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From: Dmitry S. <Sem...@gm...> - 2020-12-10 08:47:15
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Dear colleagues, It may be the bug of issue happening after the particle polishing with the relion masking 3D protocol. It seems that it has a 10x times issue. So, adjusting the volume threshold in chimera (for 3D mask protocol and then postprocessing) till no extra noise is appeared we get the value for ex. 0.00658. But if you then put this value to the relion 3D mask protocol you get completely dark images. At the same time if you set the threshold value 0.000658 you get the fine mask. I am not sure what causes that but I noticed that behaviour happening sometimes after the execution of the Bayesian polishing. Sincerely, Dmitry P.s. it will be great to have unbiased protocol for masking Or is there any exist already? |
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From: Carlos O. S. <co...@cn...> - 2020-12-09 13:03:54
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Dear all, xmipp_volume_align with the frm option is a complicated script that starts at the shell, calls a C++ program, from the C++ we call python, which in its turn calls C++ again. Under one of these calls, the libraries seen must be different from those seen when compiling. But it is difficult to tell which one. As an alternative, if the volumes are more or less aligned you may use the local align option, instead of the frm (which is a fast global alignment). Kind regards, Carlos Oscar El 09/12/2020 a las 9:07, Juha Huiskonen escribió: > Dear All, > > I am getting a strange error with xmipp_volume_align. Otherwise xmipp > binaries work ok. > > xmipp_volume_align --i1 > Runs/016895_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2 > Runs/016895_XmippProtAlignVolumeParticles/extra/inputVolume.vol > --apply > Runs/016895_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol > --mask circular -80 --frm --copyGeo > Runs/016895_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt > 00030: RuntimeError: FATAL: module compiled as little endian, but > detected different endianness at runtime > 00031: > /projappl/project_2000637/apps/scipion/3.0/software/em/xmipp/bin/xmipp_volume_align: > line 3: 65819 Segmentation fault > $XMIPP_HOME/bin/xmipp_volume_align_prog "$@" > 00032: Traceback (most recent call last): > > Any advice on how to make this run? > > Best wishes, > Juha > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Juha H. <juh...@gm...> - 2020-12-09 08:08:53
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Dear All, I am getting a strange error with xmipp_volume_align. Otherwise xmipp binaries work ok. xmipp_volume_align --i1 Runs/016895_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2 Runs/016895_XmippProtAlignVolumeParticles/extra/inputVolume.vol --apply Runs/016895_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol --mask circular -80 --frm --copyGeo Runs/016895_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt 00030: RuntimeError: FATAL: module compiled as little endian, but detected different endianness at runtime 00031: /projappl/project_2000637/apps/scipion/3.0/software/em/xmipp/bin/xmipp_volume_align: line 3: 65819 Segmentation fault $XMIPP_HOME/bin/xmipp_volume_align_prog "$@" 00032: Traceback (most recent call last): Any advice on how to make this run? Best wishes, Juha |
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From: David M. <dma...@cn...> - 2020-12-08 16:16:10
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Hi Ane-Pascale, To be honest, I can't recognize this error. The only thing that rings the bell is the last message 《Item deepLearningToolkit-0.2[scipion-em-xmipp] already exists》 which is totally weird. Can you post here the returning message for the next commands: 'scipion3 python -m pip list', 'scipion3 installp --help' and 'scipion3 installb'. Thanks and sorry for the inconveniences.. _____ Dr. David Maluenda Niubó (+34) 619.029.310 - dma...@ub... Wavefront Engineering Group Applied Physics (UB) El lun., 7 dic. 2020 10:23, Anne-Pascale JAUDIER < ann...@i2...> escribió: > Hi Gregory, > > Effectively Ihave installed it from the command line without error. > > Thanks a lot, > Anne-Pascale > > ---------------------------------------------------------------------- > Anne-Pascale Jaudier > SICS – I2BC > Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette > 01 69 82 34 74 > > ------------------------------ > *De: *"Grigory Sharov" <sha...@gm...> > *À: *"scipion-users" <sci...@li...> > *Envoyé: *Samedi 5 Décembre 2020 14:32:44 > *Objet: *Re: [scipion-users] error installing deepLearningToolkitUtils > > Hi Anne-Pascale, > > I'm not familiar with either xmipp or plugin manager code but have you > tried "*scipion installb **deepLearningToolkit*" from the command line? > It will take about 20 min to install though.. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Fri, Dec 4, 2020 at 9:13 AM Anne-Pascale JAUDIER < > ann...@i2...> wrote: > >> Hi, >> >> I have an error during the installation of the pluggin >> deepLearningToolkitUtils. >> The error is : >> >> ------------------------------------ >> /bin/sh: 1: update: not found >> 00002: Exception in thread plugin-manager: >> 00003: Traceback (most recent call last): >> 00004: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", >> line 932, in _bootstrap_inner >> 00005: self.run() >> 00006: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", >> line 870, in run >> 00007: self._target(*self._args, **self._kwargs) >> 00008: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", >> line 740, in _applyOperations >> 00009: self.reloadInstalledPlugin(op.getObjParent()) >> 00010: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", >> line 898, in reloadInstalledPlugin >> 00011: self.tree.insert(pluginName, "end", >> 00012: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", >> line 103, in insert >> 00013: ttk.Treeview.insert(self, parent, index, iid, **kw) >> 00014: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/ttk.py", >> line 1366, in insert >> 00015: res = self.tk.call(self._w, "insert", parent, index, >> 00016: _tkinter.TclError: Item >> deepLearningToolkit-0.2[scipion-em-xmipp] already exists >> >> ----------------------------- >> >> Thanks, >> Anne-Pascale >> >> ---------------------------------------------------------------------- >> Anne-Pascale Jaudier >> SICS – I2BC >> Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette >> 01 69 82 34 74 >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir > informació confidencial o protegida legalment i s’adreça exclusivament a la > persona o entitat destinatària. Si no consteu com a destinatari final o no > teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, > modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si > l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant > el missatge com els fitxers adjunts que hi pugui haver. > > Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener > información confidencial o legalmente protegida y está exclusivamente > dirigido a la persona o entidad destinataria. Si usted no consta como > destinatario final ni es la persona encargada de recibirlo, no está > autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a > revelar su contenido. Si lo ha recibido por error, informe de ello al > remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos > que pueda contener. > > This email message and any attachments it carries may contain confidential > or legally protected material and are intended solely for the individual or > organization to whom they are addressed. If you are not the intended > recipient of this message or the person responsible for processing it, then > you are not authorized to read, save, modify, send, copy or disclose any > part of it. If you have received the message by mistake, please inform the > sender of this and eliminate the message and any attachments it carries > from your account. > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: David M. <dma...@gm...> - 2020-12-08 16:11:46
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Hi Ane-Pascale, To be honest, I can't recognize this error. The only thing that rings the bell is the last message 《Item deepLearningToolkit-0.2[scipion-em-xmipp] already exists》 which is totally weird. Can you post here the returning message for the next commands: 'scipion3 python -m pip list', 'scipion3 installp --help' and 'scipion3 installb'. Thanks and sorry for the inconveniences... _____ Dr. David Maluenda Niubó (+34) 619.029.310 - dma...@ub... Wavefront Engineering Group Applied Physics (UB) El lun., 7 dic. 2020 10:23, Anne-Pascale JAUDIER < ann...@i2...> escribió: > Hi Gregory, > > Effectively Ihave installed it from the command line without error. > > Thanks a lot, > Anne-Pascale > > ---------------------------------------------------------------------- > Anne-Pascale Jaudier > SICS – I2BC > Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette > 01 69 82 34 74 > > ------------------------------ > *De: *"Grigory Sharov" <sha...@gm...> > *À: *"scipion-users" <sci...@li...> > *Envoyé: *Samedi 5 Décembre 2020 14:32:44 > *Objet: *Re: [scipion-users] error installing deepLearningToolkitUtils > > Hi Anne-Pascale, > > I'm not familiar with either xmipp or plugin manager code but have you > tried "*scipion installb **deepLearningToolkit*" from the command line? > It will take about 20 min to install though.. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Fri, Dec 4, 2020 at 9:13 AM Anne-Pascale JAUDIER < > ann...@i2...> wrote: > >> Hi, >> >> I have an error during the installation of the pluggin >> deepLearningToolkitUtils. >> The error is : >> >> ------------------------------------ >> /bin/sh: 1: update: not found >> 00002: Exception in thread plugin-manager: >> 00003: Traceback (most recent call last): >> 00004: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", >> line 932, in _bootstrap_inner >> 00005: self.run() >> 00006: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", >> line 870, in run >> 00007: self._target(*self._args, **self._kwargs) >> 00008: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", >> line 740, in _applyOperations >> 00009: self.reloadInstalledPlugin(op.getObjParent()) >> 00010: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", >> line 898, in reloadInstalledPlugin >> 00011: self.tree.insert(pluginName, "end", >> 00012: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", >> line 103, in insert >> 00013: ttk.Treeview.insert(self, parent, index, iid, **kw) >> 00014: File >> "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/ttk.py", >> line 1366, in insert >> 00015: res = self.tk.call(self._w, "insert", parent, index, >> 00016: _tkinter.TclError: Item >> deepLearningToolkit-0.2[scipion-em-xmipp] already exists >> >> ----------------------------- >> >> Thanks, >> Anne-Pascale >> >> ---------------------------------------------------------------------- >> Anne-Pascale Jaudier >> SICS – I2BC >> Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette >> 01 69 82 34 74 >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir > informació confidencial o protegida legalment i s’adreça exclusivament a la > persona o entitat destinatària. Si no consteu com a destinatari final o no > teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, > modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si > l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant > el missatge com els fitxers adjunts que hi pugui haver. > > Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener > información confidencial o legalmente protegida y está exclusivamente > dirigido a la persona o entidad destinataria. Si usted no consta como > destinatario final ni es la persona encargada de recibirlo, no está > autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a > revelar su contenido. Si lo ha recibido por error, informe de ello al > remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos > que pueda contener. > > This email message and any attachments it carries may contain confidential > or legally protected material and are intended solely for the individual or > organization to whom they are addressed. If you are not the intended > recipient of this message or the person responsible for processing it, then > you are not authorized to read, save, modify, send, copy or disclose any > part of it. If you have received the message by mistake, please inform the > sender of this and eliminate the message and any attachments it carries > from your account. > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Anne-Pascale J. <ann...@i2...> - 2020-12-07 09:23:30
