'List index out of range' during Import Particles - v2.12.4

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#1

Dear Cryosparc developers,

I have installed cryosparc V2.12.4 on a brand new workstation running scientific linux with kernel 3.10.0-1062.4.1.el7.x86_64. Although the installation procedure seems normal, when I tried to import particles I got the error of ‘list index out of range’. This is very strange because the same set of particles and star file works perfectly fine on another workstation. Does anyone have any clue of what is going on?

Thanks a lot for your inputs!


#2

Hi @chenzhao,

Can you provide us with job logs? cryosparcm joblog <project_uid> <job_uid> Also, do you happen to be importing Relion 3.1 .star files?


#3

Hi @sarulthasan,

Thank you for your reply. I am using relion 3.0.8 star file which works fine on another machine. Unfortunately, the job did not even run when showing this error (meaning it is still queued), so there is no job.log to display.

I know this is very strange problem and I have no clue of how to even troubleshot…

BTW, I have reinstalled it several times, and another lab member also tried to install using his own account, but the same problem happens to both of us…

Thanks a lot,
Chen


#4

Hi @chenzhao,

Can you please provide the output of the command_core when this error happens? cryosparcm log command_core Can you also confirm where you installed cryoSPARC? Is it in your home directory?


#5

Hi @sarulthasan,

Thank you for your suggestion. This time I did get something informative, and the error I got is the following (I erased the IP address for security purpose):

---------- Scheduler running ---------------
Jobs Queued: [u’J1’, u’J1’, u’J1’]
Licenses currently active : 0
Now trying to schedule J1
Need slots : {}
Need fixed : {}
Master direct : True
Scheduling directly onto master node XXX.XX.XX.XXX
Traceback (most recent call last):
File “cryosparc2_command/command_core/init.py”, line 187, in background_worker
scheduler_run_core() # sets last run time
File “cryosparc2_command/command_core/init.py”, line 1514, in scheduler_run_core
‘lane’ : lanes[0][‘name’],
IndexError: list index out of range
****** Scheduler Failed ****

Any ideas?

Thanks a lot,
Chen


#6

Hi @chenzhao,

Can you report the output of the command:
cryosparcm cli "get_scheduler_lanes()"