Premature exit

[cutleraging]

Hi Vadim,

I have run some label free single cell samples on my timsTOF HT using slicePASEF. I have different cell amounts per run, as you can see from the file names. When I try to run this, it seems like DiaNN prematurely exits. When I remove the 0_cell samples, it was able to run, but then exited again on the 8_cell sample. Why is this? There seems to be no info as to what went wrong.

diann.exe --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_0_cell_M1_Slot1-289_1_2757.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_0_cell_M1_Slot1-289_1_2758.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_0_cell_M2_Slot1-290_1_2762.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_0_cell_M3_Slot1-291_1_2766.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_0_cell_M4_Slot1-292_1_2770.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_1_cell_N1_Slot1-313_1_2759.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_1_cell_N2_Slot1-314_1_2763.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_1_cell_N3_Slot1-315_1_2767.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_1_cell_N4_Slot1-316_1_2771.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_2_cell_O1_Slot1-337_1_2760.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_2_cell_O2_Slot1-338_1_2764.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_2_cell_O3_Slot1-339_1_2768.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_2_cell_O4_Slot1-340_1_2772.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_8_cell_P1_Slot1-361_1_2761.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_8_cell_P2_Slot1-362_1_2765.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_8_cell_P3_Slot1-363_1_2769.d
" --f "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_8_cell_P4_Slot1-364_1_2773.d
" --lib "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\2-diann-qc\spectral-library.predicted.speclib" --threads 32 --verbose 1 --out "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\2-diann-qc\report.tsv" --qvalue 0.01 --matrices  --min-corr 2.0 --corr-diff 1.0 --time-corr-only --extracted-ms1 --out-lib "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\2-diann-qc\spectral-library.tsv" --gen-spec-lib --fasta "D:\Databases\uniprot-human-proteome_UP000005640_9606.fasta" --met-excision --cut K*,R* --missed-cleavages 1 --var-mods 1 --var-mod UniMod:35,15.994915,M --mass-acc 15 --mass-acc-ms1 15 --relaxed-prot-inf --rt-profiling --tims-scan
DIA-NN 1.9 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun  8 2024 20:00:31
Current date and time: Wed Oct 16 10:46:46 2024
CPU: GenuineIntel Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 32
Thread number set to 32
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
Only peaks with correlation sum exceeding 2 will be considered
Peaks with correlation sum below 1 from maximum will not be considered
A single score will be used until RT alignment to save memory; this can potentially lead to slower search
Fast algorithm based on MS1 feature extraction for quicker library-free search will be applied; this significantly worsens the identification performance
A spectral library will be generated
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers, GO/pathway and system-scale analyses
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
.d files will be processed as Slice-PASEF acquisitions, this mode is not compatible with dia-PASEF
Mass accuracy will be fixed to 1.5e-05 (MS2) and 1.5e-05 (MS1)
WARNING: peptidoform scoring enabled because variable modifications have been declared; to disable, use --no-peptidoforms
The following variable modifications will be scored: UniMod:35 

17 files will be processed
[0:00] Loading spectral library D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\2-diann-qc\spectral-library.predicted.speclib
[2:06] Library annotated with sequence database(s): D:\Databases\uniprot-human-proteome_UP000005640_9606.fasta
[2:08] Spectral library loaded: 20572 protein isoforms, 29398 protein groups and 5627636 precursors in 1751805 elution groups.
[2:08] Loading protein annotations from FASTA D:\Databases\uniprot-human-proteome_UP000005640_9606.fasta
[2:10] Annotating library proteins with information from the FASTA database
[2:11] Gene names missing for some isoforms
[2:11] Library contains 20572 proteins, and 20326 genes
[2:23] Initialising library

[2:54] File #1/17
[2:54] Loading run D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\1-data\241013_npop_imr90_0_cell_M1_Slot1-289_1_2757.d

DIA-NN exited
DIA-NN-plotter.exe "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\2-diann-qc\report.stats.tsv" "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\2-diann-qc\report.tsv" "D:\SharedspaceTIMSTOF\Ronnie\241013_nPOP_imr90_label-free\2-diann-qc\report.pdf"
PDF report will be generated in the background

Best, Ronnie

[vdemichev]

Hi Ronnie,

How much RAM is there in the system and how large is 241013_npop_imr90_0_cell_M1_Slot1-289_1_2757.d?

Best, Vadim

[cutleraging]

Oh I see now, they are only a couple of MB. Thanks.

Only can know the size if I look at the properties of each folder. Is there a way to display folder size in file explorer?

Ronnie

[vdemichev]

Oh I see now, they are only a couple of MB.

Means empty. No valid run would be that small. Is .tdf_bin actually there?

[cutleraging]

Yes, you are right. And no it is not. Good to know, thanks!

[li-jiamiao]

I ran it on win7. It doesn't seem to be running before it's over

diann.exe --f "E:\20241010\20241010-1.raw " --lib "" --threads 4 --verbose 1 --out "C:\DIA-NN\1.9.1/report.tsv" --qvalue 0.01 --matrices --out-lib "C:\DIA-NN\1.9.1\report-lib.parquet" --gen-spec-lib --predictor --fasta "E:\DIANN\uniprotkb_human_AND_reviewed_true_2024_07_23.fasta" --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --cut K,R --missed-cleavages 1 --unimod4 --reanalyse --relaxed-prot-inf --rt-profiling

DIA-NN exited DIA-NN-plotter.exe "C:\DIA-NN\1.9.1\report.stats.tsv" "C:\DIA-NN\1.9.1/report.tsv" "C:\DIA-NN\1.9.1\report.pdf" PDF report will be generated in the background

[vdemichev]

What does it say if ran from the command line? That is if you open Windows command prompt, navigate to the DIA-NN installation directory and type 'start diann.exe'?