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From: abhisek M. <abh...@gm...> - 2017-08-28 07:33:40
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Hi, I was recently trying to install scipion package but hitting an error every time. "./scipion install" command yields following error: scons: *** [software/em/xmipp/external/imagej/ij.jar] Source `software/em/xmipp/external/imagej.tgz' not found, needed by target `software/em/xmipp/external/imagej/ij.jar'. Seems imageJ is not available. Is there any way to overcome this issue ? Some advice regarding the same will be highly appreciated. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* |
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From: Jose M. de la R. T. <del...@gm...> - 2017-08-25 15:59:57
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Hi Dmitry, The "optimize" mode is not another protocol, but a mode, i.e, an option that you should select when filling in the protocol parameter (see attached image). The relion autopicking should be done in 3 steps: 1) Run the autopick in "optimize" mode for a subset of micrographs (either selected automatically by the protocol, covering the defocus range or you can provide a subset manually created) 2) Open again the protocol after step 1) and click on the wizard to interactively fine tune the picking parameters (interparticle distance and threshold). It should open the Xmipp picking interface, but it will launch the Relion auto-picking program and show the particles. 3) After selecting the good parameters, now you can run the auto-picking for all the input set of micrographs. All the 3 steps are done in the same protocol run (box in the processing tree). Hope this helps Best, Jose Miguel On Fri, Aug 25, 2017 at 4:52 PM, D.A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > Does anyone knows how to use relion-autopick protocol? > > It asks me to run "optimize" mode first and I have not found that in the > list of protocols > > > Any suggestions? > > Sincerely, > Dmitry > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: D.A. S. <sem...@gm...> - 2017-08-25 14:52:33
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Dear colleagues, Does anyone knows how to use relion-autopick protocol? It asks me to run "optimize" mode first and I have not found that in the list of protocols Any suggestions? Sincerely, Dmitry |
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From: Annelie O. <ann...@um...> - 2017-08-24 09:27:05
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Hi, I have installed Scipion v.1.1 and are running your suggested test to see that everything works well. Unfortunately I get error-messages when running a few of your tests, for example Medium tests Xmipp workflow and Mixed Workflow Initial volume (error messages attached). Could you please help me figure out what could be wrong. Thank you! Best regards, Annelie Annelie Olofsson, PhD ann...@um... Umeå University, Sweden |
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From: JOSUE G. B. <jg...@cn...> - 2017-08-18 15:15:17
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Hi all: The relion patch is already installed in Scipion. To install the updated relion, remove all relion-2.0 folders and files (rm -rf relion-2.0*) from software/em/ folder. Then, re-install relion from scipion (scipion install relion -j N --no-xmipp). Best, Josue Dear David, Thanks for your feedback, Juha Huiskonen also asked about this patch today. We will apply it to the distributed version with Scipion (2.0.4) and send instructions soon about how to do it for an existing installation. Best, Jose Miguel On Thu, Aug 17, 2017 at 9:34 PM, David Belnap <dbelnap@...> wrote: > Could you please instruct us how to install the RELION patch to fix the > recently discovered RELION bug (mention by Bjoern Forsberg today) in our > SCIPION installation of RELION? > > Thanks. > > David > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > scipion-users@... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: JOSE L. V. P. <jl...@cn...> - 2017-08-17 21:39:14
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Hola José Miguel ¿Qué tal por ahí? Puedes comprobar tu afiliación para ponerla en la revisión del artículo. Antes de enviarlo, os lo pasaré a todos, pero es para que vaya ya bien puesta Un salugo Vilas |
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From: JOSE L. V. P. <jl...@cn...> - 2017-08-17 21:18:34
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I am sorry for my last email I commit an error with email address Regards José Luis Vilas |
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From: Jose M. de la R. T. <del...@gm...> - 2017-08-17 20:48:01