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Hi Gregory, Effectively Ihave installed it from the command line without error. Thanks a lot, Anne-Pascale ---------------------------------------------------------------------- Anne-Pascale Jaudier SICS – I2BC Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 01 69 82 34 74 De: "Grigory Sharov" <sha...@gm...> À: "scipion-users" <sci...@li...> Envoyé: Samedi 5 Décembre 2020 14:32:44 Objet: Re: [scipion-users] error installing deepLearningToolkitUtils Hi Anne-Pascale, I'm not familiar with either xmipp or plugin manager code but have you tried " scipion installb deepLearningToolkit " from the command line? It will take about 20 min to install though.. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Fri, Dec 4, 2020 at 9:13 AM Anne-Pascale JAUDIER < [ mailto:ann...@i2... | ann...@i2... ] > wrote: Hi, I have an error during the installation of the pluggin deepLearningToolkitUtils. The error is : ------------------------------------ /bin/sh: 1: update: not found 00002: Exception in thread plugin-manager: 00003: Traceback (most recent call last): 00004: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", line 932, in _bootstrap_inner 00005: self.run() 00006: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", line 870, in run 00007: self._target(*self._args, **self._kwargs) 00008: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 740, in _applyOperations 00009: self.reloadInstalledPlugin(op.getObjParent()) 00010: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 898, in reloadInstalledPlugin 00011: self.tree.insert(pluginName, "end", 00012: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 103, in insert 00013: ttk.Treeview.insert(self, parent, index, iid, **kw) 00014: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/ttk.py", line 1366, in insert 00015: res = self.tk.call(self._w, "insert", parent, index, 00016: _tkinter.TclError: Item deepLearningToolkit-0.2[scipion-em-xmipp] already exists ----------------------------- Thanks, Anne-Pascale ---------------------------------------------------------------------- Anne-Pascale Jaudier SICS – I2BC Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 01 69 82 34 74 _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2020-12-05 13:33:15
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Hi Anne-Pascale, I'm not familiar with either xmipp or plugin manager code but have you tried "*scipion installb **deepLearningToolkit*" from the command line? It will take about 20 min to install though.. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Fri, Dec 4, 2020 at 9:13 AM Anne-Pascale JAUDIER < ann...@i2...> wrote: > Hi, > > I have an error during the installation of the pluggin > deepLearningToolkitUtils. > The error is : > > ------------------------------------ > /bin/sh: 1: update: not found > 00002: Exception in thread plugin-manager: > 00003: Traceback (most recent call last): > 00004: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", > line 932, in _bootstrap_inner > 00005: self.run() > 00006: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", > line 870, in run > 00007: self._target(*self._args, **self._kwargs) > 00008: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", > line 740, in _applyOperations > 00009: self.reloadInstalledPlugin(op.getObjParent()) > 00010: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", > line 898, in reloadInstalledPlugin > 00011: self.tree.insert(pluginName, "end", > 00012: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", > line 103, in insert > 00013: ttk.Treeview.insert(self, parent, index, iid, **kw) > 00014: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/ttk.py", > line 1366, in insert > 00015: res = self.tk.call(self._w, "insert", parent, index, > 00016: _tkinter.TclError: Item deepLearningToolkit-0.2[scipion-em-xmipp] > already exists > > ----------------------------- > > Thanks, > Anne-Pascale > > ---------------------------------------------------------------------- > Anne-Pascale Jaudier > SICS – I2BC > Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette > 01 69 82 34 74 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Anne-Pascale J. <ann...@i2...> - 2020-12-04 09:13:32
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Hi, I have an error during the installation of the pluggin deepLearningToolkitUtils. The error is : ------------------------------------ /bin/sh: 1: update: not found 00002: Exception in thread plugin-manager: 00003: Traceback (most recent call last): 00004: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", line 932, in _bootstrap_inner 00005: self.run() 00006: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", line 870, in run 00007: self._target(*self._args, **self._kwargs) 00008: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 740, in _applyOperations 00009: self.reloadInstalledPlugin(op.getObjParent()) 00010: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 898, in reloadInstalledPlugin 00011: self.tree.insert(pluginName, "end", 00012: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 103, in insert 00013: ttk.Treeview.insert(self, parent, index, iid, **kw) 00014: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/ttk.py", line 1366, in insert 00015: res = self.tk.call(self._w, "insert", parent, index, 00016: _tkinter.TclError: Item deepLearningToolkit-0.2[scipion-em-xmipp] already exists ----------------------------- Thanks, Anne-Pascale ---------------------------------------------------------------------- Anne-Pascale Jaudier SICS – I2BC Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 01 69 82 34 74 |
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From: Pablo C. <pc...@cn...> - 2020-12-03 14:38:32
|
I think Gregory is right, performance decreases with higher number of protocols. Still we need to understand the whole thing. There are projects with several 100s of protocols that perform better than others with much less number. To me it seemed impossible. There are others with 2000 (this are not em related) but my "feeling" is that: 1.- number of protocols degrades performance in any case, but specially for em data (99% of our users) 2.- Specific protocols may also affect: interactive protocols or those pointing to set items (usually volumes) may be degrading. Please take this a my impression, based also in some code I've seen. Now that Scipion3 is out we will dedicate efforts in improving performance, which is been a issue for several releases now. Sorry about this. On 3/12/20 15:17, Grigory Sharov wrote: > Hi, > > I might be wrong but my feeling is that the GUI performance linked to > the total number of protocols (and checking the whole tree?) in the > project rather than the disc space it takes, since creating a new > folder should not be a problem. Pablo or Jose, correct me if I'm wrong. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Dec 3, 2020 at 1:32 PM Dmitry A. Semchonok > <sem...@gm... <mailto:sem...@gm...>> wrote: > > Dear colleagues, > > my project grew to 3.3 tb and the speed to open any made protocol > or creation of the new one takes ages. > > Is there a way to speed up the Scipion 3 ? > Any memory dedication options? > > > Thank you. > > Sincerely, > Dmitry > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2020-12-03 14:28:20
|
Hi Dmitry, unfortunately not. What I've seen for large projects is to swith to "list" view, it seems more usable. On 3/12/20 14:30, Dmitry A. Semchonok wrote: > Dear colleagues, > > my project grew to 3.3 tb and the speed to open any made protocol or > creation of the new one takes ages. > > Is there a way to speed up the Scipion 3 ? > Any memory dedication options? > > > Thank you. > > Sincerely, > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Grigory S. <sha...@gm...> - 2020-12-03 14:18:04
