Hello,
I`ve recently acquired your software suite (3.0.1), and while I am impressed by it`s ease of use and flexibility, I have repeatedly encountered more insidious errors which make me concerned that something is not quite right with my installation.
(MacBook Pro, 2018, OsX Catalina, AND Ubuntu (64 bit), running on a VirtualBox VM)
On both my personal laptop and the virtual machine, I find routine tasks such as manual peak picking and editing peak lists seem to cause errors (causing the program to freeze), and periodically crashing. At first I thought this was just another Catalina problem, but after experiencing the same issues on the Ubuntu machine, I am curious as to the requirements of the software.
particularly, I am interested on knowing if a dedicated machine (running Ubuntu) will run the software properly, or if there may be any python preferences that can be adjusted to allow the program to run more effectively.
The error I am getting Reads, from the command line: path/to/bin/assign: line 8: 23718 killed `${ANACONDA3}`/bin/python -w ignore `{$ANALYSIS}` $*
While I am expecting that this is something wrong with my installation, system settings, or packages, I would appreciate any information on the technical limitations of the program, as I am experiencing these problems with the smaller, 2D 15N-HSQC datasets, and am concerned that the problems will become worse with larger spectra.
Hi William,
Thank you for reporting this issue. I believe is related to the particular Python distribution which probably is not compatible to your machines.
We are running on CentOS 7.5 (VM) without known issues.
Are you able to post the full error trace?
I will do my best to replicate the issue and post it in this thread. the terminal output seems not to show much else (aside from what appear to be mouse actions preceding the event), are there any log files that I should post?
Thank you very much. You can run the program in debug mode as ./assign --debug to get some extra information.
Here is the output from the crash, I think it happens when you use the vertical and horizontal traces (?), which seem to adversely affect the performance of the program. In addition, the file used is in the `.nv` format
Program licence (non-profit) valid until Tue Oct 6 11:26:22 2020
==================================================================================================================
| AnalysisAssign, version: 3.0.1.1 |
| |
| Copyright © CCPN project (http://www.ccpn.ac.uk) 2014 - 2020 |
| |
| CCPN licence. See http://www.ccpn.ac.uk/v3-software/licences. Not to be distributed without prior consent! |
| |
| Developed by: Ed Brooksbank, Luca Mureddu, Timothy J Ragan & Geerten W Vuister |
| |
| Please cite: Skinner, S.P., Fogh, R.H., Boucher, W., Ragan, T.J., Mureddu, L.G., & Vuister, G.W. |
| CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis |
| J.Biomol.Nmr (2016), 66, 111-124, http://doi.org/10.1007/s10858-016-0060-y |
| |
| DISCLAIMER: This program is offered `as-is`. Under no circumstances will the authors, CCPN, |
| the Department of Molecular and Cell Biology, or the University of Leicester be |
| liable of any damage, loss of data, loss of revenue or any other undesired |
| consequences originating from the usage of this software. |
==================================================================================================================
==> Getting user preferences
==> Language set to `English-UK`
==> Creating new, empty project
INFO : Located at /tmp/CcpnProject_eatft_op.ccpn (Logging._info:109)
DEBUG : MainWindow>> project: <PR:default> (Logging._debug1:88)
DEBUG : MainWindow>> project._appBase: <ccpn.AnalysisAssign.AnalysisAssign.Assign object at 0x7f2f39d17c70> (Logging._debug1:88)
DEBUG : GuiMainWindow: layout: <PyQt5.QtWidgets.QLayout object at 0x7f2f39d218b0> (Logging._debug1:88)
DEBUG : GuiMainWindow.moduleArea: layout: <PyQt5.QtWidgets.QVBoxLayout object at 0x7f2f39d21b80> (Logging._debug1:88)
DEBUG : MainWindow>> project._mainWindow: <GW:Main> (Logging._debug1:88)
DEBUG : MainWindow>> application from QtCore..: <ccpn.AnalysisAssign.AnalysisAssign.Assign object at 0x7f2f39d17c70> (Logging._debug1:88)
DEBUG : MainWindow>> application.project: <PR:default> (Logging._debug1:88)
DEBUG : MainWindow>> application._mainWindow: <GW:Main> (Logging._debug1:88)
DEBUG : MainWindow>> application.ui.mainWindow: <GW:Main> (Logging._debug1:88)
DEBUG : >>>framework._initialiseProject (Logging._debug1:88)
==> Done, AnalysisAssign is starting
DEBUG : >>> dropped: /media/sf_datasets/N-HSQC_10.nv (Logging._debug1:88)
INFO : Handling urls... (Logging._info:109)
DEBUG : >>> dropped: /media/sf_datasets/N-HSQC_10.nv (Logging._debug1:88)
INFO : mainWindow.createSpectrumDisplay(spectrum=`SP:N-HSQC_10`, displayAxisCodes=(), axisOrder=(), title=None, positions=(), widths=(), units=(), stripDirection=`Y`, is1D=False, position=None, relativeTo=None) (Logging._info:109)
DEBUG : SpectrumDisplayNd>> project: <PR:default>, project._appBase: <ccpn.AnalysisAssign.AnalysisAssign.Assign object at 0x7f2f39d17c70> (Logging._debug1:88)
DEBUG : GuiSpectrumDisplay>> mainWindow, name: <GW:Main> SpectrumDisplay:HN (Logging._debug1:88)
DEBUG : CcpnModule>>> <class `ccpn.ui.gui.Gui.SpectrumDisplayNd`> <GW:Main> (Logging._debug1:88)
DEBUG : StripNd>> spectrumDisplay: <GD:HN> (Logging._debug1:88)
DEBUG : GuiStrip>>> spectrumDisplay: <GD:HN> (Logging._debug1:88)
DEBUG : SpectrumViewNd>> <GV:HN.1.N-HSQC_10> <GS:HN.1> (Logging._debug1:88)
INFO : estimating noise level for spectrum SP:N-HSQC_10 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 455348.18730239844 (Logging._info:109)
INFO : spectrum.negativeContourBase = -455348.18730239844 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 643959.7813576742 (Logging._info:109)
INFO : spectrum.negativeContourBase = -643959.7813576742 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 910696.9382329618 (Logging._info:109)
INFO : spectrum.negativeContourBase = -910696.9382329618 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 1287920.35980619 (Logging._info:109)
INFO : spectrum.negativeContourBase = -1287920.35980619 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 1821395.0037229513 (Logging._info:109)
INFO : spectrum.negativeContourBase = -1821395.0037229513 (Logging._info:109)
