Exiting after loading spectral library

[JovanyBetancourt]

Hey Vlad,

I'm having an issue when I try to analyze samples using a spectral library generated from a previous search. For context, I'm trying to analyze the proteome of a fungal organism in the setting of lung infection. I generated a spectral library from fungal cultures, and I'm trying to use this spectral library to analyze infected lungs. Generating the spectral library went smoothly, but when I went to analyze the infected lungs with that spectral library I can't get passed the [Loading spectral library] step.

Any advice?

Details below: diann.exe --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_1_1.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_1_2.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_1_3.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_1_4.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_1_5.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_2_1.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_2_2.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_2_3.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_2_4.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_2_5.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_3_1.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_3_2.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_3_3.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_3_4.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_3_5.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_4_1.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_4_2.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_4_3.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_4_4.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_4_5.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_5_1.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_5_2.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_5_3.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_5_4.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_5_5.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_6_1.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_6_2.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_6_3.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_6_4.raw " --f "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\Aug_19_2024_JGM_JB_6_5.raw " --lib "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\dia_nn_cultures_oct232024\diann_report_oct232024.parquet" --threads 6 --verbose 1 --out "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\dia_nn_infected_lungs_oct232024\report.tsv" --qvalue 0.01 --matrices --out-lib "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\dia_nn_infected_lungs_oct232024\parquet.parquet" --gen-spec-lib --fasta "D:\Project 5_proteomic analysis of clinical isolates\cryptococcus_neoformans\fasta_cryptococcus_neoformans_h99_7439_proteins_oct212024.fasta" --met-excision --cut K,R --missed-cleavages 1 --unimod4 --reanalyse --relaxed-prot-inf --rt-profiling DIA-NN 1.9.1 (Data-Independent Acquisition by Neural Networks) Compiled on Jul 15 2024 15:40:36 Current date and time: Wed Oct 23 11:04:51 2024 CPU: GenuineIntel 12th Gen Intel(R) Core(TM) i5-12400F SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 Logical CPU cores: 12 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 N-terminal methionine excision enabled 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 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.

30 files will be processed [0:00] Loading spectral library D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\dia_nn_cultures_oct232024\diann_report_oct232024.parquet

DIA-NN exited DIA-NN-plotter.exe "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\dia_nn_infected_lungs_oct232024\report.stats.tsv" "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\dia_nn_infected_lungs_oct232024\report.tsv" "D:\Project 5_proteomic analysis of clinical isolates\Project 5 Raw Data\dia_nn_infected_lungs_oct232024\report.pdf" PDF report will be generated in the background

[vdemichev]

Hi Jovany,

I think this is probably not a library but the main report .parquet.

Best, Vadim

[JovanyBetancourt]

Hey Vadim,

Thank you for pointing that out! You're absolutely right I used the wrong .parquet file, the spectral library's output was in the DIA-NN program folder with the same file name. Sorry for the confusion!

Best, Jovany

Jovany Betancourt MD/PhD Candidate | Laboratory of Dr. Kirsten Nielsen Ranking Student Senator @. | @.

On Wed, Oct 23, 2024 at 2:26 PM Vadim Demichev @.***> wrote:

Hi Jovany,

I think this is probably not a library but the main report .parquet.

Best, Vadim

— Reply to this email directly, view it on GitHub https://github.com/vdemichev/DiaNN/issues/1226#issuecomment-2433260403, or unsubscribe https://github.com/notifications/unsubscribe-auth/BLIBRR4ZPGY5EC6RJ2CJ3KDZ47Z73AVCNFSM6AAAAABQPFZZ7WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZTGI3DANBQGM . You are receiving this because you authored the thread.Message ID: @.***>