|
Hi, I might be wrong but my feeling is that the GUI performance linked to the total number of protocols (and checking the whole tree?) in the project rather than the disc space it takes, since creating a new folder should not be a problem. Pablo or Jose, correct me if I'm wrong. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Dec 3, 2020 at 1:32 PM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > my project grew to 3.3 tb and the speed to open any made protocol or > creation of the new one takes ages. > > Is there a way to speed up the Scipion 3 ? > Any memory dedication options? > > > Thank you. > > Sincerely, > Dmitry > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Dmitry A. S. <sem...@gm...> - 2020-12-03 13:31:06
|
Dear colleagues, my project grew to 3.3 tb and the speed to open any made protocol or creation of the new one takes ages. Is there a way to speed up the Scipion 3 ? Any memory dedication options? Thank you. Sincerely, Dmitry |
|
From: Grigory S. <sha...@gm...> - 2020-12-01 10:01:57
|
Dear Ana, you are using wrong syntax (%(JOB_NODES)d) in your hosts.conf file. Please have a look at https://scipion-em.github.io/docs/docs/scipion-modes/host-configuration.html Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Tue, Dec 1, 2020 at 9:59 AM Ana Andreea ARTENI < ana...@i2...> wrote: > > Morning, > Can you please help us to sort out this error? > My kind regards, > > The protocols xmipp3-cl2d, relion2D-classification, relion-3D initial > _model gives the same error: > > Run.stdout: > Hostname: CRYOEM-DATA-01.calcul.i2bc.paris-saclay.fr > 00003: PID: 1378 > 00004: pyworkflow: 3.0.7 > 00005: plugin: xmipp3 > 00006: currentDir: > /data/scipion/ana-andreea.arteni/ScipionUserData/projects/TutorialBetagal > 00007: workingDir: Runs/002463_XmippProtCL2D > 00008: runMode: Restart > 00009: MPI: 8 > 00010: threads: 1 > 00011: Starting at step: 1 > 00012: Running steps > 00013: STARTED: convertInputStep, step 1, time 2020-12-01 12:35:12.105220 > 00014: FINISHED: convertInputStep, step 1, time 2020-12-01 > 12:35:17.053899 > 00015: STARTED: runJob, step 2, time 2020-12-01 12:35:17.165425 > 00016: mpirun -np %(JOB_NODES)d --map-by node %(COMMAND)s > 00017: /bin/sh: 1: Syntax error: "(" unexpected > 00018: Traceback (most recent call last): > 00019: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 187, in run > 00020: self._run() > 00021: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 238, in _run > 00022: resultFiles = self._runFunc() > 00023: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 234, in _runFunc > 00024: return self._func(*self._args) > 00025: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1338, in runJob > 00026: self._stepsExecutor.runJob(self._log, program, arguments, > **kwargs) > 00027: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > 00028: process.runJob(log, programName, params, > 00029: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 51, in runJob > 00030: return runCommand(command, env, cwd) > 00031: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 66, in runCommand > 00032: check_call(command, shell=True, stdout=sys.stdout, > stderr=sys.stderr, > 00033: File > "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", > line 364, in check_call > 00034: raise CalledProcessError(retcode, cmd) > 00035: subprocess.CalledProcessError: Command 'mpirun -np %(JOB_NODES)d > --map-by node %(COMMAND)s' returned non-zero exit status 2. > 00036: Protocol failed: Command 'mpirun -np %(JOB_NODES)d --map-by node > %(COMMAND)s' returned non-zero exit status 2. > 00037: FAILED: runJob, step 2, time 2020-12-01 12:35:17.220780 > 00038: *** Last status is failed > 00039: ------------------- PROTOCOL FAILED (DONE 2/13) > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Ana A. A. <ana...@i2...> - 2020-12-01 09:59:08
|
Morning, Can you please help us to sort out this error? My kind regards, The protocols xmipp3-cl2d, relion2D-classification, relion-3D initial _model gives the same error: Run.stdout: Hostname: CRYOEM-DATA-01.calcul.i2bc.paris-saclay.fr 00003: PID: 1378 00004: pyworkflow: 3.0.7 00005: plugin: xmipp3 00006: currentDir: /data/scipion/ana-andreea.arteni/ScipionUserData/projects/TutorialBetagal 00007: workingDir: Runs/002463_XmippProtCL2D 00008: runMode: Restart 00009: MPI: 8 00010: threads: 1 00011: Starting at step: 1 00012: Running steps 00013: STARTED: convertInputStep, step 1, time 2020-12-01 12:35:12.105220 00014: FINISHED: convertInputStep, step 1, time 2020-12-01 12:35:17.053899 00015: STARTED: runJob, step 2, time 2020-12-01 12:35:17.165425 00016: mpirun -np %(JOB_NODES)d --map-by node %(COMMAND)s 00017: /bin/sh: 1: Syntax error: "(" unexpected 00018: Traceback (most recent call last): 00019: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 187, in run 00020: self._run() 00021: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run 00022: resultFiles = self._runFunc() 00023: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc 00024: return self._func(*self._args) 00025: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1338, in runJob 00026: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00027: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob 00028: process.runJob(log, programName, params, 00029: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 51, in runJob 00030: return runCommand(command, env, cwd) 00031: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 66, in runCommand 00032: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, 00033: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", line 364, in check_call 00034: raise CalledProcessError(retcode, cmd) 00035: subprocess.CalledProcessError: Command 'mpirun -np %(JOB_NODES)d --map-by node %(COMMAND)s' returned non-zero exit status 2. 00036: Protocol failed: Command 'mpirun -np %(JOB_NODES)d --map-by node %(COMMAND)s' returned non-zero exit status 2. 00037: FAILED: runJob, step 2, time 2020-12-01 12:35:17.220780 00038: *** Last status is failed 00039: ------------------- PROTOCOL FAILED (DONE 2/13) |
|
From: Anne-Pascale J. <ann...@i2...> - 2020-12-01 09:01:11
|
Oui, tu peux réessayer.
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
De: "Ana Andreea ARTENI" <ana...@i2...>
À: "scipion-users" <sci...@li...>
Envoyé: Mardi 1 Décembre 2020 09:33:29
Objet: Re: [scipion-users] error during test sphire
Morning,
This means I can try again the protocols with the last error?
a.
From: "Anne-Pascale JAUDIER" <ann...@i2...>
To: "scipion-users" <sci...@li...>
Sent: Tuesday, 1 December, 2020 09:28:05
Subject: Re: [scipion-users] error during test sphire
Hi Pablo,
Thanks a lot, it's working now.
