-
Notifications
You must be signed in to change notification settings - Fork 13
FAQ
We will update this section summarising fixes to installation / running errors that have been submitted as tickets or found by us or users. If you find an issue, please create and Issue and we will try to get back to you as soon as possible.
- Situation: Installing developer mode with poetry. Building wheel for datrie (pyproject.toml) did not run successfully.
- Error log:
Failed to build datrie
ERROR: Failed to build one or more wheels
- Cause: In windows, datrie package requires Microsoft Visual C++ 14.0 or greater to build
- Solution: Go to the Microsoft Visual C++ Build Tools page. During the installation, make sure to select the "Desktop development with C++" workload.
Question: Why does first time running OptiNiSt take so long? After the first time, it is much faster.
- Answer: During the first time running nodes, a new conda environment is created. In the case of CaImAn or Suite2p, this takes a long time as these toolboxes are installed from scratch. On subsequent runs the cached conda environment can be used, so running workflows is much faster.
Error: func.py died with Signals.SIGKILL: 9
- Situation: When using Docker, CaImAn is executed in workflow (may occur with with nodes too)
- Error log: python /app/.snakemake/scripts/xxxxxxxxxxx.func.py' died with <Signals.SIGKILL: 9>.
- Cause: Probably the workflow execution process is out of memory.
- Related: Issue 344
- Solution:
Error: pickle data was truncated
- Situation: When a workflow is executed in which the size of the node's processing result data (.pkl) is very large (e.g., a large image + caiman)
- Error log:
File "/app/studio/app/common/core/utils/pickle_handler.py", line 13, in read
return pickle.load(f)_pickle.UnpicklingError: pickle data was truncated
- Cause: When the size of the pkl file exceeds several GB (4GB?), an exception is suspected to occur during pickle read.
- Related:
- Solution: Not solution at this time.
Error: func.py died with Signals.SIGSEGV: 11
- Situation: With Docker, suite2p freezes
- Error log:
set -euo pipefail; python /app/.snakemake/scripts/XXXXXXXXXX.func.py' died with <Signals.SIGSEGV: 11>.\n',
- Cause: Issue between Apple Silicon and certain functions. Rosetta mainly solves this, but sometimes issues remain.
- Related: Issue 365
- Solution:
- Fixed with update to use miniforge + channel_priority flexible. See here in the documentation
- Turning On / Off Rosetta in Docker may also help (in some cases turning on, in others turning off seemed to work). Go to Dockerhub, Virtual Machine Options and turn on/off Rosetta option
Error: LCCD fails with short videos
- Situation: LCCD is not robust for videos with less than 300 time-points.
- Error log:
- Cause:
- Related: Issue 408
- Solution:
Error: OptiNiSt does not currently accept 2-channel data correctly
- Situation:
- Error log:
- Cause:
- Related: Issue 411
- Solution: