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From: Pablo C. <pc...@cn...> - 2021-09-15 09:12:24
|
Forgot a "Hi Wolfgang!" or something similar. Now reading it looks rude.
Extremely far from my intention and mood ;-) . Happy em processing!
On 15/9/21 10:53, Pablo Conesa wrote:
>
> Halves imported as halves will never be seen by the spyglass. The
> "main" volume will have the two halves associated "internally" and
> protocols in need of the halves will seek for this internal structure.
> Therefore providing the "main" volume will provide, at the same time
> the internal halves associated.
>
> Now, if you want to treat any half as a volume to be chosen from any
> spyglass button, then you need to import it as a "main" map.
>
> There might be a case where a protocol does not "expect" halves to be
> associated to a volume. Only in this case you'll need to import halves
> as main volumes. But we try to prevent this to reduce number of clicks
> and improve clarity as usability.
>
> Cheers!
>
> On 15/9/21 9:31, Lugmayr, Wolfgang wrote:
>> Hi Marta,
>>
>> yes it worked, I did not expect to enter a file when the UI says "Files directory".
>> Instead I tried to enter the file somehow in the "Pattern" input field.
>> Maybe the help hints can be extended?
>>
>> Do I understand your description about half-maps attributes correctly?
>> When I need to select 2 half-maps for e.g. ResMap FSC, I have to import them from the Relion job as single imports?
>> Or is there a different way? In the spyglass selection box I cannot choose them, only the main map.
>>
>> Cheers,
>> Wolfgang
>>
>>
>> ----- Original Message -----
>> From: "Marta Martinez"<mm...@cn...>
>> To: "Mailing list for Scipion users"<sci...@li...>
>> Sent: Tuesday, 14 September, 2021 19:23:31
>> Subject: Re: [scipion-users] import volumes with half maps question
>>
>> Hi Wolfgang,
>>
>> I've tested the import volumes protocol and I've had no problems with
>> SCIPION v3.0.9-Eugenius.
>>
>> I think that you can solve your problem filling in the "Files
>> directory" with the path of the main map
>> (/Runs/000500_ProtRelionRefine3D/extra/relion_class001.mrc) and then
>> the "Path half map1" and "Path half map2" with the respective paths
>> (/Runs/000500_ProtRelionRefine3D/extra/relion_half1_class001_unfil.mrc
>> and
>> /Runs/000500_ProtRelionRefine3D/extra/relion_half2_class001_unfil.mrc). I've
>> tested this example and it works. ("Pattern" box is empty).
>>
>> However, the two half maps that you can import this way are not
>> SCIPION objects, just the main map. The half maps are attributes of
>> the main map and then they will not be recognized as maps by other
>> protocols. So, if you want to use any of those half maps as input for
>> a job in SCIPION I recommend you to import each one independently in
>> an individual import volumes protocol writing its respective whole
>> path in the box "Files directory". Sorry for the inconvenience.
>>
>> With best wishes: MARTA
>>
>>
>> Quoting "Lugmayr, Wolfgang"<w.l...@uk...>:
>>
>>> Hi,
>>>
>>> I wanted to import 2 half-maps with the import volumes job.
>>>
>>> I selected the 2 maps with full path in the file browser and no
>>> files directory or pattern:
>>> When I press execute it says:
>>> - The path and pattern can not be both empty!!!
>>>
>>> When I set also the files directory - error:
>>> - Folders can not be selected.
>>> /home/lugmayr/foldername/
>>>
>>> When I set a file pattern + a files directory - error:
>>> - You can not use the options 'Pattern' and 'Set half maps' simultaneously
>>>
>>> Do I miss something here?
>>>
>>> How do I select a half map from a relion refinement job as input for a job?
>>>
>>> Cheers,
>>> Wolfgang
>>>
>>>
>>> --
>>> Universitätsklinikum Hamburg-Eppendorf (UKE)
>>> @ Centre for Structral Systems Biology (CSSB)
>>> @ Deutsches Elektronen-Synchrotron (DESY)
>>> Notkestrasse 85 Gebäude 15
>>> 22607 Hamburg, Germany
>>> Tel.: +49 40 8998-87652
>>> Email:wol...@cs...
>>> http://www.cssb-hamburg.de/
>>>
>>>
>>> _______________________________________________
>>> 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...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Pablo C. <pc...@cn...> - 2021-09-15 08:54:03
|
Halves imported as halves will never be seen by the spyglass. The "main"
volume will have the two halves associated "internally" and protocols in
need of the halves will seek for this internal structure. Therefore
providing the "main" volume will provide, at the same time the internal
halves associated.
Now, if you want to treat any half as a volume to be chosen from any
spyglass button, then you need to import it as a "main" map.
There might be a case where a protocol does not "expect" halves to be
associated to a volume. Only in this case you'll need to import halves
as main volumes. But we try to prevent this to reduce number of clicks
and improve clarity as usability.
Cheers!
On 15/9/21 9:31, Lugmayr, Wolfgang wrote:
> Hi Marta,
>
> yes it worked, I did not expect to enter a file when the UI says "Files directory".
> Instead I tried to enter the file somehow in the "Pattern" input field.
> Maybe the help hints can be extended?
>
> Do I understand your description about half-maps attributes correctly?
> When I need to select 2 half-maps for e.g. ResMap FSC, I have to import them from the Relion job as single imports?
> Or is there a different way? In the spyglass selection box I cannot choose them, only the main map.
>
> Cheers,
> Wolfgang
>
>
> ----- Original Message -----
> From: "Marta Martinez" <mm...@cn...>
> To: "Mailing list for Scipion users" <sci...@li...>
> Sent: Tuesday, 14 September, 2021 19:23:31
> Subject: Re: [scipion-users] import volumes with half maps question
>
> Hi Wolfgang,
>
> I've tested the import volumes protocol and I've had no problems with
> SCIPION v3.0.9-Eugenius.
>
> I think that you can solve your problem filling in the "Files
> directory" with the path of the main map
> (/Runs/000500_ProtRelionRefine3D/extra/relion_class001.mrc) and then
> the "Path half map1" and "Path half map2" with the respective paths
> (/Runs/000500_ProtRelionRefine3D/extra/relion_half1_class001_unfil.mrc
> and
> /Runs/000500_ProtRelionRefine3D/extra/relion_half2_class001_unfil.mrc). I've
> tested this example and it works. ("Pattern" box is empty).
>
> However, the two half maps that you can import this way are not
> SCIPION objects, just the main map. The half maps are attributes of
> the main map and then they will not be recognized as maps by other
> protocols. So, if you want to use any of those half maps as input for
> a job in SCIPION I recommend you to import each one independently in
> an individual import volumes protocol writing its respective whole
> path in the box "Files directory". Sorry for the inconvenience.
>
> With best wishes: MARTA
>
>
> Quoting "Lugmayr, Wolfgang" <w.l...@uk...>:
>
>> Hi,
>>
>> I wanted to import 2 half-maps with the import volumes job.
>>
>> I selected the 2 maps with full path in the file browser and no
>> files directory or pattern:
>> When I press execute it says:
>> - The path and pattern can not be both empty!!!
>>
>> When I set also the files directory - error:
>> - Folders can not be selected.
>> /home/lugmayr/foldername/
>>
>> When I set a file pattern + a files directory - error:
>> - You can not use the options 'Pattern' and 'Set half maps' simultaneously
>>
>> Do I miss something here?
>>
>> How do I select a half map from a relion refinement job as input for a job?
>>
>> Cheers,
>> Wolfgang
>>
>>
>> --
>> Universitätsklinikum Hamburg-Eppendorf (UKE)
>> @ Centre for Structral Systems Biology (CSSB)
>> @ Deutsches Elektronen-Synchrotron (DESY)
>> Notkestrasse 85 Gebäude 15
>> 22607 Hamburg, Germany
>> Tel.: +49 40 8998-87652
>> Email: wol...@cs...
>> http://www.cssb-hamburg.de/
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Lugmayr, W. <w.l...@uk...> - 2021-09-15 07:31:37
|
Hi Marta,
yes it worked, I did not expect to enter a file when the UI says "Files directory".
Instead I tried to enter the file somehow in the "Pattern" input field.
Maybe the help hints can be extended?
Do I understand your description about half-maps attributes correctly?
When I need to select 2 half-maps for e.g. ResMap FSC, I have to import them from the Relion job as single imports?
Or is there a different way? In the spyglass selection box I cannot choose them, only the main map.
Cheers,
Wolfgang
----- Original Message -----
From: "Marta Martinez" <mm...@cn...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Tuesday, 14 September, 2021 19:23:31
Subject: Re: [scipion-users] import volumes with half maps question
Hi Wolfgang,
I've tested the import volumes protocol and I've had no problems with
SCIPION v3.0.9-Eugenius.
I think that you can solve your problem filling in the "Files
directory" with the path of the main map
(/Runs/000500_ProtRelionRefine3D/extra/relion_class001.mrc) and then
the "Path half map1" and "Path half map2" with the respective paths
(/Runs/000500_ProtRelionRefine3D/extra/relion_half1_class001_unfil.mrc
and
/Runs/000500_ProtRelionRefine3D/extra/relion_half2_class001_unfil.mrc). I've
tested this example and it works. ("Pattern" box is empty).
