.exe "C:\DIA-NN\1.8\report.stats.tsv" "C:\DIA-NN\1.8\report.tsv" "C:\DIA-NN\1.8\report.pdf"
PDF report will be generated in the background

image

is there a way to call dia-nn modules separately and find exactly where the issue lies?

vdemichev commented 3 years ago

And how does the output look like, if you type diann.exe --f "C:\Users\animeshs\Desktop\210902_sudhl5_tot_2_Slot1-29_1_180.d " --lib "" --threads 12 --verbose 1 --out "C:\DIA-NN\1.8\report.tsv" --qvalue 0.01 --matrices --out-lib "C:\DIA-NN\1.8\report-lib.tsv" --gen-spec-lib --predictor --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --reanalyse --smart-profiling

in powershell run as an administrator?

animesh commented 3 years ago

Yes, running as admin and the command went through without errors

(base) c:\DIA-NN\1.8>diann.exe --f "C:\Users\animeshs\Desktop\210902_sudhl5_tot_2_Slot1-29_1_180.d " --lib "" --threads 12 --verbose 1 --out "C:\DIA-NN\1.8\report.tsv" --qvalue 0.01 --matrices --out-lib "C:\DIA-NN\1.8\report-lib.tsv" --gen-spec-lib --predictor --fasta "C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --reanalyse --smart-profiling
DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Wed Sep 15 15:43:55 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2643 v3 @ 3.40GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2
Logical CPU cores: 24
Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Deep learning will be used to generate a new in silico spectral library from peptides provided
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
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
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
WARNING: MBR turned off, two or more raw files are required

1 files will be processed
[0:00] Loading FASTA C:\Users\animeshs\Desktop\Documents\DDA_PASEF\uniprot-human-iso-june21.fasta
[0:14] Processing FASTA
[0:24] Assembling elution groups
[0:42] 5158764 precursors generated
[0:42] Gene names missing for some isoforms
[0:42] Library contains 77708 proteins, and 20476 genes
[0:43] Encoding peptides for spectra and RTs prediction
[0:53] Predicting spectra and IMs
[25:29] Predicting RTs
[30:56] Decoding predicted spectra and IMs
[31:12] Decoding RTs
[31:17] Saving the library to C:\DIA-NN\1.8\report-lib.predicted.speclib
[31:29] Initialising library

[31:32] File #1/1
[31:32] Loading run C:\Users\animeshs\Desktop\210902_sudhl5_tot_2_Slot1-29_1_180.d
For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to 10 ppm.

but no outputs either it seems?

(base) c:\DIA-NN\1.8>dir
 Volume in drive C is Windows
 Volume Serial Number is 24A5-040B

 Directory of c:\DIA-NN\1.8

15-Sep-21  04:25 PM    <DIR>          .
16-Aug-21  02:08 PM    <DIR>          ..
16-Aug-21  02:08 PM           242,176 asmjit.dll
16-Aug-21  02:08 PM           355,328 c10.dll
16-Aug-21  02:08 PM         1,268,224 caffe2_detectron_ops.dll
16-Aug-21  02:08 PM            94,720 caffe2_module_test_dynamic.dll
16-Aug-21  02:08 PM             1,304 CppSQLite3 license.txt
16-Aug-21  02:08 PM        62,998,921 dia-nn-plotter.exe
16-Aug-21  02:08 PM           435,712 DIA-NN.exe
16-Aug-21  02:08 PM           115,933 DIA-NN.ico
16-Aug-21  02:08 PM            79,360 DIA-NN.Wiff.dll
16-Aug-21  02:08 PM        15,281,664 DiaNN.exe
16-Aug-21  02:08 PM             1,524 EasyTabs license.txt
16-Aug-21  02:08 PM            71,680 EasyTabs.dll
16-Aug-21  02:08 PM         3,268,096 fbgemm.dll
16-Aug-21  02:08 PM           115,933 icon.ico
16-Aug-21  02:08 PM         1,717,584 libiomp5md.dll
16-Aug-21  02:08 PM           111,952 libiompstubs5md.dll
16-Aug-21  02:08 PM             1,688 LICENSE.txt
16-Aug-21  02:08 PM             1,412 MemoryPool LICENSE.txt
16-Aug-21  02:08 PM            81,920 Microsoft.WindowsAPICodePack.dll
16-Aug-21  02:08 PM           486,400 Microsoft.WindowsAPICodePack.Shell.dll
16-Aug-21  02:08 PM         1,432,848 NDP472-KB4054531-Web.exe
16-Aug-21  02:08 PM             3,215 PyTorch LICENSE.txt
16-Aug-21  02:08 PM             9,696 README.md
15-Sep-21  04:15 PM     1,465,592,895 report-lib.predicted.speclib
16-Aug-21  02:08 PM           569,344 Svg.dll
16-Aug-21  02:08 PM            41,725 THIRD-PARTY-LICENSE-README for TIMS library.txt
16-Aug-21  02:08 PM        15,893,520 timsdata.dll
16-Aug-21  02:08 PM             9,728 torch.dll
16-Aug-21  02:08 PM       186,263,552 torch_cpu.dll
16-Aug-21  02:08 PM             8,074 unimod-license.txt
16-Aug-21  02:08 PM         1,596,865 unimod.obo
16-Aug-21  02:08 PM             5,391 Uninstall.dat
16-Aug-21  02:08 PM           947,712 Uninstall.exe
16-Aug-21  02:07 PM             3,064 Uninstall_lang.ifl
16-Aug-21  02:08 PM        14,887,048 VC_redist.x64.exe
16-Aug-21  02:08 PM             9,728 Win32Interop.Dwmapi.dll
16-Aug-21  02:08 PM            35,840 Win32Interop.Gdi32.dll
16-Aug-21  02:08 PM            90,624 Win32Interop.Kernel32.dll
16-Aug-21  02:08 PM            98,816 Win32Interop.User32.dll
16-Aug-21  02:08 PM            13,312 Win32Interop.Uxtheme.dll
              40 File(s)  1,774,244,528 bytes
               2 Dir(s)  274,656,296,960 bytes free

