Dear Vadim
When I run one.mzML file on linux, I have no problem. When I run multiple.mZML files, I report an error：
ubuntu@node188:~$ ./1/diann-linux --f data2/1.mzML --f data2/2.mzML --fasta data2/4.fasta --fasta-search --gen-spec-lib --threads 6
DIA-NN 1.7.12 (Data Independent Acquisition by Neural Networks)
Compiled on Dec 17 2023 14:45:00
Current date and time: Mon Dec 18 17:10:02 2023
Logical CPU cores: 16
Library-free search enabled
A spectral library will be generated
Thread number set to 6
Exclusion of fragments shared between heavy and light peptides from quantification is not supported in library-free mode - disabled
2 files will be processed
[0:00] Loading FASTA data2/4.fasta
[0:19] Processing FASTA
[0:22] Assembling elution groups
[1:54] 4220314 precursors generated
[1:54] Gene names missing for some isoforms
[1:54] Library contains 20404 proteins, and 20188 genes
[1:54] Initialising library
[1:55] File #1/2
[1:55] Loading run data2/1.mzML
[2:07] 1626910 library precursors are potentially detectable
[2:07] Processing...
[14:32] RT window set to 17.4244
[14:32] Peak width: 3.332
[14:32] Scan window radius set to 7
[26:48] Optimised mass accuracy: 6.19944 ppm
[36:56] Removing low confidence identifications
[36:56] Removing interfering precursors
[36:57] Training the neural network: 24286 targets, 14253 decoys
[37:00] Number of IDs at 0.01 FDR: 7791
[37:00] Calculating protein q-values
[37:00] Number of genes identified at 1% FDR: 1984 (precursor-level), 1816 (protein-level) (inference performed using proteotypic peptides only)
[37:00] Quantification
[37:01] Quantification information saved to data2/1.mzML.quant.
[37:01] File #2/2
[37:01] Loading run data2/2.mzML
[37:13] 1626910 library precursors are potentially detectable
[37:13] Processing...
[49:52] RT window set to 17.4244
[60:44] Removing low confidence identifications
[60:44] Removing interfering precursors
[60:46] Training the neural network: 23970 targets, 14953 decoys
[60:49] Number of IDs at 0.01 FDR: 7702
[60:49] Calculating protein q-values
[60:49] Number of genes identified at 1% FDR: 2003 (precursor-level), 1821 (protein-level) (inference performed using proteotypic peptides only)
[60:49] Quantification
[60:50] Quantification information saved to data2/2.mzML.quant.
[60:50] Cross-run analysis
[60:50] Reading quantification information: 2 files
[60:50] Quantifying peptides
[60:50] Assembling protein groups
Segmentation fault (core dumped)
vdemichev
commented
8 months ago
Dear Vadim When I run one.mzML file on linux, I have no problem. When I run multiple.mZML files, I report an error： ubuntu@node188:~$ ./1/diann-linux --f data2/1.mzML --f data2/2.mzML --fasta data2/4.fasta --fasta-search --gen-spec-lib --threads 6 DIA-NN 1.7.12 (Data Independent Acquisition by Neural Networks) Compiled on Dec 17 2023 14:45:00 Current date and time: Mon Dec 18 17:10:02 2023 Logical CPU cores: 16 Library-free search enabled A spectral library will be generated Thread number set to 6 Exclusion of fragments shared between heavy and light peptides from quantification is not supported in library-free mode - disabled
2 files will be processed [0:00] Loading FASTA data2/4.fasta [0:19] Processing FASTA [0:22] Assembling elution groups [1:54] 4220314 precursors generated [1:54] Gene names missing for some isoforms [1:54] Library contains 20404 proteins, and 20188 genes [1:54] Initialising library
[1:55] File #1/2 [1:55] Loading run data2/1.mzML [2:07] 1626910 library precursors are potentially detectable [2:07] Processing... [14:32] RT window set to 17.4244 [14:32] Peak width: 3.332 [14:32] Scan window radius set to 7 [26:48] Optimised mass accuracy: 6.19944 ppm [36:56] Removing low confidence identifications [36:56] Removing interfering precursors [36:57] Training the neural network: 24286 targets, 14253 decoys [37:00] Number of IDs at 0.01 FDR: 7791 [37:00] Calculating protein q-values [37:00] Number of genes identified at 1% FDR: 1984 (precursor-level), 1816 (protein-level) (inference performed using proteotypic peptides only) [37:00] Quantification [37:01] Quantification information saved to data2/1.mzML.quant.
[37:01] File #2/2 [37:01] Loading run data2/2.mzML [37:13] 1626910 library precursors are potentially detectable [37:13] Processing... [49:52] RT window set to 17.4244 [60:44] Removing low confidence identifications [60:44] Removing interfering precursors [60:46] Training the neural network: 23970 targets, 14953 decoys [60:49] Number of IDs at 0.01 FDR: 7702 [60:49] Calculating protein q-values [60:49] Number of genes identified at 1% FDR: 2003 (precursor-level), 1821 (protein-level) (inference performed using proteotypic peptides only) [60:49] Quantification [60:50] Quantification information saved to data2/2.mzML.quant.
[60:50] Cross-run analysis [60:50] Reading quantification information: 2 files [60:50] Quantifying peptides [60:50] Assembling protein groups Segmentation fault (core dumped)