However, the two half maps that you can import this way are not
SCIPION objects, just the main map. The half maps are attributes of
the main map and then they will not be recognized as maps by other
protocols. So, if you want to use any of those half maps as input for
a job in SCIPION I recommend you to import each one independently in
an individual import volumes protocol writing its respective whole
path in the box "Files directory". Sorry for the inconvenience.
With best wishes: MARTA
Quoting "Lugmayr, Wolfgang" <w.l...@uk...>:
> Hi,
>
> I wanted to import 2 half-maps with the import volumes job.
>
> I selected the 2 maps with full path in the file browser and no
> files directory or pattern:
> When I press execute it says:
> - The path and pattern can not be both empty!!!
>
> When I set also the files directory - error:
> - Folders can not be selected.
> /home/lugmayr/foldername/
>
> When I set a file pattern + a files directory - error:
> - You can not use the options 'Pattern' and 'Set half maps' simultaneously
>
> Do I miss something here?
>
> How do I select a half map from a relion refinement job as input for a job?
>
> Cheers,
> Wolfgang
>
>
> --
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Deutsches Elektronen-Synchrotron (DESY)
> Notkestrasse 85 Gebäude 15
> 22607 Hamburg, Germany
> Tel.: +49 40 8998-87652
> Email: wol...@cs...
> http://www.cssb-hamburg.de/
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Marta Martinez Gonzalez
Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
E-mail: mm...@cn...
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Colin D. <ckd...@gm...> - 2021-09-14 19:34:24
|
I do have gctf 1.06 installed but I don't see any option to do a gradient ctf estimation in the protocol. Just to clarify I'm planning to do this at the beginning of data processing, not after I have a map etc. via particle polishing. (Images below to show what I'm looking at) [image: image.png] [image: image.png] On Tue, Sep 14, 2021 at 12:19 PM Grigory Sharov <sha...@gm...> wrote: > Hi Colin, > > gctf refinement protocol only works with gctf 1.06, which is not installed > by default. You can run "scipion installb gctf-1.06" to get it. > > 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, Sep 14, 2021 at 7:29 PM Deniston, Colin < > col...@no...> wrote: > >> Hi, >> >> >> >> I want to run per-particle CTF (or generate a gradient of CTF values >> across an image) on some tilted images. However, I can’t find an option for >> this is my standard gctf – ctf estimate protocol. Could you help me locate >> it or let me know what plugin performs it I can download? Thanks! >> _______________________________________________ >> 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: Grigory S. <sha...@gm...> - 2021-09-14 19:18:59
|
Hi Colin, gctf refinement protocol only works with gctf 1.06, which is not installed by default. You can run "scipion installb gctf-1.06" to get it. 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, Sep 14, 2021 at 7:29 PM Deniston, Colin <col...@no...> wrote: > Hi, > > > > I want to run per-particle CTF (or generate a gradient of CTF values > across an image) on some tilted images. However, I can’t find an option for > this is my standard gctf – ctf estimate protocol. Could you help me locate > it or let me know what plugin performs it I can download? Thanks! > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Deniston, C. <col...@no...> - 2021-09-14 18:28:49
|
Hi, I want to run per-particle CTF (or generate a gradient of CTF values across an image) on some tilted images. However, I can't find an option for this is my standard gctf - ctf estimate protocol. Could you help me locate it or let me know what plugin performs it I can download? Thanks! |
|
From: Marta M. <mm...@cn...> - 2021-09-14 17:23:48
|
Hi Wolfgang,
I've tested the import volumes protocol and I've had no problems with
SCIPION v3.0.9-Eugenius.
I think that you can solve your problem filling in the "Files
directory" with the path of the main map
(/Runs/000500_ProtRelionRefine3D/extra/relion_class001.mrc) and then
the "Path half map1" and "Path half map2" with the respective paths
(/Runs/000500_ProtRelionRefine3D/extra/relion_half1_class001_unfil.mrc
and
/Runs/000500_ProtRelionRefine3D/extra/relion_half2_class001_unfil.mrc). I've
tested this example and it works. ("Pattern" box is empty).
However, the two half maps that you can import this way are not
SCIPION objects, just the main map. The half maps are attributes of
the main map and then they will not be recognized as maps by other
protocols. So, if you want to use any of those half maps as input for
a job in SCIPION I recommend you to import each one independently in
an individual import volumes protocol writing its respective whole
path in the box "Files directory". Sorry for the inconvenience.
With best wishes: MARTA
Quoting "Lugmayr, Wolfgang" <w.l...@uk...>:
> Hi,
>
> I wanted to import 2 half-maps with the import volumes job.
>
> I selected the 2 maps with full path in the file browser and no
> files directory or pattern:
> When I press execute it says:
> - The path and pattern can not be both empty!!!
>
> When I set also the files directory - error:
> - Folders can not be selected.
> /home/lugmayr/foldername/
>
> When I set a file pattern + a files directory - error:
> - You can not use the options 'Pattern' and 'Set half maps' simultaneously
>
> Do I miss something here?
>
> How do I select a half map from a relion refinement job as input for a job?
>
> Cheers,
> Wolfgang
>
>
> --
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Deutsches Elektronen-Synchrotron (DESY)
> Notkestrasse 85 Gebäude 15
> 22607 Hamburg, Germany
> Tel.: +49 40 8998-87652
> Email: wol...@cs...
> http://www.cssb-hamburg.de/
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Marta Martinez Gonzalez
Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
E-mail: mm...@cn...
|
|
From: Lugmayr, W. <w.l...@uk...> - 2021-09-14 16:14:12
|
Hi, I wanted to import 2 half-maps with the import volumes job. I selected the 2 maps with full path in the file browser and no files directory or pattern: When I press execute it says: - The path and pattern can not be both empty!!! When I set also the files directory - error: - Folders can not be selected. /home/lugmayr/foldername/ When I set a file pattern + a files directory - error: - You can not use the options 'Pattern' and 'Set half maps' simultaneously Do I miss something here? How do I select a half map from a relion refinement job as input for a job? Cheers, Wolfgang -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 22607 Hamburg, Germany Tel.: +49 40 8998-87652 Email: wol...@cs... http://www.cssb-hamburg.de/ |
|
From: Pablo C. <pc...@cn...> - 2021-09-13 15:52:14
|
Thanks for confirming it fixed Now, for the dataViewer, you might not need to recompile. Probably just setting JAVA_HOME in the scipion config file to a newer java runtime might work. scipion3 config --show will show you the config file. If not present add JAVA_HOME to it pointing to a modern java runtime. Not sure how you got there! On 13/9/21 15:22, Lugmayr, Wolfgang wrote: > Hi Pablo, > > yes the fix below worked on an Ab-Inito job with Scipion 3.0.9 and > cryoSPARC 3.2.0+210831 > > The "view data in cryoSPARC" open the webbrowser with the correct page > (when logged already in in cryoSPARC web). > > The dataViewer has a problem on CentOS Stream (also latest updates today): > > java -Xmx4g -d64 > -Djava.library.path=/cssbsw/em/scipion/3.0/software/em/xmipp/lib > -Dplugins.dir=/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/imagej/plugins > -cp > lib/*:/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/imagej/*:/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/lib/* > xmipp.viewer.scipion.ScipionViewer -i > "Runs/007753_ProtCryoSparcInitialModel/classes3D.sqlite" --mode > metadata --visible enabled id _size _representative._filename > --render _representative._filename --scipion 47401 7828 > Error: A JNI error has occurred, please check your installation and > try again > Exception in thread "main" java.lang.UnsupportedClassVersionError: > xmipp/viewer/scipion/ScipionViewer has been compiled by a more recent > version of the Java Runtime (class file version 60.0), this version of > the Java Runtime only recognizes class file versions up to 52.0 > > $ rpm -qa | grep jdk > java-1.8.0-openjdk-headless-1.8.0.302.b08-0.el8_4.x86_64 > copy-jdk-configs-3.7-4.el8.noarch > java-latest-openjdk-devel-16.0.1.0.9-3.rolling.el8.x86_64 > java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64 > java-latest-openjdk-headless-16.0.1.0.9-3.rolling.el8.x86_64 > java-latest-openjdk-16.0.1.0.9-3.rolling.el8.x86_64 > > Will a re-compile Xmipp help, is this a binary distribution problem or > shall i set a different JDK version as default? > > Cheers, > Wolfgang > > > ------------------------------------------------------------------------ > *From: *"Pablo Conesa" <pc...@cn...> > *To: *"Mailing list for Scipion users" > <sci...@li...> > *Sent: *Monday, 13 September, 2021 14:26:00 > *Subject: *Re: [scipion-users] Scipion 3.0.9 cryosparc2 plugin pyem error > > Hi Wolfgang!, This has been reported before and I believe is cause by > a partial update of pwem. > > I hope this fixes your issue but have no confirmation. Would be nice > to get feedback: > > > scipion3 run pip uninstall pyem > > scipion3 run pip install > git+https://github.com/asarnow/pyem.git@ed0527f98657d21d887357426b74e5240d477fae > > > > On 13/9/21 12:18, Lugmayr, Wolfgang wrote: > > Hi, > > I updated Scipion 3.0 and all plugins to the latest version. > > I run an initial model job from Scipion and with the cryoSPARC webinterface the result seems to be ok. > > But then I get the error: > Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' > > I have only relion 3.1.2 on this dedicated node. > > here are the last log lines: > 00027: Got J6 for JobId > 00028: Running: /cssbsw/em/scipion/3.0/cryosparc/cryosparc_master/bin/cryosparcm cli 'enqueue_job("P1","J6","default", "cssbuke001.desy.de", [0], "False")' > 00029: Removing intermediate results... > 00030: FINISHED: processStep, step 2, time 2021-09-13 12:12:48.450747 > 00031: STARTED: createOutputStep, step 3, time 2021-09-13 12:12:48.540652 > 00032: Creating the output... > 00033: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' > 00034: FAILED: createOutputStep, step 3, time 2021-09-13 12:12:51.351945 > 00035: *** Last status is failed > 00036: ------------------- PROTOCOL FAILED (DONE 3/3) > > Cheers, > Wolfgang > > > _______________________________________________ > 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> > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> 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 -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: David M. <dma...@ub...> - 2021-09-13 15:45:31
