Dear Colleagues,
We are processing data imported from RELION 3D classification. After motion correction, CTF estimation, particle picking and cleaning in cryosparc, we exported the particles to RELION for 3D classification. The particles in distinct STAR files corresponding to different RELION 3D classes were imported back into cryosparc, then subjected to ab initio model generation, and heterogeneous refinement. No problems till this stage. However, when we attempt to perform homogeneous refinement of the largest heterogeneous class, we run into the error below. Any advise will be greatly appreciated. Thank you.
CPU: 334.7 MB]
Traceback (most recent call last):
File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
File "cryosparc_master/cryosparc_compute/jobs/refine/newrun.py", line 125, in cryosparc_compute.jobs.refine.newrun.run_homo_refine
File "/ibbr/cryosparc/cryosparc_worker/cryosparc_compute/particles.py", line 114, in read_blobs
u_blob_paths = cache.download_and_return_cache_paths(u_rel_paths)
File "/ibbr/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache.py", line 112, in download_and_return_cache_paths
compressed_keys = get_compressed_keys(worker_hostname, rel_paths)
File "/ibbr/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache.py", line 285, in get_compressed_keys
compressed_keys = rc.cli.cache_request_check(worker_hostname, rc._project_uid, rc._job_uid, com.compress_paths(rel_paths))
File "/ibbr/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 104, in func
with make_json_request(self, "/api", data=data) as request:
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/contextlib.py", line 113, in __enter__
return next(self.gen)
File "/ibbr/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 165, in make_request
with urlopen(request, timeout=client._timeout) as response:
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 542, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(*args)
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 1383, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/urllib/request.py", line 1358, in do_open
r = h.getresponse()
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/http/client.py", line 1348, in getresponse
response.begin()
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/http/client.py", line 316, in begin
version, status, reason = self._read_status()
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/http/client.py", line 277, in _read_status
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
File "/ibbr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/socket.py", line 669, in readinto
return self._sock.recv_into(b)
socket.timeout: timed out