I am a beginner, trying to process tutorial dataset but getting error even with motion correction

I am a beginner, trying to process tutorial dataset but getting the error even with motion correction, all micrographs ending with incomplete. By any chance, did I miss any installation file? which is causing this issue? Thanks.

Hi @umarfarook12,

Can you please provide some additional information to help us determine what the issue is? If possible, please reply with the error message you got from the motion correction job and a screenshot of the ‘Parameters’ tab (when you click spacebar to inspect a job, it will be a clickable tab at the top of the dialog).


Hello Dawood,

I am not getting any error message, but you could see the output screenshot everything ended in incomplete. I am not sure, what’s going wrong here.

Hi @umarfarook12,

Thank you for the additional details. To find out if there is an error in the job log, please run the following command on the machine running cryoSPARC and report the output (replace P1 with your project number and J1 with your job number):

cryosparcm joblog P1 J1

Hi @sdawood

Please see the output below, are you asking for this?

File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 174, in _run_module_as_main
main”, fname, loader, pkg_name)
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 72, in _run_code
exec code in run_globals
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 82, in
cli = CommandClient(host, int(port))
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 33, in init
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 61, in _reload
system = self._get_callable(‘system.describe’)()
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 49, in func
r = requests.post(self.url, data = json.dumps(data, cls=NumpyEncoder), headers = header, timeout=self.timeout)
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/api.py”, line 116, in post
return request(‘post’, url, data=data, json=json, **kwargs)
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/api.py”, line 60, in request
return session.request(method=method, url=url, **kwargs)
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py”, line 533, in request
resp = self.send(prep, **send_kwargs)
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/sessions.py”, line 646, in send
r = adapter.send(request, **kwargs)
File “/ibex/scratch/projects/c2030/Umar_Arold_Lab/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/adapters.py”, line 516, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host=‘em504-02.ibex.kaust.edu.sa’, port=39002): Max retries exceeded with url: /api (Caused by NewConnectionError(’<urllib3.connection.HTTPConnection object at 0x7f001de35890>: Failed to establish a new connection: [Errno 111] Connection refused’,))

Hi @umarfarook12,

It looks like the job is having trouble accessing cryoSPARC’s API. Please ensure the following TCP ports are open to the master node and any worker nodes you have connected: https://guide.cryosparc.com/setup-configuration-and-management/cryosparc-installation-prerequisites#4-open-tcp-ports

Additionally, restarting cryoSPARC might help: cryosparcm restart