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Hi Wolfgang, Please, check /cssbsw/em/scipion/3.0/software/em/xmipp/xmipp.conf and /cssbsw/em/scipion/3.0/software/em/xmipp/xmippEnv.json to find a hint of which java had used to compile the dataViewer. Thanks, <http://ucm.es/> _____ Dr. David Maluenda Niubó Lecturer Professor Applied Physics - UB<https://www.ub.edu/portal/web/dp-fisica-aplicada> [Office 507<https://www.openstreetmap.org/?mlat=41.38427&mlon=2.11711#map=17/41.38504/2.11503>] Wavefront Engineering Group<https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA> dma...@ub...<mailto:dma...@ub...> - (+34) 619 029 310 This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Mon, Sep 13, 2021 at 3:23 PM Lugmayr, Wolfgang <w.l...@uk...<mailto:w.l...@uk...>> wrote: Hi Pablo, yes the fix below worked on an Ab-Inito job with Scipion 3.0.9 and cryoSPARC 3.2.0+210831 The "view data in cryoSPARC" open the webbrowser with the correct page (when logged already in in cryoSPARC web). The dataViewer has a problem on CentOS Stream (also latest updates today): java -Xmx4g -d64 -Djava.library.path=/cssbsw/em/scipion/3.0/software/em/xmipp/lib -Dplugins.dir=/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/imagej/plugins -cp lib/*:/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/imagej/*:/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/007753_ProtCryoSparcInitialModel/classes3D.sqlite" --mode metadata --visible enabled id _size _representative._filename --render _representative._filename --scipion 47401 7828 Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.UnsupportedClassVersionError: xmipp/viewer/scipion/ScipionViewer has been compiled by a more recent version of the Java Runtime (class file version 60.0), this version of the Java Runtime only recognizes class file versions up to 52.0 $ rpm -qa | grep jdk java-1.8.0-openjdk-headless-1.8.0.302.b08-0.el8_4.x86_64 copy-jdk-configs-3.7-4.el8.noarch java-latest-openjdk-devel-16.0.1.0.9-3.rolling.el8.x86_64 java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64 java-latest-openjdk-headless-16.0.1.0.9-3.rolling.el8.x86_64 java-latest-openjdk-16.0.1.0.9-3.rolling.el8.x86_64 Will a re-compile Xmipp help, is this a binary distribution problem or shall i set a different JDK version as default? Cheers, Wolfgang ________________________________ From: "Pablo Conesa" <pc...@cn...<mailto:pc...@cn...>> To: "Mailing list for Scipion users" <sci...@li...<mailto:sci...@li...>> Sent: Monday, 13 September, 2021 14:26:00 Subject: Re: [scipion-users] Scipion 3.0.9 cryosparc2 plugin pyem error Hi Wolfgang!, This has been reported before and I believe is cause by a partial update of pwem. I hope this fixes your issue but have no confirmation. Would be nice to get feedback: scipion3 run pip uninstall pyem scipion3 run pip install git+https://github.com/asarnow/pyem.git@ed0527f98657d21d887357426b74e5240d477fae On 13/9/21 12:18, Lugmayr, Wolfgang wrote: Hi, I updated Scipion 3.0 and all plugins to the latest version. I run an initial model job from Scipion and with the cryoSPARC webinterface the result seems to be ok. But then I get the error: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' I have only relion 3.1.2 on this dedicated node. here are the last log lines: 00027: Got J6 for JobId 00028: Running: /cssbsw/em/scipion/3.0/cryosparc/cryosparc_master/bin/cryosparcm cli 'enqueue_job("P1","J6","default", "cssbuke001.desy.de<http://cssbuke001.desy.de>", [0], "False")' 00029: Removing intermediate results... 00030: FINISHED: processStep, step 2, time 2021-09-13 12:12:48.450747 00031: STARTED: createOutputStep, step 3, time 2021-09-13 12:12:48.540652 00032: Creating the output... 00033: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' 00034: FAILED: createOutputStep, step 3, time 2021-09-13 12:12:51.351945 00035: *** Last status is failed 00036: ------------------- PROTOCOL FAILED (DONE 3/3) Cheers, Wolfgang _______________________________________________ scipion-users mailing list sci...@li...<mailto: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: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...<mailto: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. |
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From: Lugmayr, W. <w.l...@uk...> - 2021-09-13 13:22:39
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Hi Pablo, yes the fix below worked on an Ab-Inito job with Scipion 3.0.9 and cryoSPARC 3.2.0+210831 The "view data in cryoSPARC" open the webbrowser with the correct page (when logged already in in cryoSPARC web). The dataViewer has a problem on CentOS Stream (also latest updates today): java -Xmx4g -d64 -Djava.library.path=/cssbsw/em/scipion/3.0/software/em/xmipp/lib -Dplugins.dir=/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/imagej/plugins -cp lib/*:/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/imagej/*:/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/007753_ProtCryoSparcInitialModel/classes3D.sqlite" --mode metadata --visible enabled id _size _representative._filename --render _representative._filename --scipion 47401 7828 Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.UnsupportedClassVersionError: xmipp/viewer/scipion/ScipionViewer has been compiled by a more recent version of the Java Runtime (class file version 60.0), this version of the Java Runtime only recognizes class file versions up to 52.0 $ rpm -qa | grep jdk java-1.8.0-openjdk-headless-1.8.0.302.b08-0.el8_4.x86_64 copy-jdk-configs-3.7-4.el8.noarch java-latest-openjdk-devel-16.0.1.0.9-3.rolling.el8.x86_64 java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64 java-latest-openjdk-headless-16.0.1.0.9-3.rolling.el8.x86_64 java-latest-openjdk-16.0.1.0.9-3.rolling.el8.x86_64 Will a re-compile Xmipp help, is this a binary distribution problem or shall i set a different JDK version as default? Cheers, Wolfgang From: "Pablo Conesa" <pc...@cn...> To: "Mailing list for Scipion users" <sci...@li...> Sent: Monday, 13 September, 2021 14:26:00 Subject: Re: [scipion-users] Scipion 3.0.9 cryosparc2 plugin pyem error Hi Wolfgang!, This has been reported before and I believe is cause by a partial update of pwem. I hope this fixes your issue but have no confirmation. Would be nice to get feedback: scipion3 run pip uninstall pyem scipion3 run pip install git+https://github.com/asarnow/pyem.git@ed0527f98657d21d887357426b74e5240d477fae On 13/9/21 12:18, Lugmayr, Wolfgang wrote: Hi, I updated Scipion 3.0 and all plugins to the latest version. I run an initial model job from Scipion and with the cryoSPARC webinterface the result seems to be ok. But then I get the error: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' I have only relion 3.1.2 on this dedicated node. here are the last log lines: 00027: Got J6 for JobId 00028: Running: /cssbsw/em/scipion/3.0/cryosparc/cryosparc_master/bin/cryosparcm cli 'enqueue_job("P1","J6","default", "cssbuke001.desy.de", [0], "False")' 00029: Removing intermediate results... 00030: FINISHED: processStep, step 2, time 2021-09-13 12:12:48.450747 00031: STARTED: createOutputStep, step 3, time 2021-09-13 12:12:48.540652 00032: Creating the output... 00033: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' 00034: FAILED: createOutputStep, step 3, time 2021-09-13 12:12:51.351945 00035: *** Last status is failed 00036: ------------------- PROTOCOL FAILED (DONE 3/3) Cheers, Wolfgang _______________________________________________ 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 ] -- Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2021-09-13 12:26:18
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Hi Wolfgang!, This has been reported before and I believe is cause by a partial update of pwem. I hope this fixes your issue but have no confirmation. Would be nice to get feedback: scipion3 run pip uninstall pyem scipion3 run pip install git+https://github.com/asarnow/pyem.git@ed0527f98657d21d887357426b74e5240d477fae On 13/9/21 12:18, Lugmayr, Wolfgang wrote: > Hi, > > I updated Scipion 3.0 and all plugins to the latest version. > > I run an initial model job from Scipion and with the cryoSPARC webinterface the result seems to be ok. > > But then I get the error: > Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' > > I have only relion 3.1.2 on this dedicated node. > > here are the last log lines: > 00027: Got J6 for JobId > 00028: Running: /cssbsw/em/scipion/3.0/cryosparc/cryosparc_master/bin/cryosparcm cli 'enqueue_job("P1","J6","default", "cssbuke001.desy.de", [0], "False")' > 00029: Removing intermediate results... > 00030: FINISHED: processStep, step 2, time 2021-09-13 12:12:48.450747 > 00031: STARTED: createOutputStep, step 3, time 2021-09-13 12:12:48.540652 > 00032: Creating the output... > 00033: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' > 00034: FAILED: createOutputStep, step 3, time 2021-09-13 12:12:51.351945 > 00035: *** Last status is failed > 00036: ------------------- PROTOCOL FAILED (DONE 3/3) > > Cheers, > Wolfgang > > > _______________________________________________ > 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: Lugmayr, W. <w.l...@uk...> - 2021-09-13 10:18:48
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Hi,
I updated Scipion 3.0 and all plugins to the latest version.