Anne-Pascale
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
De: "Pablo Conesa" <pc...@cn...>
À: "scipion-users" <sci...@li...>
Envoyé: Lundi 30 Novembre 2020 17:21:34
Objet: Re: [scipion-users] error during test sphire
Hi Anne.
Try setting the CONDA_ACTIVATION_CMD variable like:
CONDA_ACTIVATION_CMD = . /opt/conda/etc/profile.d/conda.sh
Mind the dot (.).
If that doesn't work try:
CONDA_ACTIVATION_CMD = source /opt/conda/etc/profile.d/conda.sh
On 30/11/20 17:00, Anne-Pascale JAUDIER wrote:
Hi,
I try the following test with the following error on the command "conda activate"
The command "conda activate" is working in a interactive shell.
Thanks,
Anne-Pascale
scipion tests sphire.tests.test_protocol_janni
BQ_BEGIN
BQ_BEGIN
BQ_BEGIN
ERROR running protocol sphire - janni denoising
BQ_END
BQ_END
FAILED with error: Protocol failed: Command '/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise.py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJanniDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni_20190703.h5' returned non-zero exit status 1.
*************** LAST 50 LINES OF THE LOG *********************
threads: 1
Starting at step: 1
Running steps
STARTED: denoisingStep, step 1, time 2020-11-30 18:21:48.558591
/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise .py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJann iDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni _20190703.h5
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
-------------------------------
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
_______________________________________________
scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ]
BQ_END
--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Ana A. A. <ana...@i2...> - 2020-12-01 08:56:06
|
Soryyyy, wrong email...
Best,
ana.
From: "Ana Andreea ARTENI" <ana...@i2...>
To: "scipion-users" <sci...@li...>
Sent: Tuesday, 1 December, 2020 09:33:29
Subject: Re: [scipion-users] error during test sphire
Morning,
This means I can try again the protocols with the last error?
a.
From: "Anne-Pascale JAUDIER" <ann...@i2...>
To: "scipion-users" <sci...@li...>
Sent: Tuesday, 1 December, 2020 09:28:05
Subject: Re: [scipion-users] error during test sphire
Hi Pablo,
Thanks a lot, it's working now.
Anne-Pascale
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
De: "Pablo Conesa" <pc...@cn...>
À: "scipion-users" <sci...@li...>
Envoyé: Lundi 30 Novembre 2020 17:21:34
Objet: Re: [scipion-users] error during test sphire
Hi Anne.
Try setting the CONDA_ACTIVATION_CMD variable like:
CONDA_ACTIVATION_CMD = . /opt/conda/etc/profile.d/conda.sh
Mind the dot (.).
If that doesn't work try:
CONDA_ACTIVATION_CMD = source /opt/conda/etc/profile.d/conda.sh
On 30/11/20 17:00, Anne-Pascale JAUDIER wrote:
Hi,
I try the following test with the following error on the command "conda activate"
The command "conda activate" is working in a interactive shell.
Thanks,
Anne-Pascale
scipion tests sphire.tests.test_protocol_janni
BQ_BEGIN
BQ_BEGIN
BQ_BEGIN
ERROR running protocol sphire - janni denoising
BQ_END
BQ_END
FAILED with error: Protocol failed: Command '/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise.py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJanniDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni_20190703.h5' returned non-zero exit status 1.
*************** LAST 50 LINES OF THE LOG *********************
threads: 1
Starting at step: 1
Running steps
STARTED: denoisingStep, step 1, time 2020-11-30 18:21:48.558591
/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise .py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJann iDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni _20190703.h5
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
-------------------------------
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
_______________________________________________
scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ]
BQ_END
--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Ana A. A. <ana...@i2...> - 2020-12-01 08:33:51
|
Morning,
This means I can try again the protocols with the last error?
a.
From: "Anne-Pascale JAUDIER" <ann...@i2...>
To: "scipion-users" <sci...@li...>
Sent: Tuesday, 1 December, 2020 09:28:05
Subject: Re: [scipion-users] error during test sphire
Hi Pablo,
Thanks a lot, it's working now.
Anne-Pascale
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
De: "Pablo Conesa" <pc...@cn...>
À: "scipion-users" <sci...@li...>
Envoyé: Lundi 30 Novembre 2020 17:21:34
Objet: Re: [scipion-users] error during test sphire
Hi Anne.
Try setting the CONDA_ACTIVATION_CMD variable like:
CONDA_ACTIVATION_CMD = . /opt/conda/etc/profile.d/conda.sh
Mind the dot (.).
If that doesn't work try:
CONDA_ACTIVATION_CMD = source /opt/conda/etc/profile.d/conda.sh
On 30/11/20 17:00, Anne-Pascale JAUDIER wrote:
Hi,
I try the following test with the following error on the command "conda activate"
The command "conda activate" is working in a interactive shell.
Thanks,
Anne-Pascale
scipion tests sphire.tests.test_protocol_janni
BQ_BEGIN
BQ_BEGIN
BQ_BEGIN
ERROR running protocol sphire - janni denoising
BQ_END
BQ_END
FAILED with error: Protocol failed: Command '/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise.py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJanniDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni_20190703.h5' returned non-zero exit status 1.
*************** LAST 50 LINES OF THE LOG *********************
threads: 1
Starting at step: 1
Running steps
STARTED: denoisingStep, step 1, time 2020-11-30 18:21:48.558591
/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise .py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJann iDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni _20190703.h5
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
-------------------------------
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
_______________________________________________
scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ]
BQ_END
--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Anne-Pascale J. <ann...@i2...> - 2020-12-01 08:28:55
|
Hi Pablo,
Thanks a lot, it's working now.
Anne-Pascale
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
De: "Pablo Conesa" <pc...@cn...>
À: "scipion-users" <sci...@li...>
Envoyé: Lundi 30 Novembre 2020 17:21:34
Objet: Re: [scipion-users] error during test sphire
Hi Anne.