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Dear David, Thanks for your feedback, Juha Huiskonen also asked about this patch today. We will apply it to the distributed version with Scipion (2.0.4) and send instructions soon about how to do it for an existing installation. Best, Jose Miguel On Thu, Aug 17, 2017 at 9:34 PM, David Belnap <db...@co...> wrote: > Could you please instruct us how to install the RELION patch to fix the > recently discovered RELION bug (mention by Bjoern Forsberg today) in our > SCIPION installation of RELION? > > Thanks. > > David > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: David B. <db...@co...> - 2017-08-17 19:34:36
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Could you please instruct us how to install the RELION patch to fix the recently discovered RELION bug (mention by Bjoern Forsberg today) in our SCIPION installation of RELION? Thanks. David |
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From: Jose M. de la R. T. <del...@gm...> - 2017-08-09 20:58:34
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Ok, I'm sorry, I think I confused this protocol with another one. I will try to reproduce you same workflow to verify what is happening. On Wed, Aug 9, 2017 at 10:53 PM, David Belnap <db...@co...> wrote: > Jose Miguel, > > I don’t get another SetOfMicrographs from the ‘ctf - assign’ protocol I > ran. See attached picture. (The name for the green box underneath the > ‘Protocol Run’ window is ‘import micrographs dose weighted’.) > > David > > > On Aug 9, 2017, at 2:14 PM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > > Hi David, > > I think that after the 'ctf - assign' protocol both SetOfCTF and > SetOfMicrographs are created. The resulting micrographs are the one that > have been "linked" to CTF info. Have you used those one in the protocol > 'xmipp - particle extraction' ? (you can select Micrographs source "Other" > and provide those ones). > > Hope this helps, > Jose Miguel > > > On Wed, Aug 9, 2017 at 9:19 PM, David Belnap <db...@co...> > wrote: > >> I have a new data set made up of dose-weighted and non-dose-weighted >> micrographs. I did CTF estimation from the non-dose-weighted group and >> selected the best micrographs from that set and then used CTF assign to >> assign CTFs to the dose-weighted group. After selecting particles, I am >> ready to extract them. But, when I use “xmipp3 extract particles”, I don’t >> see any CTF object in the selection window. I do see the particle >> coordinates in that selection window. I’ve attached images. >> >> Thanks. >> >> David >> >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > |
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From: David B. <db...@co...> - 2017-08-09 20:53:42
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Jose Miguel, I don’t get another SetOfMicrographs from the ‘ctf - assign’ protocol I ran. See attached picture. (The name for the green box underneath the ‘Protocol Run’ window is ‘import micrographs dose weighted’.) David On Aug 9, 2017, at 2:14 PM, Jose Miguel de la Rosa Trevin <del...@gm...<mailto:del...@gm...>> wrote: Hi David, I think that after the 'ctf - assign' protocol both SetOfCTF and SetOfMicrographs are created. The resulting micrographs are the one that have been "linked" to CTF info. Have you used those one in the protocol 'xmipp - particle extraction' ? (you can select Micrographs source "Other" and provide those ones). Hope this helps, Jose Miguel On Wed, Aug 9, 2017 at 9:19 PM, David Belnap <db...@co...<mailto:db...@co...>> wrote: I have a new data set made up of dose-weighted and non-dose-weighted micrographs. I did CTF estimation from the non-dose-weighted group and selected the best micrographs from that set and then used CTF assign to assign CTFs to the dose-weighted group. After selecting particles, I am ready to extract them. But, when I use “xmipp3 extract particles”, I don’t see any CTF object in the selection window. I do see the particle coordinates in that selection window. I’ve attached images. Thanks. David ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://Slashdot.org>! http://sdm.link/slashdot _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users [cid:076...@en...] |
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From: Jose M. de la R. T. <del...@gm...> - 2017-08-09 20:14:45
|
Hi David, I think that after the 'ctf - assign' protocol both SetOfCTF and SetOfMicrographs are created. The resulting micrographs are the one that have been "linked" to CTF info. Have you used those one in the protocol 'xmipp - particle extraction' ? (you can select Micrographs source "Other" and provide those ones). Hope this helps, Jose Miguel On Wed, Aug 9, 2017 at 9:19 PM, David Belnap <db...@co...> wrote: > I have a new data set made up of dose-weighted and non-dose-weighted > micrographs. I did CTF estimation from the non-dose-weighted group and > selected the best micrographs from that set and then used CTF assign to > assign CTFs to the dose-weighted group. After selecting particles, I am > ready to extract them. But, when I use “xmipp3 extract particles”, I don’t > see any CTF object in the selection window. I do see the particle > coordinates in that selection window. I’ve attached images. > > Thanks. > > David > > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: David B. <db...@co...> - 2017-08-09 19:55:21
|
I have a new data set made up of dose-weighted and non-dose-weighted micrographs. I did CTF estimation from the non-dose-weighted group and selected the best micrographs from that set and then used CTF assign to assign CTFs to the dose-weighted group. After selecting particles, I am ready to extract them. But, when I use “xmipp3 extract particles”, I don’t see any CTF object in the selection window. I do see the particle coordinates in that selection window. I’ve attached images. Thanks. David [cid:6A4...@en...][cid:35B...@en...] |
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From: Burcham, R. G <rod...@va...> - 2017-08-07 17:21:02
|
Scipion Development Team: I have encountered an issue with the "xmipp3 - extract particle pairs" protocol running Scipion as distributed in SBGrid. The full run.stdout log is attached; the relevant output for the failed step is included here: 01337: STARTED: createOutputStep, step 791 01338: 2017-08-07 10:00:01.087211 01339: Traceback (most recent call last): 01340: File "/home/sbgrid/programs/x86_64-linux/scipion/1.1/pyworkflow/protocol/executor.py", line 137, in run 01341: self.step._run() # not self.step.run() , to avoid race conditions 01342: File "/home/sbgrid/programs/x86_64-linux/scipion/1.1/pyworkflow/protocol/protocol.py", line 228, in _run 01343: resultFiles = self._runFunc() 01344: File "/home/sbgrid/programs/x86_64-linux/scipion/1.1/pyworkflow/protocol/protocol.py", line 224, in _runFunc 01345: return self._func(*self._args) 01346: File "/home/sbgrid/programs/x86_64-linux/scipion/1.1/pyworkflow/em/packages/xmipp3/protocol_extract_particles_pairs.py", line 312, in createOutputStep 01347: if imgU.isEnabled() and imgT.isEnabled(): 01348: AttributeError: 'NoneType' object has no attribute 'isEnabled' 01349: Protocol failed: 'NoneType' object has no attribute 'isEnabled' 01350: FAILED: createOutputStep, step 791 01351: 2017-08-07 10:00:05.257749 01352: ------------------- PROTOCOL FAILED (DONE 791/791) Briefly, the protocol successfully performs preprocessing and particle extraction steps for each image, but fails at the final write output step. This protocol was run using Scipion version 1.1, but I have the same problem in version 1.0.1. XMIPP is version 3.2. Please advise as to what configuration or data issues may cause this error to arise. Thanks, Rodger Burcham |
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From: Grigory S. <sha...@gm...> - 2017-07-24 09:05:14
|
Hi Lars, yes, it is MPI-related. I suggest to verify that all MPI-related vars in scipion.conf file point to correct path where your 1.10.2 is installed (see here <https://github.com/I2PC/scipion/wiki/Scipion-Configuration>). After that you can check whether mpi works by simply running in command line: scipion run mpirun -np 4 hostname 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 267542 <+44%201223%20267542> e-mail: gs...@mr... On Sun, Jul 23, 2017 at 9:48 PM, Lars-Anders Carlson < lar...@um...> wrote: > Thanks for the advise, the run.stdout is attached. It seems the error may > be related to MPI? We have Open MPI 1.10.2 installed and it's working fine > for other things, but maybe we need to change something for Scipion? > > Cheers, > > Lars > > > > ------------------------------ > *From:* Grigory Sharov <sha...@gm...> > *Sent:* 23 July 2017 20:40 > *Cc:* sci...@li... > *Subject:* Re: [scipion-users] scipion 1.1 running test failure > > Not exactly. The file you should look for is ScipionUserData/projects/ > TestXmippWorkflow/Runs/***_XmippProtML2D/logs/run.stdout > > It would be great if you could attach this file here. > > 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 267542 <+44%201223%20267542> > e-mail: gs...@mr... > > On Sun, Jul 23, 2017 at 7:17 PM, Lars-Anders Carlson < > lar...@um...> wrote: > >> Hi Grigory, >> The subdirectory (of TestXmippWorkflow) Logs is empty. Is that where I'd >> expect the log files to be? >> Cheers, >> Lars >> >> On 2017-07-23 20:13, Grigory Sharov wrote: >> >>> Hello Lars, >>> >>> if you open the test project and find the failed protocol, the output >>> logs should give more details why it didn't work. >>> >>> 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 267542 <tel:+44%201223%20267542> >>> e-mail: gs...@mr... <mailto:gs...@mr...> >>> >>> On Sun, Jul 23, 2017 at 6:55 PM, Lars-Anders Carlson >>> <lar...@um... <mailto:lar...@um...>> wrote: >>> >>> Hi scipion team, >>> We've just installed Scipion 1.1 and started going through the >>> running test from Small towards Large. All the small tests were >>> successful (although with the message "Some paths do not exist in: >>> /usr/local/cuda-7.5/lib64" that others also reported - we ignored it >>> for now). But the Xmipp Workflow test failed with the message below. >>> Any idea what happened? I apologise if I'm overlooking something >>> obvious at this point.. >>> Thanks a lot in advance, >>> Lars >>> >>> >>> >>> >>> ERROR running protocol scipion - ml2d >>> FAILED with error: >>> >>> [ FAILED ] TestXmippWorkflow.testXmippWorkflow >>> >>> Traceback (most recent call last): >>> File >>> "/usr/local/bin/scipion/software/lib/python2.7/unittest/case.py", >>> line 329, in run >>> testMethod() >>> File >>> "/usr/local/bin/scipion/pyworkflow/tests/em/workflows/test_w >>> orkflow_xmipp.py", >>> line 138, in testXmippWorkflow >>> self.launchProtocol(protML2D) >>> File "/usr/local/bin/scipion/pyworkflow/tests/tests.py", line 102, >>> in launchProtocol >>> raise Exception("ERROR launching protocol.") >>> Exception: ERROR launching protocol. >>> >>> [==========] run 1 tests (139.809 secs) >>> [ FAILED ] 1 tests >>> [ PASSED ] 0 tests >>> >>> >>> >>> >>> >>> --- >>> Lars-Anders Carlson >>> Assistant Professor >>> Dept of Medical Biochemistry and Biophysics >>> Wallenberg Centre for Molecular Medicine >>> Umeå University >>> 901 87 Umeå, Sweden >>> >>> lab website including OPEN POSITIONS: >>> http://www.carlsonlab.se/ >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> 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> >>> >>> >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> -- >> Lars-Anders Carlson >> Assistant Professor >> Dept of Medical Biochemistry and Biophysics >> Wallenberg Centre for Molecular Medicine >> Umeå University >> 901 87 Umeå, Sweden >> >> lab website including OPEN POSITIONS: >> http://www.carlsonlab.se/ >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Lars-Anders C. <lar...@um...> - 2017-07-23 20:49:01
|
Thanks for the advise, the run.stdout is attached. It seems the error may be related to MPI? We have Open MPI 1.10.2 installed and it's working fine for other things, but maybe we need to change something for Scipion?
Cheers,
Lars
________________________________
From: Grigory Sharov <sha...@gm...>
Sent: 23 July 2017 20:40
Cc: sci...@li...
Subject: Re: [scipion-users] scipion 1.1 running test failure
Not exactly. The file you should look for is ScipionUserData/projects/TestXmippWorkflow/Runs/***_XmippProtML2D/logs/run.stdout
It would be great if you could attach this file here.
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 267542<tel:+44%201223%20267542>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Sun, Jul 23, 2017 at 7:17 PM, Lars-Anders Carlson <lar...@um...<mailto:lar...@um...>> wrote:
Hi Grigory,
The subdirectory (of TestXmippWorkflow) Logs is empty. Is that where I'd expect the log files to be?
Cheers,
Lars
On 2017-07-23 20:13, Grigory Sharov wrote:
Hello Lars,
if you open the test project and find the failed protocol, the output
logs should give more details why it didn't work.
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 267542<tel:%2B44%20%280%29%201223%20267542> <tel:+44%201223%20267542>
e-mail: gs...@mr...<mailto:gs...@mr...> <mailto:gs...@mr...<mailto:gs...@mr...>>
On Sun, Jul 23, 2017 at 6:55 PM, Lars-Anders Carlson
<lar...@um...<mailto:lar...@um...> <mailto:lar...@um...<mailto:lar...@um...>>> wrote:
Hi scipion team,
We've just installed Scipion 1.1 and started going through the
running test from Small towards Large. All the small tests were
successful (although with the message "Some paths do not exist in:
/usr/local/cuda-7.5/lib64" that others also reported - we ignored it
for now). But the Xmipp Workflow test failed with the message below.
Any idea what happened? I apologise if I'm overlooking something
obvious at this point..
Thanks a lot in advance,
Lars
>>> ERROR running protocol scipion - ml2d
FAILED with error:
[ FAILED ] TestXmippWorkflow.testXmippWorkflow
Traceback (most recent call last):
File
"/usr/local/bin/scipion/software/lib/python2.7/unittest/case.py",
line 329, in run
testMethod()
File
"/usr/local/bin/scipion/pyworkflow/tests/em/workflows/test_workflow_xmipp.py",
line 138, in testXmippWorkflow
self.launchProtocol(protML2D)
File "/usr/local/bin/scipion/pyworkflow/tests/tests.py", line 102,
in launchProtocol
raise Exception("ERROR launching protocol.")
