diekhans
commented
1 year ago is faToTwoBit in the conda environment?
Pankaj Dhakad @.***> writes:
Hi, I'm trying to setup CAT pipeline on a cluster and I've installed all the dependencies in a conda environment. However, When I try to run the pipeline I'm getting following error:
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 --binary-mode local
WARNING: 2023-07-13 15:26:50,820 - Will not run Task: RunCat or any dependencies due to error in complete() method: Traceback (most recent call last): File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/worker.py", line 395, in check_complete is_complete = task.complete() File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in complete return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in
return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in complete return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in complete return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 876, in flatten for result in iterator: File "/ceph/users/pdhakad/tools/Comparative-Annotation-Toolkit/cat/init.py", line 776, in requires self.validate() File "/ceph/users/pdhakad/tools/Comparative-Annotation-Toolkit/cat/init.py", line 771, in validate raise ToolMissingException('faToTwoBit tool from the Kent tools package not in global path.') cat.exceptions.ToolMissingException: faToTwoBit tool from the Kent tools package not in global path. INFO: 2023-07-13 15:26:50,827 - Informed scheduler that task RunCat_False_True_True_9d6b206223 has status UNKNOWN INFO: 2023-07-13 15:26:50,827 - Done scheduling tasks INFO: 2023-07-13 15:26:50,827 - Running Worker with 10 processes INFO: 2023-07-13 15:26:50,828 - Worker Worker(salt=292608225, workers=10, host=bigbird, username=pdhakad, pid=9391) was stopped. Shutting down Keep-Alive thread INFO: 2023-07-13 15:26:50,830 - ===== 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
===== Luigi Execution Summary =====
-- Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/297 You are receiving this because you are subscribed to this thread.
Message ID: @.***> Hi, I'm trying to setup CAT pipeline on a cluster and I've installed all the dependencies in a conda environment. However, When I try to run the pipeline I'm getting following error:
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 --binary-mode local
WARNING: 2023-07-13 15:26:50,820 - Will not run Task: RunCat or any dependencies due to error in complete() method: Traceback (most recent call last): File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-pack ages/luigi/worker.py", line 395, in check_complete is_complete = task.complete() File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-pack ages/luigi/task.py", line 815, in complete return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-pack ages/luigi/task.py", line 815, in return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-pack ages/luigi/task.py", line 815, in complete return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-pack ages/luigi/task.py", line 815, in return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-pack ages/luigi/task.py", line 815, in complete return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-pack ages/luigi/task.py", line 876, in flatten for result in iterator: File "/ceph/users/pdhakad/tools/Comparative-Annotation-Toolkit/cat/init.py", line 776, in requires self.validate() File "/ceph/users/pdhakad/tools/Comparative-Annotation-Toolkit/cat/init.py", line 771, in validate raise ToolMissingException('faToTwoBit tool from the Kent tools package not in global path.') cat.exceptions.ToolMissingException: faToTwoBit tool from the Kent tools package not in global path.
INFO: 2023-07-13 15:26:50,827 - Informed scheduler that task RunCat_False_True_True_9d6b206223 has status UNKNOWN INFO: 2023-07-13 15:26:50,827 - Done scheduling tasks INFO: 2023-07-13 15:26:50,827 - Running Worker with 10 processes INFO: 2023-07-13 15:26:50,828 - Worker Worker(salt=292608225, workers=10, host=bigbird, username=pdhakad, pid=9391) was stopped. Shutting down Keep-Alive thread INFO: 2023-07-13 15:26:50,830 - ===== 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
===== Luigi Execution Summary =====
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References
DhakadPankaj
ph09
Hi, I'm trying to setup CAT pipeline on a cluster and I've installed all the dependencies in a conda environment. However, When I try to run the pipeline I'm getting following error:
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 --binary-mode local
WARNING: 2023-07-13 15:26:50,820 - Will not run Task: RunCat or any dependencies due to error in complete() method: Traceback (most recent call last): File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/worker.py", line 395, in check_complete is_complete = task.complete() File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in complete return all(r.complete() for r in flatten(self.requires())) File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in
return all(r.complete() for r in flatten(self.requires()))
File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in complete
return all(r.complete() for r in flatten(self.requires()))
File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in
return all(r.complete() for r in flatten(self.requires()))
File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 815, in complete
return all(r.complete() for r in flatten(self.requires()))
File "/ceph/users/pdhakad/.conda/envs/cat_annotation/lib/python3.7/site-packages/luigi/task.py", line 876, in flatten
for result in iterator:
File "/ceph/users/pdhakad/tools/Comparative-Annotation-Toolkit/cat/init.py", line 776, in requires
self.validate()
File "/ceph/users/pdhakad/tools/Comparative-Annotation-Toolkit/cat/init.py", line 771, in validate
raise ToolMissingException('faToTwoBit tool from the Kent tools package not in global path.')
cat.exceptions.ToolMissingException: faToTwoBit tool from the Kent tools package not in global path.
INFO: 2023-07-13 15:26:50,827 - Informed scheduler that task RunCat_False_True_True_9d6b206223 has status UNKNOWN INFO: 2023-07-13 15:26:50,827 - Done scheduling tasks INFO: 2023-07-13 15:26:50,827 - Running Worker with 10 processes INFO: 2023-07-13 15:26:50,828 - Worker Worker(salt=292608225, workers=10, host=bigbird, username=pdhakad, pid=9391) was stopped. Shutting down Keep-Alive thread INFO: 2023-07-13 15:26:50,830 - ===== 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 =====