I run an initial model job from Scipion and with the cryoSPARC webinterface the result seems to be ok.
But then I get the error:
Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2'
I have only relion 3.1.2 on this dedicated node.
here are the last log lines:
00027: Got J6 for JobId
00028: Running: /cssbsw/em/scipion/3.0/cryosparc/cryosparc_master/bin/cryosparcm cli 'enqueue_job("P1","J6","default", "cssbuke001.desy.de", [0], "False")'
00029: Removing intermediate results...
00030: FINISHED: processStep, step 2, time 2021-09-13 12:12:48.450747
00031: STARTED: createOutputStep, step 3, time 2021-09-13 12:12:48.540652
00032: Creating the output...
00033: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2'
00034: FAILED: createOutputStep, step 3, time 2021-09-13 12:12:51.351945
00035: *** Last status is failed
00036: ------------------- PROTOCOL FAILED (DONE 3/3)
Cheers,
Wolfgang
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From: Carlos H. F. <car...@so...> - 2021-09-06 12:27:12
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Dear Gregory, Sure! The error was right in front of me!!. Thank you so much!! Best regards, Carlos. From: "Grigory Sharov" <sha...@gm...> To: "scipion-users" <sci...@li...> Sent: Monday, September 6, 2021 1:18:25 PM Subject: Re: [scipion-users] cryoSPARC not running Hi Carlos, you should put /home/impmc/ in the config file instead. 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 Mon, Sep 6, 2021 at 12:13 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: Dear all, I'm facing a problem running cryoSPARC in Scipion. Every time I try to use cryoSPARC, the following error appears: Failed to connect to cryoSPARC. Please, make sure cryoSPARC is running. Running: /home/impmc/cryosparc_master/bin/cryosparc2_master/bin/cryosparcm start might fix this. However, cryoSPARC is already running and it is located at /home/impmc/cryosparc_master/bin/; which is the same path that I put in the scipion.conf file. Does anyone have any suggestions on how to solve this problem? Thanks in advance. Best regards, Carlos Fernandes _______________________________________________ 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...> - 2021-09-06 11:18:45
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Hi Carlos, you should put /home/impmc/ in the config file instead. 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, Sep 6, 2021 at 12:13 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear all, > > I'm facing a problem running cryoSPARC in Scipion. > Every time I try to use cryoSPARC, the following error appears: > > *Failed to connect to cryoSPARC. Please, make sure cryoSPARC is running.* > *Running: > /home/impmc/cryosparc_master/bin/cryosparc2_master/bin/cryosparcm start > might fix this.* > > However, cryoSPARC is already running and it is located at /home/impmc/cryosparc_master/bin/; > which is the same path that I put in the scipion.conf file. > > Does anyone have any suggestions on how to solve this problem? > Thanks in advance. > Best regards, > Carlos Fernandes > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Carlos H. F. <car...@so...> - 2021-09-06 11:12:50
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Dear all, I'm facing a problem running cryoSPARC in Scipion. Every time I try to use cryoSPARC, the following error appears: Failed to connect to cryoSPARC. Please, make sure cryoSPARC is running. Running: /home/impmc/cryosparc_master/bin/cryosparc2_master/bin/cryosparcm start might fix this. However, cryoSPARC is already running and it is located at /home/impmc/cryosparc_master/bin/; which is the same path that I put in the scipion.conf file. Does anyone have any suggestions on how to solve this problem? Thanks in advance. Best regards, Carlos Fernandes |
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From: Pablo C. <pc...@cn...> - 2021-09-03 07:05:50
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Hi Dmitry, I've seen this then there is a movie with less frames than the rest. Sets of movies are meant to be homogeneous in terms of number of frames, but if a movie file is "partially corrupted" (I've seen tiff files partially donwloaded that motioncor is able to process) then that movie slips into the set and makes bayesian polishing fails. What can you do? 1.- Identify the corrupted movies: Probably their size will be smaller the the others. 2.- Make a subset of the movies, removing the corrupted movies 3.- Do the same for the set of particles On out side, since this has happened several times, we can try to: A:) avoid corrupted movies to slip in the sets. B:) tolerate this error in the bayesian polishing protocol and skip this case. On 2/9/21 21:36, Dmitry Semchonok wrote: > > Dear colleagues, > > The issue with Bayesian polishing – > > Logging configured. STDOUT --> > Runs/003279_ProtRelionBayesianPolishing/logs/run.stdout , STDERR --> > Runs/003279_ProtRelionBayesianPolishing/logs/run.stderr > > [32mRUNNING PROTOCOL -----------------[0m > > Protocol starts > > Hostname: localhost4.localdomain4 > > PID: 240224 > > pyworkflow: 3.0.17 > > plugin: relion > > plugin v: 3.1.3 > > currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI > > workingDir: Runs/003279_ProtRelionBayesianPolishing > > runMode: Continue > > MPI: 1 > > threads: 1 > > Starting at step: 1 > > Running steps > > [35mSTARTED[0m: convertInputStep, step 1, time 2021-09-02 21:31:33.074480 > > Converting set from > 'Runs/002848_ProtCryoSparcNonUniformRefine3D/particles.sqlite' into > 'Runs/003279_ProtRelionBayesianPolishing/input_particles.star' > > [31mProtocol failed: list index out of range[0m > > [35mFAILED[0m: convertInputStep, step 1, time 2021-09-02 21:31:33.532782 > > *** Last status is failed > > [32m------------------- PROTOCOL FAILED (DONE 1/2)[0m > > Traceback (most recent call last): > > File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 201, in run > > self._run() > > File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 252, in _run > > resultFiles = self._runFunc() > > File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _runFunc > > return self._func(*self._args) > > File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", > line 296, in convertInputStep > > tableShifts.addRow(i, shiftsX[i-a0] + xoff, > > IndexError: list index out of range > > [31mProtocol failed: list index out of range[0m > > Any idea? > > Thank you > > Sincerely, > > Dmitry > > P.s. also strange behavior of adding movies to the project – the > process just hangs without finishing. > > Could those 2 issues be connected? > > Could that happened after the SCIPION3 updates? > > > > _______________________________________________ > 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...> - 2021-09-02 19:37:11
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:612.0pt 792.0pt; margin:2.0cm 42.5pt 2.0cm 3.0cm;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=RU link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Dear colleagues,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>The issue with Bayesian polishing – <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>Logging configured. STDOUT --> Runs/003279_ProtRelionBayesianPolishing/logs/run.stdout , STDERR --> Runs/003279_ProtRelionBayesianPolishing/logs/run.stderr<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[32mRUNNING PROTOCOL -----------------[0m<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>Protocol starts<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>Hostname: localhost4.localdomain4<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>PID: 240224<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>pyworkflow: 3.0.17<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>plugin: relion<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>plugin v: 3.1.3<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>workingDir: Runs/003279_ProtRelionBayesianPolishing<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>runMode: Continue<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'> MPI: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'> threads: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'> Starting at step: 1<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'> Running steps <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[35mSTARTED[0m: convertInputStep, step 1, time 2021-09-02 21:31:33.074480<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>Converting set from 'Runs/002848_ProtCryoSparcNonUniformRefine3D/particles.sqlite' into 'Runs/003279_ProtRelionBayesianPolishing/input_particles.star'<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[31mProtocol failed: list index out of range[0m<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[35mFAILED[0m: convertInputStep, step 1, time 2021-09-02 21:31:33.532782<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>*** Last status is failed <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#0070C0'>[32m------------------- PROTOCOL FAILED (DONE 1/2)[0m<o:p></o:p></span></p><div style='mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;padding:0cm 0cm 1.0pt 0cm'><p class=MsoNormal style='border:none;padding:0cm'><o:p> </o:p></p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='color:#0070C0'>Traceback (most recent call last):<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> self._run()<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> resultFiles = self._runFunc()<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> return self._func(*self._args)<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 296, in convertInputStep<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'> tableShifts.addRow(i, shiftsX[i-a0] + xoff,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>IndexError: list index out of range<o:p></o:p></span></p><p class=MsoNormal><span style='color:#0070C0'>[31mProtocol failed: list index out of range[0m</span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US>Any idea?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Thank you<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Dmitry<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>P.s. also strange behavior of adding movies to the project – the process just hangs without finishing.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Could those 2 issues be connected?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Could that happened after the SCIPION3 updates?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Dmitry S. <sem...@gm...> - 2021-08-31 14:40:18
