Error message during AutoRefine

rasmuskf

Error message during AutoRefine

Dear cisTEAM,

During an AutoRefine run in iteration 5 out of 20 I got an error message after the "calculating reconstruction step" saying,

error: mode 32618 MRC files currently not supported. 

The GUI then immediately aborted. When trying to open the already calculated volumes in chimera I get an error message saying that "file size is too small for grid size". Any suggestion if the already calculated volume can be used? Or should I retry the AutoRefine run?

Best,

Rasmus

Thu, 03/22/2018 - 13:37

timgrant

Hi Rasmus, 

This sounds like something went wrong and the volume was not correctly written (is it possible you ran out of disk space in the scratch directory?)

I think you will have to retry the run - sorry!

Tim

Thu, 03/22/2018 - 14:26

rasmuskf

In reply to by timgrant

Hi Tim,

Disk space shouldn't be a problem. But out of curiosity, is there a way to see cisTEM's memory requirements for 3D refinements/classifications? The box sizes I use for my particles are in the 512-700 pixel range (1.1 Å/pix) and especially when I ask for multiple 3D classes it happens to me that the GUI suddenly aborts without providing any error messages.

Best,

Rasmus

Fri, 03/23/2018 - 20:30

timgrant

Hi Rasmus,

I think the memory usage should be less than 4 * the 3D size at most PER process.  So for 700 pixels, it would be ~5.2GB per process.

Tim

Hi Tim,

Thank you very much for the reply. I am using OpenSuse 15.0. When I run 3d refine I get this error msg:

Refine3D: Normal termination

   100% [=================] done! (1h:32m22s)                      

Refine3D: Normal termination

JOB CONTROL : Master Socket Disconnected!!
Running...

 JOB CONTROL: Trying to connect to 192.168.8.3:3000 (timeout = 4 sec) ...
 JOB CONTROL: Succeeded - Connection established!

We read 31240 bytes
We read 31240 bytes

 327888 data lines read

 327888 data lines read

 327888 data lines read

 327888 data lines read
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read
17:17:19: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read

 327888 data lines read
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read

 327888 data lines read

 327888 data lines read
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:20: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
Connection Timer Fired

 327888 data lines read
17:17:21: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)

 327888 data lines read

 327888 data lines read

 327888 data lines read
17:17:21: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:21: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
17:17:21: Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
Connection Timer Fired
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
Calculation thread has been waiting for something to do for 30.000000.2 seconds - going to finish
Running...

 JOB CONTROL: Trying to connect to 192.168.8.3:3000 (timeout = 4 sec) ...
 JOB CONTROL: Succeeded - Connection established!

We read 3934 bytes
We read 3934 bytes
Connection Timer Fired
Connection Timer Fired
JOB  : Master SoJOB  : Master SoJOB  : Master Socket Disconnectecket Disconnected!!
cket Disconnected!!
d!!
JOB  : Master SoJOB  : Master SoJOB  : Master Socket Disconnectecket Disconnectecket Disconnected!!
d!!
d!!
JOB  : Master Socket DisconnecteJOB  : Master Sod!!
cket DisconnecteJOB  : Master SoJOB  : Master Sod!!
cket Disconnectecket DisconnecteJOB  : Master SoJOB  : Master SoJOB  : Master Sod!!
cket Disconnected!!
d!!
cket Disconnectecket Disconnected!!
d!!
JOB  : Master SoJOB  : Master SoJOB  : Master Socket Disconnectecket Disconnectecket Disconnected!!
d!!
d!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!
JOB  : Master Socket Disconnected!!

Best regards,

Zhening

Tue, 04/20/2021 - 21:53

joana.paulino

Hello,

 

I am getting a similar error that Rasmus posted about back in 2018 when I run Find CTF.
This is happening with a small data set from at 200keV Negative Stain, so I don't think memmory space is an issue.
Any advises on how to proceed?

The error:

Error: mode 32542 MRC files not currently supported

JOB CONTROL : GUI Socket Disconnected!!
/programs/share/capsules/lib/job.sh: line 120:  9702 Aborted                 "$SB_EXECFILE" "$@"

 

 

bests

 

Joana