2D Classification Error question

Applewang · October 20, 2025, 11:04am

I am facing a question when doing 2D classification steps after I finished Extract From Micrographs.

Traceback (most recent call last): File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main File “cryosparc_master/cryosparc_compute/jobs/class2D/newrun.py”, line 89, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.run_class_2D File “/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/particles.py”, line 120, in read_blobs u_blob_paths = cache_run(u_rel_paths) File “/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache_v2.py”, line 881, in run return run_with_executor(rel_sources, executor) File “/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache_v2.py”, line 906, in run_with_executor drive = activate() File “/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache_v2.py”, line 846, in activate CacheDrive.ACTIVE = CacheDrive( File “/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache_v2.py”, line 464, in _init_ self.path.mkdir(parents=True, exist_ok=True) File “/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/pathlib.py”, line 1175, in mkdir self._accessor.mkdir(self, mode) OSError: [Errno 22] Invalid argument: ‘/media/zenglab/新加卷/cryosparc_temp/instance_zenglab-Z790-UD:61001’

Oct 20, 2025, 4:09:14 PM Encountered OS error while caching: [Errno 22] Invalid argument: ‘/media/zenglab/新加卷/cryosparc_temp/instance_zenglab-Z790-UD:61001’; dumping info

Applewang · October 20, 2025, 11:19am

And the event log is:

 License is valid.

 Launching job on lane default target zenglab-Z790-UD ...

 Running job on master node hostname zenglab-Z790-UD

 \[CPU:   87.8 MB  Avail: 124.47 GB\]

 Job J11 Started

 \[CPU:   87.8 MB  Avail: 124.47 GB\]

 Master running v4.7.1, worker running v4.7.1

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

 Working in directory: /home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_projects/MED4_8L_CP12_crosslinking_250912/CS-new-med4-8l-crosslinking-protein-250912/J11

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

 Running on lane default

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

 Resources allocated:

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

   Worker:  zenglab-Z790-UD

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

   CPU   :  \[0, 1, 2, 3\]

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

   GPU   :  \[0\]

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

   RAM   :  \[0, 1, 2\]

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

   SSD   :  True

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

 \--------------------------------------------------------------

 \[CPU:   88.1 MB  Avail: 124.47 GB\]

 Importing job module for job type class_2D_new...

 \[CPU:  268.9 MB  Avail: 124.35 GB\]

 Job ready to run

 \[CPU:  268.9 MB  Avail: 124.35 GB\]

 \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*

 \[CPU:   1.72 GB  Avail: 122.91 GB\]

 Using random seed of 922238816

 \[CPU:   1.72 GB  Avail: 122.91 GB\]

 Using pixel size from location/micrograph_psize_A for duplicate removal

 \[CPU:   1.72 GB  Avail: 122.91 GB\]

 Loading a ParticleStack with 2316132 items...

 \[CPU:   1.74 GB  Avail: 122.88 GB\]

 ────────────────────────────────────────────────────────────── SSD cache: resolving 1196 source path(s)...

 \[CPU:   1.74 GB  Avail: 122.89 GB\]

 Encountered OS error while caching: \[Errno 22\] Invalid argument: '/media/zenglab/新加卷/cryosparc_temp/instance_zenglab-Z790-UD:61001'; dumping info

 \[CPU:   1.27 GB  Avail: 122.88 GB\]

 Traceback (most recent call last):   File "cryosparc_master/cryosparc_compute/run.py", line 129, in cryosparc_master.cryosparc_compute.run.main   File "cryosparc_master/cryosparc_compute/jobs/class2D/newrun.py", line 89, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.run_class_2D   File "/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/particles.py", line 120, in read_blobs     u_blob_paths = cache_run(u_rel_paths)   File "/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache_v2.py", line 881, in run     return run_with_executor(rel_sources, executor)   File "/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache_v2.py", line 906, in run_with_executor     drive = activate()   File "/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache_v2.py", line 846, in activate     CacheDrive.ACTIVE = CacheDrive(   File "/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/cryosparc_compute/jobs/cache_v2.py", line 464, in \__init_\_     self.path.mkdir(parents=True, exist_ok=True)   File "/home/zenglab/home/zenglab/wxy/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/pathlib.py", line 1175, in mkdir     self.\_accessor.mkdir(self, mode) OSError: \[Errno 22\] Invalid argument: '/media/zenglab/新加卷/cryosparc_temp/instance_zenglab-Z790-UD:61001'

My SSD cache path is /media/zenglab/新加卷, which has 500GB. Is it because there isn’t enough space？

rbs_sci · October 20, 2025, 11:32am

A quick test is disable caching and see whether it’ll run.

But I suspect that it’s caused by the UTF-8 characters in the path (新加卷)… or something has gone wrong with the mount.

edit: what format is the /media drive?

Applewang · October 21, 2025, 12:56pm

Hi rbs. I run out df -hT /media/zenglab/新加卷/cryosparc_temp/ which is the SSD path. The result is /dev/nvme0n1p2 ntfs3 469G 3.7G 466G 1% /media/zenglab/新加卷
and the df -hT /media is /dev/sda4 ext4 5.0T 1.1T 3.7T 23% /