Try setting the CONDA_ACTIVATION_CMD variable like:
CONDA_ACTIVATION_CMD = . /opt/conda/etc/profile.d/conda.sh
Mind the dot (.).
If that doesn't work try:
CONDA_ACTIVATION_CMD = source /opt/conda/etc/profile.d/conda.sh
On 30/11/20 17:00, Anne-Pascale JAUDIER wrote:
Hi,
I try the following test with the following error on the command "conda activate"
The command "conda activate" is working in a interactive shell.
Thanks,
Anne-Pascale
scipion tests sphire.tests.test_protocol_janni
BQ_BEGIN
BQ_BEGIN
BQ_BEGIN
ERROR running protocol sphire - janni denoising
BQ_END
BQ_END
FAILED with error: Protocol failed: Command '/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise.py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJanniDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni_20190703.h5' returned non-zero exit status 1.
*************** LAST 50 LINES OF THE LOG *********************
threads: 1
Starting at step: 1
Running steps
STARTED: denoisingStep, step 1, time 2020-11-30 18:21:48.558591
/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise .py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJann iDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni _20190703.h5
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
-------------------------------
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
_______________________________________________
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Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
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From: Pablo C. <pc...@cn...> - 2020-11-30 16:21:46
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Hi Anne. Try setting the CONDA_ACTIVATION_CMD variable like: CONDA_ACTIVATION_CMD = . /opt/conda/etc/profile.d/conda.sh Mind the dot (.). If that doesn't work try: CONDA_ACTIVATION_CMD = source /opt/conda/etc/profile.d/conda.sh On 30/11/20 17:00, Anne-Pascale JAUDIER wrote: > Hi, > > I try the following test with the following error on the command "conda activate" > The command "conda activate" is working in a interactive shell. > > Thanks, > Anne-Pascale > > scipion tests sphire.tests.test_protocol_janni > >>>> ERROR running protocol sphire - janni denoising > FAILED with error: Protocol failed: Command '/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise.py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJanniDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni_20190703.h5' returned non-zero exit status 1. > > *************** LAST 50 LINES OF THE LOG ********************* > > threads: 1 > Starting at step: 1 > Running steps > STARTED: denoisingStep, step 1, time 2020-11-30 18:21:48.558591 > /opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise .py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJann iDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni _20190703.h5 > > CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. > To initialize your shell, run > > $ conda init <SHELL_NAME> > > Currently supported shells are: > - bash > - fish > - tcsh > - xonsh > - zsh > ------------------------------- > > ---------------------------------------------------------------------- > Anne-Pascale Jaudier > SICS – I2BC > Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette > 01 69 82 34 74 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry S. <Sem...@gm...> - 2020-11-30 16:15:33
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Dear Grigory, I guess I spotted the issue — the original files were stored under the symbolic link (in the protocol — import movies) and later were removed from there. So that possibly cased the issue. Please let me fix it — I will report if that was the case. Thank you! Sincerely, Dmitry > On 30. Nov 2020, at 16:20, Grigory Sharov <sha...@gm...> wrote: > > Hi Dmitry, > > could you please send me: > > - Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star , > - first hundred lines of Runs/037414_ProtRelionBayesianPolishing/input_particles.star and > - any star file from Runs/037414_ProtRelionBayesianPolishing/input/ folder? > > then we can go from there. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Mon, Nov 30, 2020 at 3:13 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > Dear colleagues, > > > A compatibility question: > > > I have a project done by SCIPION 2.0: including relion particle polishing > > Now when I open it with SCIPION 3.0 all works fine except Bayesian polishing. > > > The error is : > > Using dose per frame from Runs/037414_ProtRelionBayesianPolishing/input/FoilHole_15002836_Data_15054168_15054170_20200615_191823_Fractions.star: 1 e/A^2 > > 02673: in: /home/user/Data/Software/Scipion3/software/em/relion-3.1.0/src/jaz/micrograph_handler.cpp, line 211 > > 02674: ERROR: > > 02675: ERROR: Not a single movie contains the requested number of frames (119) > > 02676: === Backtrace === > > 02677: relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x453571] > > 02678: relion_motion_refine(_ZN17MicrographHandler20findLongEnoughMoviesERKSt6vectorI13MetaDataTableSaIS1_EEii+0x44d) [0x53272d] > > 02679: relion_motion_refine(_ZN13MotionRefiner4initEv+0xee3) [0x47db43] > > 02680: relion_motion_refine(main+0x31) [0x428841] > > 02681: /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd0b7c19555] > > 02682: relion_motion_refine() [0x42955f] > > 02683: ================== > > 02684: ERROR: > > 02685: ERROR: Not a single movie contains the requested number of frames (119) > > 02686: Traceback (most recent call last): > > 02687: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 187, in run > > 02688: self._run() > > 02689: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run > > 02690: resultFiles = self._runFunc() > > 02691: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc > > 02692: return self._func(*self._args) > > 02693: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 309, in trainOrPolishStep > > 02694: self.runJob(prog, args) > > 02695: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1338, in runJob > > 02696: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) > > 02697: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob > > 02698: process.runJob(log, programName, params, > > 02699: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 51, in runJob > > 02700: return runCommand(command, env, cwd) > > 02701: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 66, in runCommand > > 02702: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, > > 02703: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", line 364, in check_call > > 02704: raise CalledProcessError(retcode, cmd) > > 02705: subprocess.CalledProcessError: Command 'relion_motion_refine --i Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o Runs/037414_ProtRelionBayesianPolishing/extra --f Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1. > > 02706: Protocol failed: Command 'relion_motion_refine --i Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o Runs/037414_ProtRelionBayesianPolishing/extra --f Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1. > > 02707: FAILED: trainOrPolishStep, step 2, time 2020-11-30 16:07:27.531346 > > 02708: *** Last status is failed > > 02709: ------------------- PROTOCOL FAILED (DONE 2/2) > > > > Could that be a consequence that the motion correction was done in relion-motioncor protocol in SCIPION 2.0 and SCIPION 3.0 has the newer relion-motion correction protocol? (The indirect sign I see in the output relion-motioncor file). > > > Thank you in advance. > > > Sincerely, > > Dmitry > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Anne-Pascale J. <ann...@i2...> - 2020-11-30 16:01:10
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Hi,
I try the following test with the following error on the command "conda activate"
The command "conda activate" is working in a interactive shell.