INFO : get(`PL:N-HSQC_10.1`).pickPeaksRegion(regionToPick={`H`: [5.2, 12.25], `N`: [101.04, 133.03]}, doPos=True, doNeg=False, minLinewidth=None, exclusionBuffer=None, minDropFactor=0.1, checkAllAdjacent=True, fitMethod=`parabolic`, excludedRegions=None, excludedDiagonalDims=None, excludedDiagonalTransform=None, estimateLineWidths=False) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[10.117713514715433, 115.11061589606106]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[9.623358689248562, 113.40151057951152]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[9.304569128900766, 116.7571929693222]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[10.169, 10.159], [117.132, 117.257]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[10.210116285830736, 113.27645409293473]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[9.115143448114395, 112.42190143465996]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[9.031980954110622, 115.94432580657303]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[10.538146123290062, 118.73725400678813]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[9.637219104915857, 110.96290909126401]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[9.466273978352547, 111.60903427191079]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.583827514201403, 110.50436864048243]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.784543544054031, 112.63032891228795]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.83331499621272, 112.10926021821797]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[9.239887189120054, 110.58773963153362]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.950145845301449, 122.89537155255675]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.002093392424285, 119.06864344328642]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.101888387463987, 117.47042170353234]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.466140119358897, 120.89196683652699]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.3044180776923895, 121.29714981280267]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.975984703749418, 115.91722194291651]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.961015454493463, 117.53795384801924]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.626702221110463, 116.1873439271003]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.184099019505084, 114.84163142740726]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.520693087950349, 111.55920163728297]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.592140106775332, 111.27762538846582]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.688988748355769, 115.61077145952731]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.009994847991038, 116.18315855879337]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.158391828357708, 115.23067065142095]) (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 1287920.35980619 (Logging._info:109)
INFO : spectrum.negativeContourBase = -1287920.35980619 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 910696.9382329619 (Logging._info:109)
INFO : spectrum.negativeContourBase = -910696.9382329619 (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.865503261447884, 118.04788589570671]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.277109783724882, 118.87069596257061]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.678561840672046, 119.55935021489859]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.624670305696782, 120.1496244110167]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.70043086935766, 120.1227937657386]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.769162102369592, 120.24800344370306]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.793374241271522, 120.08254779782146]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.480959545762744, 119.91262037772685]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.894127980573103, 120.35085425060242]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.910529752087314, 120.6504631228745]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.908186641870998, 120.16303973365575]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.878507245797664, 120.04677360411733]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.8558571803732775, 119.97522521670908]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.8699158416711725, 119.36259214952588]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.865229621238541, 119.76505182869732]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.982385132054333, 118.74548730812967]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.937866037944332, 118.69182601757348]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.915215972519945, 118.64710827544332]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.7996225351816975, 118.839394566603]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.807432902569417, 118.83045101817697]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[7.703, 7.701], [118.263, 118.249]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.485646389890462, 118.68734916299582]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.485646389890462, 118.74995400197804]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.60123982722871, 117.95397819206119]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.583275982236955, 117.92267577257007]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.398951311886776, 118.10601851530373]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.534851704433095, 119.29998223017901]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.484084316412918, 118.08813141845167]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.3591181905940175, 119.58170852717012]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.312256174220238, 117.1803635219112]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.328657945734449, 117.53810545895249]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.1466763856005855, 117.07751271501184]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.524115673266351, 114.8193620457314]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.70428876474034, 115.04275916749611]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.642318402067758, 115.10846420330927]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.42542213271372, 116.09403974050656]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.701993566122837, 116.35685988375917]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.625104412436485, 116.30429585510865]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.605595224187709, 116.50798146612942]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.61362841934897, 116.01519369753078]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.722650353680365, 115.33186132507399]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.7593735315604135, 115.33186132507399]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[7.523, 7.897], [114.353, 115.713]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.198903978802264, 116.73137845750898]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.232184358756058, 116.7379489610903]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.224151163594797, 116.3962827748619]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.09791523963213, 116.37000076053664]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.061192061752081, 116.33057773904875]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[7.3, 8.034], [114.445, 115.141]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[7.49, 7.903], [114.721, 115.621]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.400880977045745, 115.72609420819208]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.309073032345623, 115.18731291452423]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.289563844096847, 113.84693018393591]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.381371788796969, 113.78122514812276]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.708437591791153, 113.76808414096013]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.701551995938644, 113.42641795473173]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.041682393406518, 115.26615895750001]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[8.042, 8.042], [115.49, 115.509]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.004959215526469, 116.88250283850357]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.097914759535342, 