Exception: ERROR launching protocol.
[==========] run 1 tests (139.809 secs)
[ FAILED ] 1 tests
[ PASSED ] 0 tests
---
Lars-Anders Carlson
Assistant Professor
Dept of Medical Biochemistry and Biophysics
Wallenberg Centre for Molecular Medicine
Umeå University
901 87 Umeå, Sweden
lab website including OPEN POSITIONS:
http://www.carlsonlab.se/
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
<mailto:sci...@li...<mailto:sci...@li...>>
https://lists.sourceforge.net/lists/listinfo/scipion-users
<https://lists.sourceforge.net/lists/listinfo/scipion-users>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Lars-Anders Carlson
Assistant Professor
Dept of Medical Biochemistry and Biophysics
Wallenberg Centre for Molecular Medicine
Umeå University
901 87 Umeå, Sweden
lab website including OPEN POSITIONS:
http://www.carlsonlab.se/
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Jose M. de la R. T. <del...@gm...> - 2017-07-23 18:46:03
|
Hi Lars,
As Grigory mentioned, you should look at which protocol failed and then
look into its log file.
After launching the logs....you can run the following command (assuming
that you are running
scipion script from the installation folder):
./scipion last &
This should open the last project (the failed one) and then you can check
which protocol
failed...and look its log in
ScipionUserData/TestProjectName/Runs/0000xxx_FailledProtocol/logs/
Hope this helps,
Jose Miguel
On Sun, Jul 23, 2017 at 8:40 PM, Grigory Sharov <sha...@gm...>
wrote:
> Not exactly. The file you should look for is ScipionUserData/projects/
> TestXmippWorkflow/Runs/***_XmippProtML2D/logs/run.stdout
>
> It would be great if you could attach this file here.
>
> 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 267542 <+44%201223%20267542>
> e-mail: gs...@mr...
>
> On Sun, Jul 23, 2017 at 7:17 PM, Lars-Anders Carlson <
> lar...@um...> wrote:
>
>> Hi Grigory,
>> The subdirectory (of TestXmippWorkflow) Logs is empty. Is that where I'd
>> expect the log files to be?
>> Cheers,
>> Lars
>>
>> On 2017-07-23 20:13, Grigory Sharov wrote:
>>
>>> Hello Lars,
>>>
>>> if you open the test project and find the failed protocol, the output
>>> logs should give more details why it didn't work.
>>>
>>> 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 267542 <tel:+44%201223%20267542>
>>> e-mail: gs...@mr... <mailto:gs...@mr...>
>>>
>>> On Sun, Jul 23, 2017 at 6:55 PM, Lars-Anders Carlson
>>> <lar...@um... <mailto:lar...@um...>> wrote:
>>>
>>> Hi scipion team,
>>> We've just installed Scipion 1.1 and started going through the
>>> running test from Small towards Large. All the small tests were
>>> successful (although with the message "Some paths do not exist in:
>>> /usr/local/cuda-7.5/lib64" that others also reported - we ignored it
>>> for now). But the Xmipp Workflow test failed with the message below.
>>> Any idea what happened? I apologise if I'm overlooking something
>>> obvious at this point..
>>> Thanks a lot in advance,
>>> Lars
>>>
>>>
>>>
>>> >>> ERROR running protocol scipion - ml2d
>>> FAILED with error:
>>>
>>> [ FAILED ] TestXmippWorkflow.testXmippWorkflow
>>>
>>> Traceback (most recent call last):
>>> File
>>> "/usr/local/bin/scipion/software/lib/python2.7/unittest/case.py",
>>> line 329, in run
>>> testMethod()
>>> File
>>> "/usr/local/bin/scipion/pyworkflow/tests/em/workflows/test_w
>>> orkflow_xmipp.py",
>>> line 138, in testXmippWorkflow
>>> self.launchProtocol(protML2D)
>>> File "/usr/local/bin/scipion/pyworkflow/tests/tests.py", line 102,
>>> in launchProtocol
>>> raise Exception("ERROR launching protocol.")
>>> Exception: ERROR launching protocol.