(base) c:\DIA-NN\1.8>
(base) c:\DIA-NN\1.8>dir C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d\*.*
 Volume in drive C is Windows
 Volume Serial Number is 24A5-040B

 Directory of C:\Users\animeshs\Desktop\Documents\DDA_PASEF\HeLa_200ng_Slot1-1_1_56.d

13-Sep-21  10:19 PM    <DIR>          .
13-Sep-21  10:19 PM    <DIR>          ..
13-Sep-21  10:20 PM    <DIR>          2021-08-15_19-05-33_One-column-separation
13-Sep-21  10:20 PM    <DIR>          2021-08-15_19-05-33_Waiting-for-Oven-Temperature,-open-context-menu-to-stop-waiting
15-Aug-21  09:38 PM               223 4f954600-6711-41a7-b8cd-9a6cd63c5e82_1.mcf
15-Aug-21  09:38 PM            26,624 4f954600-6711-41a7-b8cd-9a6cd63c5e82_1.mcf_idx
13-Sep-21  10:20 PM    <DIR>          56.m
15-Aug-21  09:30 PM             9,892 analysis.0.DataAnalysis.method
15-Aug-21  09:30 PM        17,799,071 analysis.0.result_c
15-Aug-21  09:30 PM               104 analysis.content
15-Aug-21  09:22 PM       258,625,536 analysis.tdf
15-Aug-21  09:22 PM     4,641,734,656 analysis.tdf_bin
15-Aug-21  09:37 PM        24,143,745 BackgroundLinePos.ami
15-Aug-21  07:22 PM           120,832 chromatography-data-pre.sqlite
15-Aug-21  09:22 PM         2,571,264 chromatography-data.sqlite
15-Aug-21  09:22 PM                 0 chromatography-data.sqlite-journal
15-Aug-21  09:28 PM        28,550,821 DensViewPos.ami
15-Aug-21  09:28 PM                 0 HeLa_200ng_Slot1-1_1_56.d
15-Aug-21  09:38 PM       636,529,313 HeLa_200ng_Slot1-1_1_56_5.3.342.mgf
15-Aug-21  09:30 PM           198,647 HeLa_200ng_Slot1-1_1_56_BPC 350.0000-2200.0000 +All MS.xy
15-Aug-21  09:30 PM           212,077 HeLa_200ng_Slot1-1_1_56_TIC +All MS FullScan.xy
15-Aug-21  09:30 PM         1,110,237 HeLa_200ng_Slot1-1_1_56_TIC +All MSn.xy
16-Aug-21  11:11 AM                56 LockInfo
16-Aug-21  11:11 AM                 0 ProjectCreationHelper
15-Aug-21  07:22 PM             5,344 SampleInfo.xml
15-Aug-21  09:30 PM            24,576 Storage.mcf_idx
16-Aug-21  11:11 AM                 0 SyncHelper
              22 File(s)  5,611,663,018 bytes
               5 Dir(s)  274,250,305,536 bytes free

(base) c:\DIA-NN\1.8>
vdemichev commented 3 years ago

There's an .mgf file. Are you 100% sure it's diaPASEF, and not DDA PASEF?

Best, Vadim

animesh commented 3 years ago

My bad @vdemichev, it is a DDA_PASEF! Surprisingly the orbitrap DDA data went somehow fine?