hi, w installed CAT using docker, failure with following error when I try to run test_data.
luigi --module cat RunCat --hal=test_data/vertebrates.hal --ref-genome=mm10 --workers=10 --config=test_data/test.config --work-dir test_install --out-dir test_install --local-scheduler --augustus --augustus-cgp --augustus-pb --assembly-hub
WARNING: 2022-10-09 00:27:16,732 - Will not run Task: RunCat or any dependencies due to error in complete() method:
Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/toil/lib/memoize.py", line 35, in new_f
return memory[args]
KeyError: (Task: RunCat,)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/misc.py", line 155, in is_exec
pl.wait()
File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/pipeline.py", line 1127, in wait
self.raiseIfExcept()
File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/pipeline.py", line 1085, in raiseIfExcept
p.raiseIfExcept()
File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/pipeline.py", line 749, in raiseIfExcept
raise self.exceptInfo[0].with_traceback(self.exceptInfo[2])
tools.pipeline.ProcException: process exited 1: which docker
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/luigi/worker.py", line 401, in check_complete
is_complete = task.complete()
File "/usr/local/lib/python3.8/dist-packages/luigi/task.py", line 822, in complete
return all(r.complete() for r in flatten(self.requires()))
File "/usr/local/lib/python3.8/dist-packages/luigi/task.py", line 883, in flatten
for result in iterator:
File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/cat/init.py", line 652, in requires
self.load_docker()
File "/usr/local/lib/python3.8/dist-packages/toil/lib/memoize.py", line 37, in new_f
r = f(*args)
File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/cat/init.py", line 392, in load_docker
if not tools.misc.is_exec('docker'):
File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/misc.py", line 158, in is_exec
raise Exception("{0} not found. Either install {0}, or install CAT's dependencies and use --binary-mode local.".format(binary_mode))
Exception: docker not found. Either install docker, or install CAT's dependencies and use --binary-mode local.
INFO: 2022-10-09 00:27:16,740 - Informed scheduler that task RunCat_False_True_True_8b43c26b62 has status UNKNOWN
INFO: 2022-10-09 00:27:16,741 - Done scheduling tasks
INFO: 2022-10-09 00:27:16,741 - Running Worker with 10 processes
INFO: 2022-10-09 00:27:16,741 - Worker Worker(salt=228861317, workers=10, host=887c6b30229b, username=root, pid=94) was stopped. Shutting down Keep-Alive thread
INFO: 2022-10-09 00:27:16,743 -
===== Luigi Execution Summary =====
Scheduled 1 tasks of which:
1 failed scheduling:
1 RunCat(...)
Did not run any tasks
This progress looks :( because there were tasks whose scheduling failed
hi, w installed CAT using docker, failure with following error when I try to run test_data.
luigi --module cat RunCat --hal=test_data/vertebrates.hal --ref-genome=mm10 --workers=10 --config=test_data/test.config --work-dir test_install --out-dir test_install --local-scheduler --augustus --augustus-cgp --augustus-pb --assembly-hub WARNING: 2022-10-09 00:27:16,732 - Will not run Task: RunCat or any dependencies due to error in complete() method: Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/toil/lib/memoize.py", line 35, in new_f return memory[args] KeyError: (Task: RunCat,)
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/misc.py", line 155, in is_exec pl.wait() File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/pipeline.py", line 1127, in wait self.raiseIfExcept() File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/pipeline.py", line 1085, in raiseIfExcept p.raiseIfExcept() File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/pipeline.py", line 749, in raiseIfExcept raise self.exceptInfo[0].with_traceback(self.exceptInfo[2]) tools.pipeline.ProcException: process exited 1: which docker
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/luigi/worker.py", line 401, in check_complete is_complete = task.complete() File "/usr/local/lib/python3.8/dist-packages/luigi/task.py", line 822, in complete return all(r.complete() for r in flatten(self.requires())) File "/usr/local/lib/python3.8/dist-packages/luigi/task.py", line 883, in flatten for result in iterator: File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/cat/init.py", line 652, in requires self.load_docker() File "/usr/local/lib/python3.8/dist-packages/toil/lib/memoize.py", line 37, in new_f r = f(*args) File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/cat/init.py", line 392, in load_docker if not tools.misc.is_exec('docker'): File "/usr/local/lib/python3.8/dist-packages/cat-2.0-py3.8.egg/tools/misc.py", line 158, in is_exec raise Exception("{0} not found. Either install {0}, or install CAT's dependencies and use --binary-mode local.".format(binary_mode)) Exception: docker not found. Either install docker, or install CAT's dependencies and use --binary-mode local.
INFO: 2022-10-09 00:27:16,740 - Informed scheduler that task RunCat_False_True_True_8b43c26b62 has status UNKNOWN INFO: 2022-10-09 00:27:16,741 - Done scheduling tasks INFO: 2022-10-09 00:27:16,741 - Running Worker with 10 processes INFO: 2022-10-09 00:27:16,741 - Worker Worker(salt=228861317, workers=10, host=887c6b30229b, username=root, pid=94) was stopped. Shutting down Keep-Alive thread INFO: 2022-10-09 00:27:16,743 - ===== Luigi Execution Summary =====
Scheduled 1 tasks of which:
Did not run any tasks This progress looks :( because there were tasks whose scheduling failed
===== Luigi Execution Summary =====