>>>
>>> [==========] run 1 tests (139.809 secs)
>>> [ FAILED ] 1 tests
>>> [ PASSED ] 0 tests
>>>
>>>
>>>
>>>
>>>
>>> ---
>>> Lars-Anders Carlson
>>> Assistant Professor
>>> Dept of Medical Biochemistry and Biophysics
>>> Wallenberg Centre for Molecular Medicine
>>> Umeå University
>>> 901 87 Umeå, Sweden
>>>
>>> lab website including OPEN POSITIONS:
>>> http://www.carlsonlab.se/
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> 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>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>> --
>> Lars-Anders Carlson
>> Assistant Professor
>> Dept of Medical Biochemistry and Biophysics
>> Wallenberg Centre for Molecular Medicine
>> Umeå University
>> 901 87 Umeå, Sweden
>>
>> lab website including OPEN POSITIONS:
>> http://www.carlsonlab.se/
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
|
|
From: Grigory S. <sha...@gm...> - 2017-07-23 18:40:42
|
Not exactly. The file you should look for is
ScipionUserData/projects/TestXmippWorkflow/Runs/***_XmippProtML2D/logs/run.stdout
It would be great if you could attach this file here.
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 267542 <+44%201223%20267542>
e-mail: gs...@mr...
On Sun, Jul 23, 2017 at 7:17 PM, Lars-Anders Carlson <
lar...@um...> wrote:
> Hi Grigory,
> The subdirectory (of TestXmippWorkflow) Logs is empty. Is that where I'd
> expect the log files to be?
> Cheers,
> Lars
>
> On 2017-07-23 20:13, Grigory Sharov wrote:
>
>> Hello Lars,
>>
>> if you open the test project and find the failed protocol, the output
>> logs should give more details why it didn't work.
>>
>> 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 267542 <tel:+44%201223%20267542>
>> e-mail: gs...@mr... <mailto:gs...@mr...>
>>
>> On Sun, Jul 23, 2017 at 6:55 PM, Lars-Anders Carlson
>> <lar...@um... <mailto:lar...@um...>> wrote:
>>
>> Hi scipion team,
>> We've just installed Scipion 1.1 and started going through the
>> running test from Small towards Large. All the small tests were
>> successful (although with the message "Some paths do not exist in:
>> /usr/local/cuda-7.5/lib64" that others also reported - we ignored it
>> for now). But the Xmipp Workflow test failed with the message below.
>> Any idea what happened? I apologise if I'm overlooking something
>> obvious at this point..
>> Thanks a lot in advance,
>> Lars
>>
>>
>>
>> >>> ERROR running protocol scipion - ml2d
>> FAILED with error:
>>
>> [ FAILED ] TestXmippWorkflow.testXmippWorkflow
>>
>> Traceback (most recent call last):
>> File
>> "/usr/local/bin/scipion/software/lib/python2.7/unittest/case.py",
>> line 329, in run
>> testMethod()
>> File
>> "/usr/local/bin/scipion/pyworkflow/tests/em/workflows/test_
>> workflow_xmipp.py",
>> line 138, in testXmippWorkflow
>> self.launchProtocol(protML2D)
>> File "/usr/local/bin/scipion/pyworkflow/tests/tests.py", line 102,
>> in launchProtocol
>> raise Exception("ERROR launching protocol.")
>> Exception: ERROR launching protocol.
>>
>> [==========] run 1 tests (139.809 secs)
>> [ FAILED ] 1 tests
>> [ PASSED ] 0 tests
>>
>>
>>
>>
>>
>> ---
>> Lars-Anders Carlson
>> Assistant Professor
>> Dept of Medical Biochemistry and Biophysics
>> Wallenberg Centre for Molecular Medicine
>> Umeå University
>> 901 87 Umeå, Sweden
>>
>> lab website including OPEN POSITIONS:
>> http://www.carlsonlab.se/
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> 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>
>>
>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
> --
> Lars-Anders Carlson
> Assistant Professor
> Dept of Medical Biochemistry and Biophysics
> Wallenberg Centre for Molecular Medicine
> Umeå University
> 901 87 Umeå, Sweden
>
> lab website including OPEN POSITIONS:
> http://www.carlsonlab.se/
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Lars-Anders C. <lar...@um...> - 2017-07-23 18:18:26
|
Hi Grigory,
The subdirectory (of TestXmippWorkflow) Logs is empty. Is that where I'd
expect the log files to be?
Cheers,
Lars
On 2017-07-23 20:13, Grigory Sharov wrote:
> Hello Lars,
>
> if you open the test project and find the failed protocol, the output
> logs should give more details why it didn't work.
