Skyline-Daily v. 3.7.1.11208 CLI mProphet NullPointerException | wbarshop | 2017-08-24 20:18 | |||||||||||||||||||||||||||||||||
Hello Skyline Team! The aforementioned version of Skyline-Daily fails to correctly apply mProphet model to the data, returning a NullPointerException (as shown in the partial output below). The same command set//data works just fine under the stable v. 3.7 release. This is only the case when the analysis is done through the CLI (SkylineCmd). For reference, the command is included here: SkylineCmd --timestamp --in=combined_analysis.sky --full-scan-rt-filter-tolerance=2.0 --add-library-path=filtered.blib --import-fasta=C:\pulsar\files\staging\1953\inputs\dataset_3491.dat_corrected.fasta --decoys-add=reverse --import-all=. --reintegrate-model-name=REVERSEcombinedanalysis180434961000 --reintegrate-create-model --reintegrate-overwrite-peaks --report-add=WOHL_MSSTATS_REPORT.skyr --report-conflict-resolution=overwrite --report-name=Wohl_MSstats_Input --report-file=MSstats_input.csv --chromatogram-file=C:\pulsar\files\staging\1953\outputs\dataset_3732.dat --chromatogram-precursors --chromatogram-products --chromatogram-base-peaks --chromatogram-tics --out=docker_protection_temporary.sky Please let me know if you would like me to upload my data directly to the Skyline team to use as a test case. ========================================================================== [2017/08/24 19:49:43] 0% - Updating peak statistics [2017/08/24 19:49:45] 6% [2017/08/24 19:49:48] 12% [2017/08/24 19:49:50] 18% [2017/08/24 19:49:52] 24% [2017/08/24 19:49:54] 30% [2017/08/24 19:49:57] 36% [2017/08/24 19:49:59] 43% [2017/08/24 19:50:01] 49% [2017/08/24 19:50:03] 55% [2017/08/24 19:50:05] 61% [2017/08/24 19:50:07] 67% [2017/08/24 19:50:09] 73% [2017/08/24 19:50:12] 79% [2017/08/24 19:50:14] 84% [2017/08/24 19:50:16] 90% [2017/08/24 19:50:18] 95% [2017/08/24 19:50:49] 100% [2017/08/24 19:50:49] Creating scoring model REVERSEcombinedanalysis180434961000 [2017/08/24 19:50:51] Calculating peak group scores [2017/08/24 19:50:54] 5% [2017/08/24 19:50:56] 7% [2017/08/24 19:50:58] 9% [2017/08/24 19:51:01] 12% [2017/08/24 19:51:03] 14% [2017/08/24 19:51:05] 16% [2017/08/24 19:51:08] 19% [2017/08/24 19:51:11] 22% [2017/08/24 19:51:14] 25% [2017/08/24 19:51:16] 28% [2017/08/24 19:51:19] 31% [2017/08/24 19:51:21] 34% [2017/08/24 19:51:24] 37% [2017/08/24 19:51:26] 40% [2017/08/24 19:51:28] 43% [2017/08/24 19:51:31] 46% [2017/08/24 19:51:34] 49% [2017/08/24 19:51:37] 52% [2017/08/24 19:51:40] 55% [2017/08/24 19:51:43] 58% [2017/08/24 19:51:46] 61% [2017/08/24 19:51:49] 64% [2017/08/24 19:51:51] 67% [2017/08/24 19:51:54] 69% [2017/08/24 19:51:56] 71% [2017/08/24 19:51:58] 73% [2017/08/24 19:52:00] 75% [2017/08/24 19:52:02] 77% [2017/08/24 19:52:04] 79% [2017/08/24 19:52:06] 81% [2017/08/24 19:52:09] 84% [2017/08/24 19:52:11] 87% [2017/08/24 19:52:14] 90% [2017/08/24 19:52:16] 92% [2017/08/24 19:52:18] 94% [2017/08/24 19:52:20] 96% [2017/08/24 19:52:22] 98% [2017/08/24 19:52:23] 100% [2017/08/24 19:52:26] 0% - Training peak scoring model [2017/08/24 19:52:30] 9% - Training scoring model (iteration 1 of 10) [2017/08/24 19:52:33] 18% - Training scoring model (iteration 2 of 10 - 242,066 peaks at 2% FDR) [2017/08/24 19:52:36] 27% - Training scoring model (iteration 3 of 10 - 245,356 peaks at 2% FDR) [2017/08/24 19:52:39] 36% - Training scoring model (iteration 4 of 10 - 245,739 peaks at 2% FDR) [2017/08/24 19:52:42] 45% - Training scoring model (iteration 5 of 10 - 245,791 peaks at 2% FDR) [2017/08/24 19:52:45] 54% - Training scoring model (iteration 6 of 10 - 245,824 peaks at 2% FDR) [2017/08/24 19:52:48] 63% - Training scoring