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CCPEM  November 2020

CCPEM November 2020

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Subject:

Re: motion correction job in Relion

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Fri, 13 Nov 2020 22:43:51 +0000

Content-Type:

text/plain

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Parts/Attachments

text/plain (208 lines)

Hi,

It is easier to count STAR files in your "movies" folder. The number should be
the same as the input movies.

But this is not the right way to proceed. You should stop the job,
repair the job submission script and continue the job.

Best regards,

Takanori Nakane

On 2020/11/13 22:40, Yahui Yan wrote:
> Hi Takanori,
> 
> Thanks for the reply.
> 
> Since I do not have the run.out file to monitor the process, I am monitoring how many .mrc files generated  in the 'movies' folder (which is the 
> motion correction job folder). I have imported 7259 movies. I am wondering how many .mrc files will generate in the 'movies' folder? The job has run 
> for a day now. I hope to estimate the leftover running time if possible.
> 
> Kind regards,
> Yahui
> 
> On Fri, Nov 13, 2020 at 11:22 AM Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>> wrote:
> 
>     Hi,
> 
>     The program writes to standard output and standard error.
>     It is the responsibility of your queue system to redirect
>     them into run.out and run.err. In other words, probably
>     your job submission template is not properly set up.
> 
>     Best regards,
> 
>     Takanori Nakane
> 
>     P.S. Please don't remove CC to CCPEM.
> 
>     On 2020/11/13 11:19, Yahui Yan wrote:
>      > Hi Takanori,
>      >
>      > Thanks for your quick reply.
>      >
>      > In my job folder (MotionCorr/job008/), I used command 'ls -a' and got:
>      > .
>      > ..
>      > default_pipeline.star
>      > job_pipeline.star
>      > job.star
>      > movies
>      > note.txt
>      > run_submit.script
>      >
>      > Which one of them shows the progress bar?
>      >
>      > Thanks very much!
>      >
>      > Kind regards,
>      > Yahui
>      >
>      >
>      > On Fri, Nov 13, 2020 at 10:36 AM Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>
>     <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>      >
>      >     Hi,
>      >
>      >     In the job directory (i.e. MotionCorr/jobXXX).
>      >
>      >     Takanori
>      >
>      >     On 2020/11/13 10:35, Yahui Yan wrote:
>      >      > Hi Takanori,
>      >      >
>      >      > Could you please tell me where to find the 'run.out' to see the progress? I can't find it in my Relion project folder.
>      >      >
>      >      > Many thanks,
>      >      > Yahui
>      >      >
>      >      >
>      >      > On Wed, Nov 11, 2020 at 4:52 PM Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>
>     <mailto:[log in to unmask] <mailto:[log in to unmask]>> <mailto:[log in to unmask] <mailto:[log in to unmask]>
>      >     <mailto:[log in to unmask] <mailto:[log in to unmask]>>>> wrote:
>      >      >
>      >      >     Hi,
>      >      >
>      >      >      > I found  half of the sub-folders in the 'mnt' folder (similar file path names to my image files) have new files (*.mrc, *star,*.log,
>      >     etc) written.
>      >      >
>      >      >     The fact that you have "mnt/XXX/YYY" subdirectories suggests you have imported
>      >      >     movies in a non-recommended way. Please read
>      >      > https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#What_is_the_right_way_to_import_files_outside_the_project_directory.3F
>     <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#What_is_the_right_way_to_import_files_outside_the_project_directory.3F>
>      >     <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#What_is_the_right_way_to_import_files_outside_the_project_directory.3F
>     <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#What_is_the_right_way_to_import_files_outside_the_project_directory.3F>>
>      >      >     <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#What_is_the_right_way_to_import_files_outside_the_project_directory.3F
>     <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#What_is_the_right_way_to_import_files_outside_the_project_directory.3F>
>      >     <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#What_is_the_right_way_to_import_files_outside_the_project_directory.3F
>     <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#What_is_the_right_way_to_import_files_outside_the_project_directory.3F>>>.
>      >      >
>      >      >      > I
>      >      >      > guess other empty subfolders will be filled up when relevant images are processed.
>      >      >
>      >      >     Yes.
>      >      >
>      >      >      > I assume it would give a bit of estimation of time needed to finish the job.
>      >      >
>      >      >     A progress bar is displayed in run.out.
>      >      >
>      >      >     Another tips is to use "--do_at_most XXX". This terminates the job
>      >      >     after processing XXX movies, so you can get a STAR file quicker.
>      >      >     Of course you have to continue the job several times to process the remaining.
>      >      >     This is intended to be used within a loop of RELION scheduler for on-the-fly
>      >      >     processing.
>      >      >
>      >      >     Best regards,
>      >      >
>      >      >     Takanori Nakane
>      >      >
>      >      >      > Kind regards,
>      >      >      > Yahui
>      >      >      >
>      >      >      >
>      >      >      >
>      >      >      > On Wed, Nov 11, 2020 at 4:24 PM Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>
>     <mailto:[log in to unmask] <mailto:[log in to unmask]>>
>      >     <mailto:[log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
>     <mailto:[log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
>      >      >     <mailto:[log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask]
>     <mailto:[log in to unmask]>>>>> wrote:
>      >      >      >
>      >      >      >     Hi,
>      >      >      >
>      >      >      >     You can open individual micrographs (*.mrc) or plots (*.eps) but
>      >      >      >     the STAR file is generated only at the end.
>      >      >      >
>      >      >      >     Takanori
>      >      >      >
>      >      >      >     On 2020/11/11 16:12, Yahui Yan wrote:
>      >      >      >      > Dear all,
>      >      >      >      >
>      >      >      >      > I am running the motion correction job for a 7200 movies dataset. It has been running for 5.5 hours.
>      >      >      >      >
>      >      >      >      > How can I check the progress of the running job to see what has been done?
>      >      >      >      >
>      >      >      >      > I can see it is running on the cluster job list.
>      >      >      >      >
>      >      >      >      > In the Relion interface, this job is on the 'Running jobs' column. And nothing on the 'Display' pull down list yet.
>      >      >      >      >
>      >      >      >      > I can see there are some files generated in the job folder:
>      >      >      >      > default_pipeline.star
>      >      >      >      > job_pipeline.star
>      >      >      >      > job.star
>      >      >      >      > mnt
>      >      >      >      > note.txt
>      >      >      >      > run_submit.script
>      >      >      >      >
>      >      >      >      >
>      >      >      >      > Thanks very much for answering my silly question.
>      >      >      >      >
>      >      >      >      > Kind regards,
>      >      >      >      > Yahui
>      >      >      >      >
>      >      >      >      >
>      >      >      >      >
>      >      >      >
>      >      >
>      >     
>       ------------------------------------------------------------------------------------------------------------------------------------------------------
>      >      >      >      >
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