>
> 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 267542 <tel:+44%201223%20267542>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
> On Sun, Jul 23, 2017 at 6:55 PM, Lars-Anders Carlson
> <lar...@um... <mailto:lar...@um...>> wrote:
>
> Hi scipion team,
> We've just installed Scipion 1.1 and started going through the
> running test from Small towards Large. All the small tests were
> successful (although with the message "Some paths do not exist in:
> /usr/local/cuda-7.5/lib64" that others also reported - we ignored it
> for now). But the Xmipp Workflow test failed with the message below.
> Any idea what happened? I apologise if I'm overlooking something
> obvious at this point..
> Thanks a lot in advance,
> Lars
>
>
>
> >>> ERROR running protocol scipion - ml2d
> FAILED with error:
>
> [ FAILED ] TestXmippWorkflow.testXmippWorkflow
>
> Traceback (most recent call last):
> File
> "/usr/local/bin/scipion/software/lib/python2.7/unittest/case.py",
> line 329, in run
> testMethod()
> File
> "/usr/local/bin/scipion/pyworkflow/tests/em/workflows/test_workflow_xmipp.py",
> line 138, in testXmippWorkflow
> self.launchProtocol(protML2D)
> File "/usr/local/bin/scipion/pyworkflow/tests/tests.py", line 102,
> in launchProtocol
> raise Exception("ERROR launching protocol.")
> Exception: ERROR launching protocol.
>
> [==========] run 1 tests (139.809 secs)
> [ FAILED ] 1 tests
> [ PASSED ] 0 tests
>
>
>
>
>
> ---
> Lars-Anders Carlson
> Assistant Professor
> Dept of Medical Biochemistry and Biophysics
> Wallenberg Centre for Molecular Medicine
> Umeå University
> 901 87 Umeå, Sweden
>
> lab website including OPEN POSITIONS:
> http://www.carlsonlab.se/
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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>
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
--
Lars-Anders Carlson
Assistant Professor
Dept of Medical Biochemistry and Biophysics
Wallenberg Centre for Molecular Medicine
Umeå University
901 87 Umeå, Sweden
lab website including OPEN POSITIONS:
http://www.carlsonlab.se/
|
|
From: Grigory S. <sha...@gm...> - 2017-07-23 18:14:24
|
Hello Lars,
if you open the test project and find the failed protocol, the output logs
should give more details why it didn't work.
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 267542 <+44%201223%20267542>
e-mail: gs...@mr...
On Sun, Jul 23, 2017 at 6:55 PM, Lars-Anders Carlson <
lar...@um...> wrote:
> Hi scipion team,
> We've just installed Scipion 1.1 and started going through the running
> test from Small towards Large. All the small tests were successful
> (although with the message "Some paths do not exist in:
> /usr/local/cuda-7.5/lib64" that others also reported - we ignored it for
> now). But the Xmipp Workflow test failed with the message below. Any idea
> what happened? I apologise if I'm overlooking something obvious at this
> point..
> Thanks a lot in advance,
> Lars
>
>
>
> >>> ERROR running protocol scipion - ml2d
> FAILED with error:
>
> [ FAILED ] TestXmippWorkflow.testXmippWorkflow
>
> Traceback (most recent call last):
> File "/usr/local/bin/scipion/software/lib/python2.7/unittest/case.py",
> line 329, in run
> testMethod()
> File "/usr/local/bin/scipion/pyworkflow/tests/em/workflows/test_workflow_xmipp.py",
> line 138, in testXmippWorkflow
> self.launchProtocol(protML2D)
> File "/usr/local/bin/scipion/pyworkflow/tests/tests.py", line 102, in
> launchProtocol
> raise Exception("ERROR launching protocol.")
> Exception: ERROR launching protocol.
>
> [==========] run 1 tests (139.809 secs)
> [ FAILED ] 1 tests
> [ PASSED ] 0 tests
>
>
>
>
>
> ---
> Lars-Anders Carlson
> Assistant Professor
> Dept of Medical Biochemistry and Biophysics
> Wallenberg Centre for Molecular Medicine
> Umeå University
> 901 87 Umeå, Sweden
>
> lab website including OPEN POSITIONS:
> http://www.carlsonlab.se/
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Lars-Anders C. <lar...@um...> - 2017-07-23 17:55:37
|
Hi scipion team,
We've just installed Scipion 1.1 and started going through the running test from Small towards Large. All the small tests were successful (although with the message "Some paths do not exist in: /usr/local/cuda-7.5/lib64" that others also reported - we ignored it for now). But the Xmipp Workflow test failed with the message below. Any idea what happened? I apologise if I'm overlooking something obvious at this point..
