Closed jflucier closed 1 year ago
vdemichev
commented
1 year ago Well, you can try running again with library generation set to 'IDs, RT and IM profiling' - then it will not need to load the raw files. What happened is some error accessing that raw file on the disk...
jflucier
commented
1 year ago I performed 2 tests:
1) I rerun the whole pipleine with 5 files and it pass without problem 2) I rerun the above analysis and specified the --lib with the report-lib.tsv that was generated before the previous crash and it also pass without problem
I did not find the command line options to specify 'IDs, RT and IM profiling' in the documentation
thanks for your help
kostrouc
commented
4 months ago Is Dia-NN compatible with .d Bruker files?
I am observing this same error when running with Dia-NN 1.8.1 in Linux. There is no log written but I do have the printed output. I have tried replacing --smart-profiling with --rt-profiling as suggested but this was not successful.
(base) kostrouchov@ip$sudo /usr/diann/1.8.1/diann-1.8.1 --cfg ./20240412_fasta_config.txt--
A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs Fixed-width center of each elution peak will be used for quantification Interference removal from fragment elution curves disabled Normalisation disabled MaxLFQ-based protein quantification disabled WARNING: unrecognised option [--] Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1) Exclusion of fragments shared between heavy and light peptides from quantification is not supported in FASTA digest mode - disabled; to enable, generate an in silico predicted spectral library and analyse with this library WARNING: it's strongly recommended to use deep learning spectra/RTs prediction. If impossible because some unsupported modifications need to be searched, consider using either (i) the --strip-unknown-mods command or (ii) a 'training library' specified with the --learn-lib command. A training library might facilitate about 1.5x more IDs, deep learning - about 2x-3x more IDs. 153 files will be processed [0:00] Loading FASTA /mnt/data/kostrouchov/diann_fasta/20240105.fasta [0:46] Processing FASTA [1:22] Assembling elution groups [2:05] 21021765 precursors generated [2:06] Gene names missing for some isoforms [2:06] Library contains 174633 proteins, and 65427 genes [2:08] Initialising library [2:34] First pass: generating a spectral library from DIA data [2:34] File #1/153 [2:34] Loading run /mnt/data/kostrouchov/Tims_DIA-PASEF/Tims_DIA-PASEF_S2-D8_1_182.d terminate called after throwing an instance of 'CppSQLite3Exception'
(base) kostrouchov@ip:/mnt/data/kostrouchov/Tims_DIA-PASEF/Tim_DIA-PASEF_S2-D8_1_182.d$ ls
182.m analysis.tdf chromatography-data-pre.sqlite chromatography-data.sqlite-journal SampleInfo.xml analysis.tdf_bin chromatography-data.sqlite desktop.ini
(base) kostrouchov@ip:/mnt/data/kostrouchov/Tims_DIA-PASEF/Tim_DIA-PASEF_S2-D8_1_182.d/182.m$ ls
InstrumentSetup.isset backup-2024-03-24.m diaSettings.diasqlite lock.file prmSettings.prmsqlite Maldi.method desktop.ini hystar.method microTOFQImpacTemAcquisition.method submethods.xml
Hi
I have build a singularity image from DIANN docker image v1.8.1
I have run sucessfully on a single sample diaNN. See execution log and submission: diann-singlesample.slurm.log diann-singlesample.submit.sh.gz
I have retried to submit with multiple samples acquisition (40 samples) and the execution fails with the following error:
Again, you can taker a look at full log and submission script: diann-multiplesamples.slurm.log diann-multiplesamples.submit.sh.gz
If i look at output folder, I see:
Can you guide me i how to give a command to I bypass speclib creation since already in ouptut folder?
Any help debugging this is appreciated.