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} pre {mso-style-priority:99; mso-style-link:"\0421\0442\0430\043D\0434\0430\0440\0442\043D\044B\0439 HTML \0417\043D\0430\043A"; margin:0cm; font-size:10.0pt; font-family:"Courier New";} span.HTML {mso-style-name:"\0421\0442\0430\043D\0434\0430\0440\0442\043D\044B\0439 HTML \0417\043D\0430\043A"; mso-style-priority:99; mso-style-link:"\0421\0442\0430\043D\0434\0430\0440\0442\043D\044B\0439 HTML"; font-family:"Courier New";} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:612.0pt 792.0pt; margin:2.0cm 42.5pt 2.0cm 3.0cm;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=RU link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Dear Pablo,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I deleted the </span><span style='background:yellow;mso-highlight:yellow'>pyem-0.4 folder</span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US>And run the command </span><span style='background:yellow;mso-highlight:yellow'>scipion3 installb pyem</span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US>Please see the log below.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I will re-run the SCIPION3 – cryosparc process and further inform you about the results.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Dmitry<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>[panos@cryoem01 ~]$ scipion3 installb pyem<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Scipion v3.0.9 - Eugenius<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Error retrieving plugin relion binaries: CUDA_LIB (or RELION_CUDA_LIB) is defined, but not CUDA_BIN (or RELION_CUDA_BIN), please execute scipion config --update<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Building pyem-0.4 ...<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> Skipping command: wget -nv -c -O /opt/Scipion3/software/em/void.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>mv -v /opt/Scipion3/software/em/void.tgz.part /opt/Scipion3/software/em/void.tgz<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> All targets exist.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>cd /opt/Scipion3/software/em<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>mkdir /opt/Scipion3/software/em/pyem-0.4<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> Skipping command: tar -xf void.tgz -C pyem-0.4<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> All targets exist.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>cd /opt/Scipion3/software/em/pyem-0.4<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>pip install git+https://github.com/asarnow/pyem.git@ed0527f98657d21d887357426b74e5240d477fae && touch pyem-0.4_installed<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Collecting git+https://github.com/asarnow/pyem.git@ed0527f98657d21d887357426b74e5240d477fae<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> Cloning https://github.com/asarnow/pyem.git (to revision ed0527f98657d21d887357426b74e5240d477fae) to /tmp/pip-req-build-tozvidgn<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> Running command git clone -q https://github.com/asarnow/pyem.git /tmp/pip-req-build-tozvidgn<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> Running command git rev-parse -q --verify 'sha^ed0527f98657d21d887357426b74e5240d477fae'<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> Running command git fetch -q https://github.com/asarnow/pyem.git ed0527f98657d21d887357426b74e5240d477fae<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> Running command git checkout -q ed0527f98657d21d887357426b74e5240d477fae<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: future in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (0.18.2)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: numba in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (0.47.0)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: numpy in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (1.18.4)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: scipy in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (1.6.2)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: matplotlib in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (3.2.2)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: seaborn in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (0.11.1)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: pandas in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (1.2.4)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: pathos in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (0.2.7)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: pyfftw in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (0.12.0)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: healpy in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (1.14.0)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: natsort in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pyem==0.4) (7.1.1)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: six in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from healpy->pyem==0.4) (1.15.0)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: astropy in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from healpy->pyem==0.4) (4.2.1)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: pyerfa in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from astropy->healpy->pyem==0.4) (1.7.2)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from matplotlib->pyem==0.4) (2.4.7)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from matplotlib->pyem==0.4) (1.3.1)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: python-dateutil>=2.1 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from matplotlib->pyem==0.4) (2.8.1)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: cycler>=0.10 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from matplotlib->pyem==0.4) (0.10.0)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: llvmlite>=0.31.0dev0 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from numba->pyem==0.4) (0.31.0)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: setuptools in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from numba->pyem==0.4) (52.0.0.post20210125)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: pytz>=2017.3 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pandas->pyem==0.4) (2021.1)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: multiprocess>=0.70.11 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pathos->pyem==0.4) (0.70.11.1)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: ppft>=1.6.6.3 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pathos->pyem==0.4) (1.6.6.3)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: dill>=0.3.3 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pathos->pyem==0.4) (0.3.3)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Requirement already satisfied: pox>=0.2.9 in /usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages (from pathos->pyem==0.4) (0.2.9)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> Skipping command: Link 'pyem-0.4 -> pyem-0.4'<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'> All targets exist.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='color:#00B0F0'>Done (4.12 seconds)<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Dmitry<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='border:none;padding:0cm'><b>От: </b><a href="mailto:pc...@cn...">Pablo Conesa</a><br><b>Отправлено: </b>31 августа 2021 г. в 17:15<br><b>Кому: </b><a href="mailto:sci...@li...">sci...@li...</a><br><b>Тема: </b>Re: [scipion-users] Cryosparc 2D - Scipion issue</p></div><p class=MsoNormal><o:p> </o:p></p><p>I posted a possible solution there:</p><p>"Have you got software/em/pyem-0.4 folder.<br><br>If so, try to remove it and then run scipion3 installb pyem"</p><p><o:p> </o:p></p><p><o:p> </o:p></p><div><p class=MsoNormal>On 31/8/21 13:40, Jose Miguel de la Rosa Trevin wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>I had a similar issue than Dmitry....at some point the same error that here...but then another one. Reported last Friday here: <o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><a href="https://github.com/scipion-em/scipion-em-cryosparc2/issues/91">https://github.com/scipion-em/scipion-em-cryosparc2/issues/91</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Tue, Aug 31, 2021 at 11:29 AM Pablo Conesa <<a href="mailto:pc...@cn...">pc...@cn...</a>> wrote:<o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><p>Hi!</p><p>It seems there is a mismatch of versions. Could you please send the output of:</p><p><o:p> </o:p></p><p>scipion3 run pip list </p><p><o:p> </o:p></p><p>And the output of:</p><p>ls -l <SCIPION_HOME>/software/em | grep pyem</p><p><o:p> </o:p></p><div><p class=MsoNormal>On 25/8/21 8:07, <a href="mailto:pc...@cn..." target="_blank">pc...@cn...</a> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>Hi Dmitry, give us some time. Probably until next week to investigate.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <a href="mailto:sem...@gm..." target="_blank"><sem...@gm...></a> escribió:<o:p></o:p></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p>Dear colleagues,</p><p> </p><p>After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly.</p><p> </p><p>Could you please advice how to fix that?</p><p> </p><p> </p><p>Thank you</p><p> </p><p>Sincerely,</p><p>Dmitry</p><p> </p><p> </p><p> </p><p>Creating the output...</p><p>00032: Traceback (most recent call last):</p><p>00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run</p><p>00034: self._run()</p><p>00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run</p><p>00036: resultFiles = self._runFunc()</p><p>00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc</p><p>00038: return self._func(*self._args)</p><p>00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep</p><p>00040: convertCs2Star(args)</p><p>00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star</p><p>00042: df = star.remove_deprecated_relion2(df, inplace=True)</p><p>00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</p><p>00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</p><p>00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:<a href="tel:23.830243" target="_blank">23.830243</a></p><p>00046: *** Last status is failed</p><p>00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True.</p><p>00048: ------------------- PROTOCOL FAILED (DONE 3/3)</p><p> </p><p> </p></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><pre>Hi Dmitry, give us some time. Probably until next week to investigate.</pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <a href="mailto:sem...@gm..." target="_blank"><sem...@gm...