Big Fatsa Document

[zhh-pedestrian]

Dear Vadim,

Firstly, I would like to express my gratitude for developing an exceptional software tool. I encountered an issue while attempting to predict spectral information with a 2.83GB sequence file, as DIA-NN failed to execute successfully. Could you please advise on what might be causing this problem and how I can resolve it?

Here is the detailed process of my attempt:

Skyline found: Skyline (64 bit) 24.1.0.199
MSFileReader not found, Thermo .raw data processing unavailable

Command line used:

diann.exe --lib "" --threads 8 --verbose 1 --out "F:\1_Darkprotein\Output\DIA_NN_36M\report.tsv" --qvalue 0.01 --matrices  --out-lib "F:\1_Darkprotein\Output\DIA_NN_36M\test03.parquet" --gen-spec-lib --predictor --fasta "F:\1_Darkprotein\Input\uniprotkb_human_2024_12_02.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 1.9.2 (Data-Independent Acquisition by Neural Networks)
Compiled on Oct 17 2024 21:58:43
Current date and time: Fri Dec 6 10:26:25 2024
CPU: AuthenticAMD AMD Ryzen 7 6800H with Radeon Graphics
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 SSE4a
Logical CPU cores: 16
Thread number set to 8
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
DIA-NN will carry out FASTA digest for in silico lib generation
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
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
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
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
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
WARNING: MBR turned off, two or more raw files are required

0 files will be processed
[0:00] Loading FASTA F:\1_Darkprotein\Input\uniprotkb_human_2024_12_02.fasta
[124:55] Processing FASTA
[126:48] Assembling elution groups

DIA-NN exited

Best regards,
Zhang

[vdemichev]

Hi Zhang,

Most likely out of memory, this is a huge FASTA.

Best,
Vadim