Thanks,
Anne-Pascale
scipion tests sphire.tests.test_protocol_janni
>>> ERROR running protocol sphire - janni denoising
FAILED with error: Protocol failed: Command '/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise.py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJanniDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni_20190703.h5' returned non-zero exit status 1.
*************** LAST 50 LINES OF THE LOG *********************
threads: 1
Starting at step: 1
Running steps
STARTED: denoisingStep, step 1, time 2020-11-30 18:21:48.558591
/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise .py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJann iDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni _20190703.h5
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
-------------------------------
----------------------------------------------------------------------
Anne-Pascale Jaudier
SICS – I2BC
Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
01 69 82 34 74
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From: Grigory S. <sha...@gm...> - 2020-11-30 15:21:17
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Hi Dmitry, could you please send me: - Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star , - first hundred lines of Runs/037414_ProtRelionBayesianPolishing/input_particles.star and - any star file from Runs/037414_ProtRelionBayesianPolishing/input/ folder? then we can go from there. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Nov 30, 2020 at 3:13 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear colleagues, > > > > A compatibility question: > > > > I have a project done by SCIPION 2.0: including relion particle polishing > > Now when I open it with SCIPION 3.0 all works fine except Bayesian > polishing. > > > The error is : > > Using dose per frame from > Runs/037414_ProtRelionBayesianPolishing/input/FoilHole_15002836_Data_15054168_15054170_20200615_191823_Fractions.star: > 1 e/A^2 > > 02673: in: > /home/user/Data/Software/Scipion3/software/em/relion-3.1.0/src/jaz/micrograph_handler.cpp, > line 211 > > 02674: ERROR: > > 02675: ERROR: Not a single movie contains the requested number of frames > (119) > > 02676: === Backtrace === > > 02677: relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x453571] > > 02678: > relion_motion_refine(_ZN17MicrographHandler20findLongEnoughMoviesERKSt6vectorI13MetaDataTableSaIS1_EEii+0x44d) > [0x53272d] > > 02679: relion_motion_refine(_ZN13MotionRefiner4initEv+0xee3) [0x47db43] > > 02680: relion_motion_refine(main+0x31) [0x428841] > > 02681: /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd0b7c19555] > > 02682: relion_motion_refine() [0x42955f] > > 02683: ================== > > 02684: ERROR: > > 02685: ERROR: Not a single movie contains the requested number of frames > (119) > > 02686: Traceback (most recent call last): > > 02687: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 187, in run > > 02688: self._run() > > 02689: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 238, in _run > > 02690: resultFiles = self._runFunc() > > 02691: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 234, in _runFunc > > 02692: return self._func(*self._args) > > 02693: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", > line 309, in trainOrPolishStep > > 02694: self.runJob(prog, args) > > 02695: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1338, in runJob > > 02696: self._stepsExecutor.runJob(self._log, program, arguments, > **kwargs) > > 02697: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > > 02698: process.runJob(log, programName, params, > > 02699: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 51, in runJob > > 02700: return runCommand(command, env, cwd) > > 02701: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 66, in runCommand > > 02702: check_call(command, shell=True, stdout=sys.stdout, > stderr=sys.stderr, > > 02703: File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", line > 364, in check_call > > 02704: raise CalledProcessError(retcode, cmd) > > 02705: subprocess.CalledProcessError: Command 'relion_motion_refine --i > Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o > Runs/037414_ProtRelionBayesianPolishing/extra --f > Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref > 0.96120 --corr_mic > Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star > --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac > 0.500 --params3 --j 14 ' returned non-zero exit status 1. > > 02706: Protocol failed: Command 'relion_motion_refine --i > Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o > Runs/037414_ProtRelionBayesianPolishing/extra --f > Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref > 0.96120 --corr_mic > Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star > --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac > 0.500 --params3 --j 14 ' returned non-zero exit status 1. > > 02707: FAILED: trainOrPolishStep, step 2, time 2020-11-30 16:07:27.531346 > > 02708: *** Last status is failed > > 02709: ------------------- PROTOCOL FAILED (DONE 2/2) > > > > > > Could that be a consequence that the motion correction was done in > relion-motioncor protocol in SCIPION 2.0 and SCIPION 3.0 has the newer > relion-motion correction protocol? (The indirect sign I see in the output > relion-motioncor file). > > > > Thank you in advance. > > > > Sincerely, > > Dmitry > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2020-11-30 15:13:35
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Dear colleagues, A compatibility question: I have a project done by SCIPION 2.0: including relion particle polishing Now when I open it with SCIPION 3.0 all works fine except Bayesian polishing. The error is : Using dose per frame from Runs/037414_ProtRelionBayesianPolishing/input/FoilHole_15002836_Data_15054168_15054170_20200615_191823_Fractions.star: 1 e/A^2 02673: in: /home/user/Data/Software/Scipion3/software/em/relion-3.1.0/src/jaz/micrograph_handler.cpp, line 211 02674: ERROR: 02675: ERROR: Not a single movie contains the requested number of frames (119) 02676: === Backtrace === 02677: relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x453571] 02678: relion_motion_refine(_ZN17MicrographHandler20findLongEnoughMoviesERKSt6vectorI13MetaDataTableSaIS1_EEii+0x44d) [0x53272d] 02679: relion_motion_refine(_ZN13MotionRefiner4initEv+0xee3) [0x47db43] 02680: relion_motion_refine(main+0x31) [0x428841] 02681: /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd0b7c19555] 02682: relion_motion_refine() [0x42955f] 