></a> escribió:<o:p></o:p></pre><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>Dear colleagues,</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly.</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>Could you please advice how to fix that?</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>Thank you</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>Sincerely,</pre><pre><o:p> </o:p></pre><pre>Dmitry</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>Creating the output...</pre><pre><o:p> </o:p></pre><pre>00032: Traceback (most recent call last):</pre><pre><o:p> </o:p></pre><pre>00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run</pre><pre><o:p> </o:p></pre><pre>00034: self._run()</pre><pre><o:p> </o:p></pre><pre>00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run</pre><pre><o:p> </o:p></pre><pre>00036: resultFiles = self._runFunc()</pre><pre><o:p> </o:p></pre><pre>00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc</pre><pre><o:p> </o:p></pre><pre>00038: return self._func(*self._args)</pre><pre><o:p> </o:p></pre><pre>00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep</pre><pre><o:p> </o:p></pre><pre>00040: convertCs2Star(args)</pre><pre><o:p> </o:p></pre><pre>00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star</pre><pre><o:p> </o:p></pre><pre>00042: df = star.remove_deprecated_relion2(df, inplace=True)</pre><pre><o:p> </o:p></pre><pre>00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</pre><pre><o:p> </o:p></pre><pre>00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</pre><pre><o:p> </o:p></pre><pre>00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:23.830243</pre><pre><o:p> </o:p></pre><pre>00046: *** Last status is failed</pre><pre><o:p> </o:p></pre><pre>00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True.</pre><pre><o:p> </o:p></pre><pre>00048: ------------------- PROTOCOL FAILED (DONE 3/3)</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre> </pre></blockquote></blockquote><div><p class=MsoNormal>-- <br>Pablo Conesa - <strong><span style='font-family:"Calibri",sans-serif'>Madrid <a href="http://scipion.i2pc.es" target="_blank">Scipion</a> team</span></strong><o:p></o:p></p></div></div><p class=MsoNormal>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><o:p></o:p></p></blockquote></div><p class=MsoNormal><br><br><br><o:p></o:p></p><pre>_______________________________________________</pre><pre>scipion-users mailing list</pre><pre><a href="mailto:sci...@li...">sci...@li...</a></pre><pre><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre></blockquote><p class=MsoNormal>-- <br>Pablo Conesa - <strong><span style='font-family:"Calibri",sans-serif'>Madrid <a href="http://scipion.i2pc.es">Scipion</a> team</span></strong><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Pablo C. <pc...@cn...> - 2021-08-31 14:15:19
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I posted a possible solution there: "Have you got software/em/pyem-0.4 folder. If so, try to remove it and then run scipion3 installb pyem" On 31/8/21 13:40, Jose Miguel de la Rosa Trevin wrote: > I had a similar issue than Dmitry....at some point the same error that > here...but then another one. Reported last Friday here: > > https://github.com/scipion-em/scipion-em-cryosparc2/issues/91 > <https://github.com/scipion-em/scipion-em-cryosparc2/issues/91> > > > > > > On Tue, Aug 31, 2021 at 11:29 AM Pablo Conesa <pc...@cn... > <mailto:pc...@cn...>> wrote: > > Hi! > > It seems there is a mismatch of versions. Could you please send > the output of: > > > scipion3 run pip list > > > And the output of: > > ls -l <SCIPION_HOME>/software/em | grep pyem > > > On 25/8/21 8:07, pc...@cn... <mailto:pc...@cn...> > wrote: >> Hi Dmitry, give us some time. Probably until next week to >> investigate. >> >> El 23 ago. 2021 22:22, "Dmitry A. Semchonok" >> <sem...@gm...> <mailto:sem...@gm...> escribió: >> >> >> Dear colleagues, >> >> After the installation of the latest modules for the >> cryosparc//relion the 2D classification in SCIPION3 is >> finishing with the error, although in cryosparc itself the 2D >> classification finished correctly. >> >> Could you please advice how to fix that? >> >> Thank you >> >> Sincerely, >> >> Dmitry >> >> Creating the output... >> >> 00032: Traceback (most recent call last): >> >> 00033: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 197, in run >> >> 00034: self._run() >> >> 00035: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 248, in _run >> >> 00036: resultFiles = self._runFunc() >> >> 00037: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", >> line 244, in _runFunc >> >> 00038: return self._func(*self._args) >> >> 00039: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", >> line 282, in createOutputStep >> >> 00040: convertCs2Star(args) >> >> 00041: File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", >> line 99, in convertCs2Star >> >> 00042: df = star.remove_deprecated_relion2(df, >> inplace=True) >> >> 00043: AttributeError: module 'pyem.star' has no attribute >> 'remove_deprecated_relion2' >> >> 00044: Protocol failed: module 'pyem.star' has no attribute >> 'remove_deprecated_relion2' >> >> 00045: FAILED: createOutputStep, step 3, time 2021-08-22 >> 13:57:23.830243 <tel:23.830243> >> >> 00046: *** Last status is failed >> >> 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN >> is set to True. >> >> 00048: ------------------- PROTOCOL FAILED (DONE 3/3) >> >> >> >> Hi Dmitry, give us some time. Probably until next week to investigate. >> >> >> El 23 ago. 2021 22:22, "Dmitry A. Semchonok"<sem...@gm...> <mailto:sem...@gm...> escribió: >>> Dear colleagues, >>> >>> >>> >>> After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly. >>> >>> >>> >>> Could you please advice how to fix that? >>> >>> >>> >>> >>> >>> Thank you >>> >>> >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> >>> >>> >>> >>> >>> Creating the output... >>> >>> 00032: Traceback (most recent call last): >>> >>> 00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run >>> >>> 00034: self._run() >>> >>> 00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run >>> >>> 00036: resultFiles = self._runFunc() >>> >>> 00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc >>> >>> 00038: return self._func(*self._args) >>> >>> 00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep >>> >>> 00040: convertCs2Star(args) >>> >>> 00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star >>> >>> 00042: df = star.remove_deprecated_relion2(df, inplace=True) >>> >>> 00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2' >>> >>> 00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' >>> >>> 00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:23.830243 >>> >>> 00046: *** Last status is failed >>> >>> 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True. >>> >>> 00048: ------------------- PROTOCOL FAILED (DONE 3/3) >>> >>> >>> >>> > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > 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 -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry S. <sem...@gm...> - 2021-08-31 14:06:09
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} pre {mso-style-priority:99; mso-style-link:"\0421\0442\0430\043D\0434\0430\0440\0442\043D\044B\0439 HTML \0417\043D\0430\043A"; margin:0cm; font-size:10.0pt; font-family:"Courier New";} span.HTML {mso-style-name:"\0421\0442\0430\043D\0434\0430\0440\0442\043D\044B\0439 HTML \0417\043D\0430\043A"; mso-style-priority:99; mso-style-link:"\0421\0442\0430\043D\0434\0430\0440\0442\043D\044B\0439 HTML"; font-family:"Courier New";} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:612.0pt 792.0pt; margin:2.0cm 42.5pt 2.0cm 3.0cm;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=RU link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Dear colleagues,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Here are my results<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p><span style='background:yellow;mso-highlight:yellow'>scipion3 run pip list</span> </p><p><span style='color:#002060'>[panos@cryoem01 ~]$ scipion3 run pip list <o:p></o:p></span></p><p><span style='color:#002060'>Scipion v3.0.9 - Eugenius<o:p></o:p></span></p><p><span style='color:#002060'>** Running command: pip "list"<o:p></o:p></span></p><p><span style='color:#002060'>Package Version<o:p></o:p></span></p><p><span style='color:#002060'>--------------------- -------------------<o:p></o:p></span></p><p><span style='color:#002060'>appdirs 1.4.4<o:p></o:p></span></p><p><span style='color:#002060'>arcp 0.2.1<o:p></o:p></span></p><p><span style='color:#002060'>argcomplete 1.12.3<o:p></o:p></span></p><p><span style='color:#002060'>astropy 4.2.1<o:p></o:p></span></p><p><span style='color:#002060'>attrs 20.3.0<o:p></o:p></span></p><p><span style='color:#002060'>bagit 1.8.1<o:p></o:p></span></p><p><span style='color:#002060'>bibtexparser 1.2.0<o:p></o:p></span></p><p><span style='color:#002060'>bioblend 0.16.0<o:p></o:p></span></p><p><span style='color:#002060'>biopython 1.76<o:p></o:p></span></p><p><span style='color:#002060'>boto 2.49.0<o:p></o:p></span></p><p><span style='color:#002060'>CacheControl 0.12.6<o:p></o:p></span></p><p><span style='color:#002060'>certifi 2020.12.5<o:p></o:p></span></p><p><span style='color:#002060'>chardet 3.0.4<o:p></o:p></span></p><p><span style='color:#002060'>coloredlogs 15.0.1<o:p></o:p></span></p><p><span style='color:#002060'>configparser 5.0.0<o:p></o:p></span></p><p><span style='color:#002060'>cwltool 3.1.20210628163208<o:p></o:p></span></p><p><span style='color:#002060'>cycler 0.10.0<o:p></o:p></span></p><p><span style='color:#002060'>decorator 4.4.2<o:p></o:p></span></p><p><span style='color:#002060'>dill 0.3.3<o:p></o:p></span></p><p><span style='color:#002060'>distlib 0.3.1<o:p></o:p></span></p><p><span style='color:#002060'>empiar-depositor 1.6b23<o:p></o:p></span></p><p><span style='color:#002060'>emtable 0.0.7<o:p></o:p></span></p><p><span style='color:#002060'>filelock 3.0.12<o:p></o:p></span></p><p><span style='color:#002060'>future 0.18.2<o:p></o:p></span></p><p><span style='color:#002060'>galaxy2cwl 0.1.4<o:p></o:p></span></p><p><span style='color:#002060'>gxformat2 0.15.0<o:p></o:p></span></p><p><span style='color:#002060'>healpy 1.14.0<o:p></o:p></span></p><p><span style='color:#002060'>humanfriendly 9.2<o:p></o:p></span></p><p><span style='color:#002060'>idna 2.10<o:p></o:p></span></p><p><span style='color:#002060'>isodate 0.6.0<o:p></o:p></span></p><p><span style='color:#002060'>Jinja2 3.0.1<o:p></o:p></span></p><p><span style='color:#002060'>joblib 1.0.1<o:p></o:p></span></p><p><span style='color:#002060'>jsonschema 3.2.0<o:p></o:p></span></p><p><span style='color:#002060'>kiwisolver 