Re: [scipion-users] Scipion 3.0.9 cryosparc2 plugin pyem error

[Pablo C. <pc...@cn...>]

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*