02683: ================== 02684: ERROR: 02685: ERROR: Not a single movie contains the requested number of frames (119) 02686: Traceback (most recent call last): 02687: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 187, in run 02688: self._run() 02689: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 238, in _run 02690: resultFiles = self._runFunc() 02691: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 234, in _runFunc 02692: return self._func(*self._args) 02693: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 309, in trainOrPolishStep 02694: self.runJob(prog, args) 02695: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1338, in runJob 02696: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 02697: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob 02698: process.runJob(log, programName, params, 02699: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 51, in runJob 02700: return runCommand(command, env, cwd) 02701: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 66, in runCommand 02702: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, 02703: File "/home/user/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", line 364, in check_call 02704: raise CalledProcessError(retcode, cmd) 02705: subprocess.CalledProcessError: Command 'relion_motion_refine --i Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o Runs/037414_ProtRelionBayesianPolishing/extra --f Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1. 02706: Protocol failed: Command 'relion_motion_refine --i Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o Runs/037414_ProtRelionBayesianPolishing/extra --f Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.96120 --corr_mic Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1. 02707: FAILED: trainOrPolishStep, step 2, time 2020-11-30 16:07:27.531346 02708: *** Last status is failed 02709: ------------------- PROTOCOL FAILED (DONE 2/2) Could that be a consequence that the motion correction was done in relion-motioncor protocol in SCIPION 2.0 and SCIPION 3.0 has the newer relion-motion correction protocol? (The indirect sign I see in the output relion-motioncor file). Thank you in advance. Sincerely, Dmitry |
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From: Pablo C. <pc...@cn...> - 2020-11-26 12:17:39
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Great! On 26/11/20 12:23, Dmitry A. Semchonok wrote: > Dear colleagues, > > I am not sure how but currently the issue is solved. Probably it was > connected with ScipionUserData being copied from the other scipion > installation. > > Thank you! > > Sincerely, > Dmitry > > On November 26, 2020 11:54:51 AM Pablo Conesa <pc...@cn...> wrote: > >> Ok, let me understand. >> >> Dmitry, you have folder >> "/home/user/Data/ScipionUserData/projects/scratch/" that does not >> contain project.sqlite (thus the warning) >> >> Now, why is that folder there? What does it contain? Is that an >> actual project? >> >> >> On 26/11/20 11:46, Grigory Sharov wrote: >>> Honestly not sure if there's a solution besides editing sqlite >>> files. Maybe Pablo or Jose Miguel can reply to the thread. >>> >>> Best regards, >>> Grigory >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >>> e-mail: gs...@mr... <mailto:gs...@mr...> >>> >>> >>> On Wed, Nov 25, 2020 at 3:55 PM Dmitry A. Semchonok >>> <sem...@gm... <mailto:sem...@gm...>> wrote: >>> >>> Dear Grigory, >>> >>> Yes, it probably was removed unintrendedly. >>> >>> Sincerely, >>> Dmitry >>> >>> On November 25, 2020 4:19:35 PM Grigory Sharov >>> <sha...@gm... <mailto:sha...@gm...>> wrote: >>> >>>> Hi, >>>> >>>> did you remove >>>> /home/user/Data/ScipionUserData/projects/scratch/ folder? >>>> >>>> Best regards, >>>> Grigory >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >>>> e-mail: gs...@mr... >>>> <mailto:gs...@mr...> >>>> >>>> >>>> On Wed, Nov 25, 2020 at 9:50 AM Dmitry Semchonok >>>> <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>>> >>>> Dear colleagues, >>>> >>>> Small question. >>>> >>>> I have an issue with some error message in the terminal. >>>> >>>> How to remove it? >>>> >>>> Thank you! >>>> >>>> >>>> Sincerely, >>>> Dmitry >>>> >>>> >>>> ERROR loading project: scratch >>>> Project database not found at >>>> '/home/user/Data/ScipionUserData/projects/scratch/project.sqlite' >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> <mailto:sci...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> <mailto:scipion-users%40lists.sourceforge.net> >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> -- >> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:scipion-users%40lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry A. S. <sem...@gm...> - 2020-11-26 11:24:00
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Dear colleagues, I am not sure how but currently the issue is solved. Probably it was connected with ScipionUserData being copied from the other scipion installation. Thank you! Sincerely, Dmitry On November 26, 2020 11:54:51 AM Pablo Conesa <pc...@cn...> wrote: > Ok, let me understand. > Dmitry, you have folder > "/home/user/Data/ScipionUserData/projects/scratch/" that does not contain > project.sqlite (thus the warning) > Now, why is that folder there? What does it contain? Is that an actual project? > > On 26/11/20 11:46, Grigory Sharov wrote: >> Honestly not sure if there's a solution besides editing sqlite files. Maybe >> Pablo or Jose Miguel can reply to the thread. >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 >> e-mail: gs...@mr... >> >> >> On Wed, Nov 25, 2020 at 3:55 PM Dmitry A. Semchonok <sem...@gm...> >> wrote: >> Dear Grigory, >> >> Yes, it probably was removed unintrendedly. >> >> Sincerely, >> Dmitry >> >> On November 25, 2020 4:19:35 PM Grigory Sharov <sha...@gm...> >> wrote: >>> Hi, >>> >>> did you remove /home/user/Data/ScipionUserData/projects/scratch/ folder? >>> >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 >>> e-mail: gs...@mr... >>> >>> >>> On Wed, Nov 25, 2020 at 9:50 AM Dmitry Semchonok <Sem...@gm...> wrote: >>> Dear colleagues, >>> >>> Small question. >>> >>> I have an issue with some error message in the terminal. >>> >>> How to remove it? >>> >>> Thank you! >>> >>> >>> Sincerely, >>> Dmitry >>> >>> >>> >>> ERROR loading project: scratch >>> Project database not found at >>> '/home/user/Data/ScipionUserData/projects/scratch/project.sqlite' >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > Pablo Conesa - Madrid Scipion team > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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