ifiddes
commented
4 years ago If you are compiling binaries yourself and not using docker, you need to run CAT with --binary-mode local.
Ian Fiddes, PhD
On Sun, Mar 29, 2020 at 7:28 PM YPGG1234 notifications@github.com wrote:
Hi,
Recently I have installing cat, I think I had installed everthing except little bit wrong with Augustus (I got it from bioconda, version 3.3.2, but I think it cannot config as you said). When I run :
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
I got :
03-30 10:10:19 luigi-interface WARNING Will not run Task: RunCat or any dependencies due to error in complete() method: Traceback (most recent call last): File "/home/liran/Software/miniconda2/envs/C-A-T/lib/python2.7/site-packages/luigi/worker.py", line 409, in check_complete is_complete = task.complete() File "/home/liran/Software/miniconda2/envs/C-A-T/lib/python2.7/site-packages/luigi/task.py", line 826, in complete return all(r.complete() for r in flatten(self.requires())) File "/home/liran/Software/miniconda2/envs/C-A-T/lib/python2.7/site-packages/luigi/task.py", line 887, in flatten for result in iterator: File "/home/liran/Software/C-A-T/Comparative-Annotation-Toolkit/cat/init.py", line 624, in requires pipeline_args = self.get_pipeline_args() File "/home/liran/Software/C-A-T/Comparative-Annotation-Toolkit/cat/init.py", line 211, in get_pipeline_args if not tools.misc.is_exec('docker'): File "/home/liran/Software/C-A-T/Comparative-Annotation-Toolkit/tools/misc.py", line 80, in is_exec raise ToolMissingException("{0} not found. Either install {0}, or install CAT's dependencies and use --binary-mode local.".format(binary_mode)) ToolMissingException: docker not found. Either install docker, or install CAT's dependencies and use --binary-mode local.
03-30 10:10:19 luigi-interface INFO Informed scheduler that task RunCat_False_True_True_a22c0dbb99 has status UNKNOWN 03-30 10:10:19 luigi-interface INFO Done scheduling tasks 03-30 10:10:19 luigi-interface INFO Running Worker with 10 processes 03-30 10:10:19 luigi-interface INFO Worker Worker(salt=976387333, workers=10, host=subnet190-2.nwsuaf.edu.cn, username=liran, pid=31552) was stopped. Shutting down Keep-Alive thread 03-30 10:10:19 luigi-interface INFO ===== 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 =====
When I check out the log dir, I got :
luigi-server.log 2020-03-30 09:52:08,921 luigi.scheduler[22095] INFO: No prior state file exists at /var/lib/luigi-server/state.pickle. Starting with empty state
luigi-server-2020-03-30.err socket.error: [Errno 98] Address already in use
Can you help me to sovle it? Thank you
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YPGG1234
diekhans
Hi,
Recently I have installing cat, I think I had installed everthing except little bit wrong with Augustus (I got it from bioconda, version 3.3.2, but I think it cannot config as you said). When I run :
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-hubI got :
When I check out the log dir, I got :
luigi-server.log
2020-03-30 09:52:08,921 luigi.scheduler[22095] INFO: No prior state file exists at /var/lib/luigi-server/state.pickle. Starting with empty stateluigi-server-2020-03-30.err
socket.error: [Errno 98] Address already in useCan you help me to sovle it? Thank you