Dear all,
I have been trying Topaz on my data and wanted to perform the manual pick approach before training. After successful denoising, I loaded the micrographs onto a manual pick but they do not appear in the interface. This also happens if I try to run an Inspect Picks job.
Is there any way of solving this? Here are some screenshots:
I am using Cryosparc 3.0.4 if that helps.
Thank you very much in advance
David
Hi @DavidF,
To help us debug this, when you encounter this error (by opening up the job dialog), can you reply with the results of the following commands:
cryosparcm log command_core
cryosparcm log webapp
Thanks,
Suhail
Hi Suhail,
This is the output of cryosparcm log command_core
[EXPORT_JOB] : Creating .csg file for denoised_micrographs
[EXPORT_JOB] : Done. Exported in 0.01s
[EXPORT_JOB] : Updating job manifest…
[EXPORT_JOB] : Done. Updated in 0.01s
[EXPORT_JOB] : Exported P4 J554 in 0.06s
[EXPORT_JOB] : Request to export P4 J576
[EXPORT_JOB] : Exporting job to /data/cm01/cmihr1/dafernan/P7/J576
[EXPORT_JOB] : Exporting all of job’s images in the database to /data/cm01/cmihr1/dafernan/P7/J576/gridfs_data…
[EXPORT_JOB] : Done. Exported 0 images in 0.00s
[EXPORT_JOB] : Exporting all job’s streamlog events…
[EXPORT_JOB] : Done. Exported 1 files in 0.00s
[EXPORT_JOB] : Exporting job metafile…
[EXPORT_JOB] : Done. Exported in 0.00s
[EXPORT_JOB] : Updating job manifest…
[EXPORT_JOB] : Done. Updated in 0.01s
[EXPORT_JOB] : Exported P4 J576 in 0.01s
---------- Scheduler running ---------------
Jobs Queued: [(‘P4’, ‘J576’)]
Licenses currently active : 0
Now trying to schedule J576
Need slots : {}
Need fixed : {}
Master direct : True
Scheduling directly onto master node cmproc1.esrf.fr
Failed to connect link: HTTP Error 502: Bad Gateway
Not a commercial instance - heartbeat set to 12 hours.
Changed job P4.J576 status launched
Running project UID P4 job UID J576
Running job on master node directly
Running job using: /home/esrf/cryosparc/cryosparc2_master/bin/cryosparcm
---------- Scheduler finished ---------------
Changed job P4.J576 status started
Changed job P4.J576 status running
Changed job P4.J576 status waiting
As for the cryosparcm log webapp
job_connect_group
{“project_uid”:“P4”,“source_group”:“J554.denoised_micrographs”,“dest_group”:“J576.micrographs”}
enqueue_job
{“project_uid”:“P4”,“job_uid”:“J576”,“lane”:“default”}
==== [jobs] project query user 5dfca322234ba3279ac8f512 David Fernandez false
==== [workspace] project query user 5dfca322234ba3279ac8f512 David Fernandez false
==== [jobs] project query user 5dfca322234ba3279ac8f512 David Fernandez false
==== [jobs] project query user 5dfca322234ba3279ac8f512 David Fernandez false
==== [jobs] project query user 5dfca322234ba3279ac8f512 David Fernandez false
[PUB] job.events.checkpoints: { project_uid: ‘P4’, job_uid: ‘J576’, type: ‘checkpoint’ }
[PUB] job.events: { project_uid: ‘P4’, job_uid: ‘J576’ } 100 0
[PUB] events.countAfterCheckpoint
I am unaware whether this is the correct output since when I create a text file from the commands, this file is enormous. However this seems to be the part related to the manual pick (J576) job.
I hope this helps.
Thanks for your time,
David
Hi @DavidF,
Apologies for the delay! Thank you for the logs - based on their contents it doesn’t seem to be an issue with the cryoSPARC setup but rather the job process itself. Please report the output of the following command (replace the project or job ID with the applicable one):
cryosparcm joblog P4 J576