vdemichev
commented
3 months ago Hi Victor,
A general comment: using --monitor-mod on so many modifications is usually not a good idea.
The reason for the problem is likely (i) a bug in DIA-NN or (ii) DIA-NN is out of memory. In either case, please just try beta 39 here https://osf.io/q8kfc/?view_only=5e77d3c62563468280fd09265583dbbd. Also, can just use Peptidoform scoring instead of --monitor-mod in it (there's an option in GUI), if you need to be confident in specific peptidoforms.
Best, Vadim
Hi,
I am using DIA-NN 1.8.1 in Windows 11 Pro with 13th Gen Intel(R) Core(TM) i7-13700 (processors 16, threads 24) for DIA analysis of 51 Thermo raw data files. First attempts were successful exploring the library-free approach and hybrid DDA+DIA library from Fragpipe.
However, I encounter an error with two samples in my last analysis: 1 Fragpipe library generation with 10 DDA files and 51 DIA files (previous analysis only included QC samples in the library) 2 Run DIA-NN by command line using Fragpipe library All of the samples can be analyzed except two samples ( "D:\DIA_Raw\24NP00480034.mzML" and "D:\DIA_Raw\24NP00480035.mzML" in log file) that previously were not having any problem. I checked if the mzML and raw files were corrupted by generating new input files from the original stored files and the error persisted. I changed verbose to 4 expecting to see some error message but DIA-NN stops in the quantification step without any error message. Please, find attached the log file log_file_2samples_quant.txt with my last attempt with already generated quant files for the rest of the samples. Independently, if I run alone these two samples or each sample separated, DIA-NN also stops in Quantification without error message. Also, if it would help, I could share both problematic files raw and mzML. Please, could you help to figure out what could be the problem?
Many thanks in advance, Victor