116.9416373707354]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.315958628198132, 116.849650320597]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.25398826552555, 116.44884960213676]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.173656313912943, 116.90221434924752]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.16332792013418, 116.50141363078728]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.166770718060434, 116.12689492665231]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.215354570304044, 115.16390125430189]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.238146154471906, 115.39174387627281]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.23452844269923, 115.69415317452513]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[8.18, 8.182], [115.682, 115.684]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.171580257854657, 115.2819651584141]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.173750884918263, 115.10590495052747]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.451733906171285, 116.75293307611719]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.432759834919125, 118.51451259036548]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.408642738300841, 118.49196878192015]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.398306839750148, 118.64132151287049]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[8.3633616589359, 118.61877770442516]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.891355478903279, 118.59622817626223]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.878559020231478, 120.51809288118966]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.867238750390243, 120.31238062912598]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.985363045474514, 121.25640024221502]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.930238253204152, 120.96896668453701]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.919410169008188, 121.20285869715735]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.740746967261657, 121.69036480668001]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.711708014190663, 121.53537612361833]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.630497382720932, 121.22258078143932]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.815066999697592, 121.377569464501]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.7801218188833445, 121.37193351238966]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.874621462775394, 122.05951966997236]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.769785920332652, 121.546648027841]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.654614479339216, 120.99150674487464]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.547810194315389, 120.74634282803163]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.445435352099594, 121.07605148549192]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.429193225805648, 121.83408704446629]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.389818330237176, 122.08770002331585]) (Logging._info:109)
DEBUG : CcpnModule>>> <class `ccpn.ui.gui.modules.PeakTable.PeakTableModule`> <GW:Main> (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : application.showPeakTable() (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.468568033480551, 121.64245980652049]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.509911627683323, 121.2253993502818]) (Logging._info:109)
DEBUG : Closing <pyqtgraph.dockarea.Container.HContainer object at 0x7f2f0633ef70> (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 643959.7813576742 (Logging._info:109)
INFO : spectrum.negativeContourBase = -643959.7813576742 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 455348.18730239844 (Logging._info:109)
INFO : spectrum.negativeContourBase = -455348.18730239844 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 321979.69140625 (Logging._info:109)
INFO : spectrum.negativeContourBase = -321979.69140625 (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[7.157, 7.217], [123.92, 123.81]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.066548800095916, 124.03832614421844]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.991794866509736, 124.08064521849155]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.9506802030373365, 123.91983273625374]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.216056667268276, 123.58974395692348]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.172450206009671, 124.28377677500248]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.172450206009671, 124.28377677500248]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.9556637986097485, 124.89317144453526]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.742615087889135, 124.81699711084366]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.707729918882251, 124.49537214636803]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.691533233271912, 124.19067481160164]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.6093039063271135, 124.74928659200668]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[6.761, 6.761], [124.978, 124.978]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[6.915, 6.819], [125.401, 125.435]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.9494343041442335, 125.40100033581257]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.523793693864718, 122.35402698814869]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.6770392577163875, 123.14116176962852]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.721891617868096, 123.3612209558487]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[7.564, 7.656], [123.564, 123.556]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickRegion(selectedRegion=[[7.45, 7.468], [123.209, 123.336]]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.40418740012683, 123.03113217651844]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.199859981657937, 124.20760244131088]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.199859981657937, 124.20760244131088]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.425367681309581, 124.35995110869408]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.231007453985512, 126.54361534118652]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.142548632575199, 126.62825348973274]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.072778294561431, 126.55207915604115]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[6.9731063831131905, 124.563082665205]) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.037893125554547, 124.58847410976887]) (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 455348.18730239844 (Logging._info:109)
INFO : spectrum.negativeContourBase = -455348.18730239844 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 643959.7813576742 (Logging._info:109)
INFO : spectrum.negativeContourBase = -643959.7813576742 (Logging._info:109)
DEBUG : Added undoPoint (Logging._debug1:88)
DEBUG : Added undoPoint (Logging._debug1:88)
INFO : spectrum = project.getByPid(SP:N-HSQC_10) (Logging._info:109)
INFO : spectrum.positiveContourBase = 910696.9382329618 (Logging._info:109)
