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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Job hung at "running gene mapper..." #119

Closed CypherAce closed 1 year ago

CypherAce commented 2 years ago

As the title describes, I'm having an issue that I'm at a loss to diagnose. I have completely nuked and reinstalled my installation of open-cravat on this linux system twice at this point. When I try to run any job, it simply hangs and never gets past the "running gene mapper..." step of the process. I know the files in question are fine because I was able to run them on a brand new windows installation I setup as a test. I just don't know what the issue is at this point.

CypherAce commented 2 years ago

I'll add, for the sake of thoroughness, that the hang also occurs in example input I generate with OC itself and I have checked and the hg38 mapper is installed.

kmoad commented 2 years ago

Could you send the output of oc config cravat and oc config system. Also, the log files for the job. They should be something like INPUTFILENAME.log.

Also, you could try nuking and re-installing the mapper module

oc module uninstall hg38
oc module install hg38
skoul9 commented 1 year ago

I am facing a similar issue.

I installed Open Cravat on my workspace in a cluster environment and on my local machine (Mac OS) using pip. I can run the example-input on my local machine, but on the cluster, the program hangs at the mapper step, and an error is reported saying that a new thread can not be started. I raised the RAM and number of cores to ensure it is not due to a computing resource limitation, but I need help getting past that step. Can I modify environment settings or OC options to make it work?

I don't know if this is an error related to the mapper or if it coincides with the mapping step.

Exception in thread Thread-1: Traceback (most recent call last): File ".../python/3.9.10/lib/python3.9/threading.py", line 973, in _bootstrap_inner self.run() File ".../python/3.9.10/lib/python3.9/threading.py", line 910, in run self._target(*self._args, **self._kwargs) File ".../python/3.9.10/lib/python3.9/multiprocessing/managers.py", line 194, in accepter t.start() File ".../python/3.9.10/lib/python3.9/threading.py", line 892, in start _start_new_thread(self._bootstrap, ()) RuntimeError: can't start new thread

Please note that I have deleted some portions in the path of threading.py.

skoul9 commented 1 year ago

Adding the "mp" parameter suppressed the error.