model (iteration 7 of 10 - 245,828 peaks at 2% FDR) [2017/08/24 19:52:51] 72% - Training scoring model (iteration 8 of 10 - 245,831 peaks at 2% FDR) [2017/08/24 19:52:54] 81% - Training scoring model (iteration 9 of 10 - 245,831 peaks at 2% FDR) [2017/08/24 19:52:57] 90% - Training scoring model (iteration 10 of 10 - 245,832 peaks at 2% FDR) [2017/08/24 19:52:57] 100% [2017/08/24 19:53:05] 7% - Calculating score contributions [2017/08/24 19:53:05] 100% [2017/08/24 19:53:05] Intensity: -0.3061 (-11.6 %) [2017/08/24 19:53:05] Retention time difference: -0.3580 (5.6 %) [2017/08/24 19:53:05] Retention time difference squared: 0.0057 (-0.1 %) [2017/08/24 19:53:05] Library intensity dot-product: 5.1910 (49.3 %) [2017/08/24 19:53:05] Shape (weighted): 1.7624 (20.8 %) [2017/08/24 19:53:05] Co-elution (weighted): -0.0448 (1.3 %) [2017/08/24 19:53:05] Co-elution count: -0.0136 (-0.6 %) [2017/08/24 19:53:05] Signal to noise: 0.1551 (5.1 %) [2017/08/24 19:53:05] Product mass error: -0.0513 (-0.4 %) [2017/08/24 19:53:05] Precursor-product shape score: -0.0254 (-0.3 %) [2017/08/24 19:53:05] Precursor mass error: -0.1419 (-0.4 %) [2017/08/24 19:53:05] Precursor isotope dot product: 2.7389 (26.1 %) [2017/08/24 19:53:05] Identified count: 0.5870 (5.2 %) [2017/08/24 19:53:09] Adjusting peak boundaries [2017/08/24 19:53:11] 6% [2017/08/24 19:53:13] 12% [2017/08/24 19:53:15] 18% [2017/08/24 19:53:17] 24% [2017/08/24 19:53:20] 30% [2017/08/24 19:53:22] 36% [2017/08/24 19:53:24] 42% [2017/08/24 19:53:26] 48% [2017/08/24 19:53:28] 55% [2017/08/24 19:53:31] 62% [2017/08/24 19:53:33] 68% [2017/08/24 19:53:35] 74% [2017/08/24 19:53:37] 80% [2017/08/24 19:53:40] 85% [2017/08/24 19:53:42] 90% [2017/08/24 19:53:44] 95% [2017/08/24 19:53:45] 100% [2017/08/24 19:53:45] Error: Failed to reintegrate peaks successfully. [2017/08/24 19:53:46] System.NullReferenceException: Object reference not set to an instance of an object. at pwiz.Skyline.Model.DocNodeChildren.IsOrderSame(DocNodeChildren previousChildren) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\DocNodeChildren.cs:line 45 at pwiz.Skyline.Model.DocNodeChildren..ctor(IEnumerable`1 items, IList`1 previous) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\DocNodeChildren.cs:line 20 at pwiz.Skyline.Model.DocNodeParent.set_Children(IList`1 value) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\DocNode.cs:line 384 at pwiz.Common.SystemUtil.Immutable.ChangeProp[TIm](TIm immutable, SetLambda`1 set) in c:\proj\pwiz_x64\pwiz_tools\Shared\Common\SystemUtil\Immutable.cs:line 192 at pwiz.Skyline.Model.DocNodeParent.ChangeChildren(IList`1 children, IList`1 counts, Int32 indexReplaced) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\DocNode.cs:line 0 at pwiz.Skyline.Model.DocNodeParent.ChangeChildrenChecked(IList`1 children, Boolean changeAutoManage) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\DocNode.cs:line 1170 at pwiz.Skyline.Model.SrmDocument.RegroupMolecules(IList`1 children, PeptideDocNode[] moleculeNodes, Func`3 rankChildren) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 803 at pwiz.Skyline.Model.SrmDocument.ChangeSettingsInternal(SrmSettings settingsNew, SrmSettingsChangeMonitor progressMonitor) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 995 at pwiz.Skyline.Model.MProphetResultsHandler.ChangePeaks(IProgressMonitor progressMonitor) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\MProphetResultsHandler.cs:line 177 at pwiz.Skyline.CommandLine.Reintegrate(ModelAndFeatures modelAndFeatures, Boolean isOverwritePeaks, Boolean logTraining) in c:\proj\pwiz_x64\pwiz_tools\Skyline\CommandLine.cs:line 1511 |
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