INFO : spectrum.negativeContourBase = -910696.9382329618 (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4948, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4942, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4971, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4974, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5022, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5059, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5058, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5090, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5107, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5109, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5110, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1321], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5227, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1291], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5213, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1088], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5255, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1087], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 996], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5351, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1014], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5487, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5486, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5485, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5476, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1013], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5474, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 972], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5116, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5119, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5244, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 955], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5445, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 908], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5370, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 815], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5273, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 785], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5179, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 786], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 962], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5118, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 956], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5144, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 953], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5153, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 954], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5152, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5151, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 949], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5139, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5138, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 950], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5141, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5147, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5148, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 952], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.216056667268276, 125.6041318923235]) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1397], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5203, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5204, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1389], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[5036, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4977, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1172], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4702, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1112], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4689, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1095], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4797, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1097], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4802, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1096], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4827, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`GS:HN.1`).peakPickPosition(inPosition=[7.743071593111381, 123.51356875896454]) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1255], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4565, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1144], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4900, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1307], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4473, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1304], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4477, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1296], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[4511, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1661], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[3980, 1], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[1, 1660], xDim=1, yDim=2) (Logging._info:109)
INFO : get(`SP:N-HSQC_10`).getPlaneData(position=[3978, 1], xDim=1, yDim=2) (Logging._info:109)
/home/thyran/Documents/ccpnmr3.0.1/bin/assign: line 8: 2691 Killed `${ANACONDA3}`/bin/python -W ignore `${ANALYSIS}` $*
Thank you for the trace.
Can I ask you which Ubuntu version are you running?
If this will not cause any inconvenience, would you like to try a CentOS VM until we find the source of these crashes on Ubuntu?
We have one ready in our 3.0.0 download webpage:
http://www.ccpn.ac.uk/download/3.0.0/ccpnmr3.0.0VM.zip
you will need download again the 3.0.1 from:
http://www.ccpn.ac.uk/download/3.0.1/ccp...entOS7.tgz
The Ubuntu version is 20.04 focal (64 bit, if the system type doesn`t already make that clear in some way). I appreciate the help!
On the topic of your VM release, is the release compatible with the guest additions module in VirtualBox?
Hi William and Luca,
just a couple more thoughts:
One is that you can always try using the NMRBox version (https://nmrbox.org/) if you are struggling with your local installation. Anyone can register for an account and you basically run everything remotely on the NMRBox servers.
With respect to Ubuntu, we do have a version compiled on an Ubuntu VM (16.04) (http://www.ccpn.ac.uk/download/3.0.1/ccp...u16.04.tgz). I can`t remember the details, but there were some issues when Ed did the build on a newer version of Ubuntu (I think older versions struggled). So there could be some mismatch somewhere. Could it be worth trying a 16.04 Ubuntu VM?
Best wishes,
Vicky
Dear William,
I have created an Ubuntu 20.04 VM and downloaded/installed the 3.0.1 (including updates) which was built on Ubuntu 16 .
I was not able to reproduce any crashes.
I haven`t installed any additional `guest support` on Ubuntu 20.04. Not sure what you need from the guest addition in particular, but I noticed both mouse pointer/ displays and sharing files are (for me) quite well supported in Vbox 6.1 without any additions (both for Ubuntu and CentOS VM).
Related to this, I have followed this https://www.if-not-true-then-false.com/2...-hat-rhel/
for installing Guest additions on CentOS VM, but I actually corrupted the VM! So I would not recommend.
Do you have any other Anaconda/Miniconda or Python installation in your machine? I wonder if there is some conflict.
Can I also ask you if you have the AutoBackup enabled from Preferences?