1.3.1<o:p></o:p></span></p><p><span style='color:#002060'>littleutils 0.2.2<o:p></o:p></span></p><p><span style='color:#002060'>llvmlite 0.31.0<o:p></o:p></span></p><p><span style='color:#002060'>lockfile 0.12.2<o:p></o:p></span></p><p><span style='color:#002060'>lxml 4.6.3<o:p></o:p></span></p><p><span style='color:#002060'>MarkupSafe 2.0.1<o:p></o:p></span></p><p><span style='color:#002060'>matplotlib 3.2.2<o:p></o:p></span></p><p><span style='color:#002060'>mistune 0.8.4<o:p></o:p></span></p><p><span style='color:#002060'>mpi4py 3.0.3<o:p></o:p></span></p><p><span style='color:#002060'>mrcfile 1.3.0<o:p></o:p></span></p><p><span style='color:#002060'>msgpack 1.0.2<o:p></o:p></span></p><p><span style='color:#002060'>multiprocess 0.70.11.1<o:p></o:p></span></p><p><span style='color:#002060'>mypy-extensions 0.4.3<o:p></o:p></span></p><p><span style='color:#002060'>natsort 7.1.1<o:p></o:p></span></p><p><span style='color:#002060'>networkx 2.5.1<o:p></o:p></span></p><p><span style='color:#002060'>numba 0.47.0<o:p></o:p></span></p><p><span style='color:#002060'>numpy 1.18.4<o:p></o:p></span></p><p><span style='color:#002060'>outdated 0.2.0<o:p></o:p></span></p><p><span style='color:#002060'>pandas 1.2.4<o:p></o:p></span></p><p><span style='color:#002060'>pathos 0.2.7<o:p></o:p></span></p><p><span style='color:#002060'>peppercorn 0.6<o:p></o:p></span></p><p><span style='color:#002060'>Pillow 7.1.2<o:p></o:p></span></p><p><span style='color:#002060'>pip 21.0.1<o:p></o:p></span></p><p><span style='color:#002060'>plotter 1.3.18<o:p></o:p></span></p><p><span style='color:#002060'>pox 0.2.9<o:p></o:p></span></p><p><span style='color:#002060'>ppft 1.6.6.3<o:p></o:p></span></p><p><span style='color:#002060'>prov 1.5.1<o:p></o:p></span></p><p><span style='color:#002060'>psutil 5.7.0<o:p></o:p></span></p><p><span style='color:#002060'>pydot 1.4.2<o:p></o:p></span></p><p><span style='color:#002060'>pyem 0.4<o:p></o:p></span></p><p><span style='color:#002060'>pyerfa 1.7.2<o:p></o:p></span></p><p><span style='color:#002060'>pyFFTW 0.12.0<o:p></o:p></span></p><p><span style='color:#002060'>pyparsing 2.4.7<o:p></o:p></span></p><p><span style='color:#002060'>pyrsistent 0.17.3<o:p></o:p></span></p><p><span style='color:#002060'>python-dateutil 2.8.1<o:p></o:p></span></p><p><span style='color:#002060'>pytz 2021.1<o:p></o:p></span></p><p><span style='color:#002060'>PyWavelets 1.1.1<o:p></o:p></span></p><p><span style='color:#002060'>PyYAML 5.4.1<o:p></o:p></span></p><p><span style='color:#002060'>rdflib 5.0.0<o:p></o:p></span></p><p><span style='color:#002060'>rdflib-jsonld 0.5.0<o:p></o:p></span></p><p><span style='color:#002060'>requests 2.23.0<o:p></o:p></span></p><p><span style='color:#002060'>requests-toolbelt 0.9.1<o:p></o:p></span></p><p><span style='color:#002060'>rocrate 0.3.1<o:p></o:p></span></p><p><span style='color:#002060'>ruamel.yaml 0.17.10<o:p></o:p></span></p><p><span style='color:#002060'>ruamel.yaml.clib 0.2.6<o:p></o:p></span></p><p><span style='color:#002060'>schema-salad 8.1.20210627200047<o:p></o:p></span></p><p><span style='color:#002060'>scikit-learn 0.22.1<o:p></o:p></span></p><p><span style='color:#002060'>scipion-app 3.0.9<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em 3.0.13<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-cistem 3.1.0<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-cryosparc2 3.2.12<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-eman2 3.3.2<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-empiar 3.0.6<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-gctf 3.0.12<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-motioncorr 3.1.1<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-relion 3.1.3<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-sphire 3.0.7<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-tomo 3.0.6<o:p></o:p></span></p><p><span style='color:#002060'>scipion-em-xmipp 21.6.1<o:p></o:p></span></p><p><span style='color:#002060'>scipion-installer 1.0.14<o:p></o:p></span></p><p><span style='color:#002060'>scipion-pyworkflow 3.0.17<o:p></o:p></span></p><p><span style='color:#002060'>scipy 1.6.2<o:p></o:p></span></p><p><span style='color:#002060'>SCons 4.1.0.post1<o:p></o:p></span></p><p><span style='color:#002060'>seaborn 0.11.1<o:p></o:p></span></p><p><span style='color:#002060'>setuptools 52.0.0.post20210125<o:p></o:p></span></p><p><span style='color:#002060'>shellescape 3.8.1<o:p></o:p></span></p><p><span style='color:#002060'>six 1.15.0<o:p></o:p></span></p><p><span style='color:#002060'>tifffile 2021.4.8<o:p></o:p></span></p><p><span style='color:#002060'>tkcolorpicker 2.1.3<o:p></o:p></span></p><p><span style='color:#002060'>typing-extensions 3.10.0.0<o:p></o:p></span></p><p><span style='color:#002060'>urllib3 1.25.11<o:p></o:p></span></p><p><span style='color:#002060'>virtualenv 20.4.4<o:p></o:p></span></p><p><span style='color:#002060'>wheel 0.36.2<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p><span style='background:yellow;mso-highlight:yellow'>ls -l <SCIPION_HOME>/software/em | grep pyem</span></p><p><span style='color:#002060'>[panos@cryoem01 ~]$ ls -l <SCIPION_HOME>/software/em | grep pyem<o:p></o:p></span></p><p><span style='color:#002060'>bash: SCIPION_HOME: No such file or directory<o:p></o:p></span></p><p><span style='color:#002060'>[panos@cryoem01 ~]$<o:p></o:p></span></p><p><span style='color:#002060'><o:p> </o:p></span></p><p><span style='color:#002060'><o:p> </o:p></span></p><p><span style='color:black'><o:p> </o:p></span></p><p><span lang=EN-US style='color:black'>Thank you!<o:p></o:p></span></p><p><span style='color:#002060'><o:p> </o:p></span></p><p><span lang=EN-US style='color:black'>Sincerely,</span><span style='color:black'><o:p></o:p></span></p><p><span lang=EN-US style='color:black'>Dmitry</span><span style='color:black'><o:p></o:p></span></p><p><span style='color:#002060'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Отправлено из приложения "<a href="https://go.microsoft.com/fwlink/?LinkId=550986">Почта</a>" для Windows</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='border:none;padding:0cm'><b>От: </b><a href="mailto:pc...@cn...">Pablo Conesa</a><br><b>Отправлено: </b>31 августа 2021 г. в 12:29<br><b>Кому: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Тема: </b>Re: [scipion-users] Cryosparc 2D - Scipion issue</p></div><p class=MsoNormal><o:p> </o:p></p><p>Hi!</p><p>It seems there is a mismatch of versions. Could you please send the output of:</p><p><o:p> </o:p></p><p>scipion3 run pip list </p><p><o:p> </o:p></p><p>And the output of:</p><p>ls -l <SCIPION_HOME>/software/em | grep pyem</p><p><o:p> </o:p></p><div><p class=MsoNormal>On 25/8/21 8:07, <a href="mailto:pc...@cn...">pc...@cn...</a> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>Hi Dmitry, give us some time. Probably until next week to investigate.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <a href="mailto:sem...@gm..."><sem...@gm...></a> escribió:<o:p></o:p></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p style='margin:0cm;overflow-wrap:!important'>Dear colleagues,<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly.<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>Could you please advice how to fix that?<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>Thank you<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>Sincerely,<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>Dmitry<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>Creating the output...<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00032: Traceback (most recent call last):<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00034: self._run()<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00036: resultFiles = self._runFunc()<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00038: return self._func(*self._args)<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00040: convertCs2Star(args)<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00042: df = star.remove_deprecated_relion2(df, inplace=True)<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2'<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2'<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:<a href="tel:23.830243">23.830243</a><o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00046: *** Last status is failed<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True.<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'>00048: ------------------- PROTOCOL FAILED (DONE 3/3)<o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> <o:p></o:p></p><p style='margin:0cm;overflow-wrap:!important'> </p></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><pre>Hi Dmitry, give us some time. Probably until next week to investigate.</pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <a href="mailto:sem...@gm..."><sem...@gm...></a> escribió:<o:p></o:p></pre><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>Dear colleagues,</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly.</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>Could you please advice how to fix that?</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>Thank you</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>Sincerely,</pre><pre><o:p> </o:p></pre><pre>Dmitry</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre>Creating the output...</pre><pre><o:p> </o:p></pre><pre>00032: Traceback (most recent call last):</pre><pre><o:p> </o:p></pre><pre>00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run</pre><pre><o:p> </o:p></pre><pre>00034: self._run()</pre><pre><o:p> </o:p></pre><pre>00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run</pre><pre><o:p> </o:p></pre><pre>00036: resultFiles = self._runFunc()</pre><pre><o:p> </o:p></pre><pre>00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc</pre><pre><o:p> </o:p></pre><pre>00038: return self._func(*self._args)</pre><pre><o:p> </o:p></pre><pre>00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep</pre><pre><o:p> </o:p></pre><pre>00040: convertCs2Star(args)</pre><pre><o:p> </o:p></pre><pre>00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star</pre><pre><o:p> </o:p></pre><pre>00042: df = star.remove_deprecated_relion2(df, inplace=True)</pre><pre><o:p> </o:p></pre><pre>00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</pre><pre><o:p> </o:p></pre><pre>00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</pre><pre><o:p> </o:p></pre><pre>00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:23.830243</pre><pre><o:p> </o:p></pre><pre>00046: *** Last status is failed</pre><pre><o:p> </o:p></pre><pre>00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True.</pre><pre><o:p> </o:p></pre><pre>00048: ------------------- PROTOCOL FAILED (DONE 3/3)</pre><pre><o:p> </o:p></pre><pre> </pre><pre><o:p> </o:p></pre><pre> <o:p></o:p></pre></blockquote><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre></blockquote><p class=MsoNormal>-- <br>Pablo Conesa - <strong><span style='font-family:"Calibri",sans-serif'>Madrid <a href="http://scipion.i2pc.es">Scipion</a> team</span></strong><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Jose M. de la R. T. <del...@gm...> - 2021-08-31 11:41:13