Thanks a lot in advance,
Lars
>>> ERROR running protocol scipion - ml2d
FAILED with error:
[ FAILED ] TestXmippWorkflow.testXmippWorkflow
Traceback (most recent call last):
File "/usr/local/bin/scipion/software/lib/python2.7/unittest/case.py", line 329, in run
testMethod()
File "/usr/local/bin/scipion/pyworkflow/tests/em/workflows/test_workflow_xmipp.py", line 138, in testXmippWorkflow
self.launchProtocol(protML2D)
File "/usr/local/bin/scipion/pyworkflow/tests/tests.py", line 102, in launchProtocol
raise Exception("ERROR launching protocol.")
Exception: ERROR launching protocol.
[==========] run 1 tests (139.809 secs)
[ FAILED ] 1 tests
[ PASSED ] 0 tests
---
Lars-Anders Carlson
Assistant Professor
Dept of Medical Biochemistry and Biophysics
Wallenberg Centre for Molecular Medicine
Umeå University
901 87 Umeå, Sweden
lab website including OPEN POSITIONS:
http://www.carlsonlab.se/
|
|
From: Jose M. de la R. T. <del...@gm...> - 2017-07-21 08:03:05
|
Dear Samson, Have you tried to launch scipion from the folder where do you installed it? If you installed in path /path/to/scipion, then you should do: cd /path/to/scipion ./scipion and this should launch the GUI. Please not that we do not add anything to the .bashrc, so if you want to make scipion available as a command you should add the following line to your .bashrc (or equivalent in your system) to point to the scipion main script: alias scipion='/path/to/scipion/scipion' Regarding helical processing, there is an ongoing work to add the Relion helical programs, but still is not ready to use. We will inform when is it available here in the list. Best, Jose Miguel On Fri, Jul 21, 2017 at 9:03 AM, Pablo Conesa <su...@bc...> wrote: > Hi Samson, > > Could you provide some more information? Is there anything written in the > console? In hat case, could you please send it? > > All the best, Pablo. > Scipion team > > Activo Vie, 21 Julio at 9:01 AM , Samson Ali <a.s...@gm...> > Escrito: > Dear Sirs, > I have installed scipion unto my computer according as stated in the > installation guide but I cannot launch the scipion program. Please can you > help? Can I do helical processing on scipion? > I look forward to hearing from you soon. > Thanks. > > Samson > (IMCB, Singapore) > > 185:553135 > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Pablo C. <su...@bc...> - 2017-07-21 07:03:20
|
Hi Samson,
Could you provide some more information? Is there anything written in the console? In hat case, could you please send it?
All the best, Pablo.
Scipion team
Activo Vie, 21 Julio at 9:01 AM
, Samson Ali <a.s...@gm...> Escrito:
Dear Sirs, I have installed scipion unto my computer according as stated in the installation guide but I cannot launch the scipion program. Please can you help? Can I do helical processing on scipion?
I look forward to hearing from you soon.
Thanks.
Samson
(IMCB, Singapore)
|
|
From: Samson A. <a.s...@gm...> - 2017-07-20 14:16:16
|
Dear Sirs, I have installed scipion unto my computer according as stated in the installation guide but I cannot launch the scipion program. Please can you help? Can I do helical processing on scipion? I look forward to hearing from you soon. Thanks. Samson (IMCB, Singapore) |
|
From: Carlos O. S. <co...@cn...> - 2017-07-07 05:46:01
|
Dear Dieter, On 07/07/17 06:52, Dieter Blaas wrote: > Dear colleagues, > > I am trying to window a stack of particle images and a > corresponding volume from 450 x 450 x 450 px to 200 x 200 x 200 but > shifted on z by 100 px up. Are the following commands correct? > > 1) for the stack of particle images: > > xmipp_transform_window -i subtracted.mrcs --corners -100 -100 -0 99 -o > subtracted_200_new.mrcs" > > 2) for the volume: > > "xmipp_transform_window -i run_class001.mrc:mrc --corners -100 -100 -0 > 99 99 199 -o run_class001.mrc:mrc" > > I am somewhat intrigued by the message issued on running on the stack > of particle images: > These commands look correct. > "Output File: subtracted_200_new.mrcs > New window: from (z0,y0,x0)=(0,-100,-100) to (zF,yF,xF)=(0,99,0)" > > what does it do with the z-axis here? This is a problem with the feedback message, it is written always as if it were a 3D window, even if the actual work is performed in 2D. If the result is correct, don't worry about this message. Kind regards, Carlos Oscar > > thanks, best regards, Dieter > > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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