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I had a similar issue than Dmitry....at some point the same error that here...but then another one. Reported last Friday here: https://github.com/scipion-em/scipion-em-cryosparc2/issues/91 On Tue, Aug 31, 2021 at 11:29 AM Pablo Conesa <pc...@cn...> wrote: > Hi! > > It seems there is a mismatch of versions. Could you please send the output > of: > > > scipion3 run pip list > > > And the output of: > > ls -l <SCIPION_HOME>/software/em | grep pyem > > > On 25/8/21 8:07, pc...@cn... wrote: > > Hi Dmitry, give us some time. Probably until next week to investigate. > > El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <sem...@gm...> > <sem...@gm...> escribió: > > > Dear colleagues, > > > > After the installation of the latest modules for the cryosparc//relion the > 2D classification in SCIPION3 is finishing with the error, although in > cryosparc itself the 2D classification finished correctly. > > > > Could you please advice how to fix that? > > > > > > Thank you > > > > Sincerely, > > Dmitry > > > > > > > > Creating the output... > > 00032: Traceback (most recent call last): > > 00033: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 197, in run > > 00034: self._run() > > 00035: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _run > > 00036: resultFiles = self._runFunc() > > 00037: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 244, in _runFunc > > 00038: return self._func(*self._args) > > 00039: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", > line 282, in createOutputStep > > 00040: convertCs2Star(args) > > 00041: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", > line 99, in convertCs2Star > > 00042: df = star.remove_deprecated_relion2(df, inplace=True) > > 00043: AttributeError: module 'pyem.star' has no attribute > 'remove_deprecated_relion2' > > 00044: Protocol failed: module 'pyem.star' has no attribute > 'remove_deprecated_relion2' > > 00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:23.830243 > > 00046: *** Last status is failed > > 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to > True. > > 00048: ------------------- PROTOCOL FAILED (DONE 3/3) > > > > > > > > Hi Dmitry, give us some time. Probably until next week to investigate. > > > El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <sem...@gm...> <sem...@gm...> escribió: > > Dear colleagues, > > > > After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly. > > > > Could you please advice how to fix that? > > > > > > Thank you > > > > Sincerely, > > Dmitry > > > > > > > > Creating the output... > > 00032: Traceback (most recent call last): > > 00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run > > 00034: self._run() > > 00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run > > 00036: resultFiles = self._runFunc() > > 00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc > > 00038: return self._func(*self._args) > > 00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep > > 00040: convertCs2Star(args) > > 00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star > > 00042: df = star.remove_deprecated_relion2(df, inplace=True) > > 00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2' > > 00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' > > 00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:23.830243 > > 00046: *** Last status is failed > > 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True. > > 00048: ------------------- PROTOCOL FAILED (DONE 3/3) > > > > > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2021-08-31 09:29:26
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Hi! It seems there is a mismatch of versions. Could you please send the output of: scipion3 run pip list And the output of: ls -l <SCIPION_HOME>/software/em | grep pyem On 25/8/21 8:07, pc...@cn... wrote: > Hi Dmitry, give us some time. Probably until next week to investigate. > > El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <sem...@gm...> > escribió: > > > Dear colleagues, > > After the installation of the latest modules for the > cryosparc//relion the 2D classification in SCIPION3 is finishing > with the error, although in cryosparc itself the 2D classification > finished correctly. > > Could you please advice how to fix that? > > Thank you > > Sincerely, > > Dmitry > > Creating the output... > > 00032: Traceback (most recent call last): > > 00033: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 197, in run > > 00034: self._run() > > 00035: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _run > > 00036: resultFiles = self._runFunc() > > 00037: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 244, in _runFunc > > 00038: return self._func(*self._args) > > 00039: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", > line 282, in createOutputStep > > 00040: convertCs2Star(args) > > 00041: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", > line 99, in convertCs2Star > > 00042: df = star.remove_deprecated_relion2(df, inplace=True) > > 00043: AttributeError: module 'pyem.star' has no attribute > 'remove_deprecated_relion2' > > 00044: Protocol failed: module 'pyem.star' has no attribute > 'remove_deprecated_relion2' > > 00045: FAILED: createOutputStep, step 3, time 2021-08-22 > 13:57:23.830243 <tel:23.830243> > > 00046: *** Last status is failed > > 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is > set to True. > > 00048: ------------------- PROTOCOL FAILED (DONE 3/3) > > > > Hi Dmitry, give us some time. Probably until next week to investigate. > > > El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <sem...@gm...> escribió: >> >> Dear colleagues, >> >> >> >> After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly. >> >> >> >> Could you please advice how to fix that? >> >> >> >> >> >> Thank you >> >> >> >> Sincerely, >> >> Dmitry >> >> >> >> >> >> >> >> Creating the output... >> >> 00032: Traceback (most recent call last): >> >> 00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run >> >> 00034: self._run() >> >> 00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run >> >> 00036: resultFiles = self._runFunc() >> >> 00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc >> >> 00038: return self._func(*self._args) >> >> 00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep >> >> 00040: convertCs2Star(args) >> >> 00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star >> >> 00042: df = star.remove_deprecated_relion2(df, inplace=True) >> >> 00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2' >> >> 00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' >> >> 00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:23.830243 >> >> 00046: *** Last status is failed >> >> 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True. >> >> 00048: ------------------- PROTOCOL FAILED (DONE 3/3) >> >> >> >> > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: <pc...@cn...> - 2021-08-25 06:08:03
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<div dir='auto'>Hi Dmitry, give us some time. Probably until next week to investigate.</div><div class="gmail_extra"><br><div class="gmail_quote">El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <sem...@gm...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div> <div dir="auto"><br /></div><div dir="auto"><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Dear colleagues,</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly.</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Could you please advice how to fix that?</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Thank you</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Sincerely,</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Dmitry</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Creating the output...</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00032: Traceback (most recent call last):</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00034: self._run()</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00036: resultFiles = self._runFunc()</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00038: return self._func(*self._args)</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00040: convertCs2Star(args)</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00042: df = star.remove_deprecated_relion2(df, inplace=True)</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:<a href="tel:23.830243" style="overflow-wrap:!important;color:rgb( 0 , 151 , 167 ) !important">23.830243</a></span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00046: *** Last status is failed</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True.</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00048: ------------------- PROTOCOL FAILED (DONE 3/3)</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"> </p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"> </p></div></div> </blockquote></div><br></div> |
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From: Dmitry A. S. <sem...@gm...> - 2021-08-23 20:23:03
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Dear colleagues, After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly. Could you please advice how to fix that? Thank you Sincerely, Dmitry Creating the output... 00032: Traceback (most recent call last): 00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run 00034: self._run() 00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run 00036: resultFiles = self._runFunc() 00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc 00038: return self._func(*self._args) 00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep 00040: convertCs2Star(args) 00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star 00042: df = star.remove_deprecated_relion2(df, inplace=True) 00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2' 00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' 00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:23.830243 00046: *** Last status is failed 00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True. 00048: ------------------- PROTOCOL FAILED (DONE 3/3) |
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