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November 15, 2019 05:47
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| $ toil-cwl-runner --preserve-environment PATH --singularity ./example.cwl ./example-job.cwl | |
| /usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: | |
| DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. | |
| Please upgrade your Python as the Python 2.7 version of cwltool won't be | |
| maintained after that date. | |
| """, category=CWLToolDeprecationWarning) | |
| INFO:cwltool:Resolved './example.cwl' to 'file:///usr/people/pvh/toil/example.cwl' | |
| WARNING:toil.batchSystems.singleMachine:Limiting maxCores to CPU count of system (24). | |
| WARNING:toil.batchSystems.singleMachine:Limiting maxMemory to physically available memory (33714651136). | |
| WARNING:toil.batchSystems.singleMachine:Limiting maxDisk to physically available disk (119865921536). | |
| INFO:toil:Running Toil version 3.20.0-cf34ca3416697f2abc816b2538f20ee29ba16932. | |
| INFO:toil.leader:Issued job 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P with job batch system ID: 0 and cores: 1, disk: 3.0 G, and memory: 2.0 G | |
| DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/tmp/tmp6Z25vF'. | |
| INFO:toil.worker:Redirecting logging to /tmp/toil-cca549db-0a73-4c28-b1e8-8156c2ce2080-fdb23d803088485fa8951979ad4e693f/tmpJwp1iA/worker_log.txt | |
| INFO:toil.leader:Job ended successfully: 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P | |
| WARNING:toil.leader:The job seems to have left a log file, indicating failure: 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P | |
| WARNING:toil.leader:1/O/job5Fne_P INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- | |
| WARNING:toil.leader:1/O/job5Fne_P INFO:toil:Running Toil version 3.20.0-cf34ca3416697f2abc816b2538f20ee29ba16932. | |
| WARNING:toil.leader:1/O/job5Fne_P /usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: | |
| WARNING:toil.leader:1/O/job5Fne_P DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. | |
| WARNING:toil.leader:1/O/job5Fne_P Please upgrade your Python as the Python 2.7 version of cwltool won't be | |
| WARNING:toil.leader:1/O/job5Fne_P maintained after that date. | |
| WARNING:toil.leader:1/O/job5Fne_P | |
| WARNING:toil.leader:1/O/job5Fne_P """, category=CWLToolDeprecationWarning) | |
| WARNING:toil.leader:1/O/job5Fne_P ['singularity', 'pull', '--force', '--name', 'busybox:latest.img', 'docker://busybox:latest'] | |
| WARNING:toil.leader:1/O/job5Fne_P INFO:cwltool:['singularity', 'pull', '--force', '--name', 'busybox:latest.img', 'docker://busybox:latest'] | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: pull for Docker Hub is not guaranteed to produce the | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: same image on repeated pull. Use Singularity Registry | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: (shub://) to pull exactly equivalent images. | |
| WARNING:toil.leader:1/O/job5Fne_P Docker image path: index.docker.io/library/busybox:latest | |
| WARNING:toil.leader:1/O/job5Fne_P Cache folder set to /usr/people/pvh/.singularity/docker | |
| WARNING:toil.leader:1/O/job5Fne_P Importing: base Singularity environment | |
| WARNING:toil.leader:1/O/job5Fne_P Exploding layer: sha256:0f8c40e1270f10d085dda8ce12b7c5b17cd808f055df5a7222f54837ca0feae0.tar.gz | |
| WARNING:toil.leader:1/O/job5Fne_P Exploding layer: sha256:29ade4f96a9909940ce0251b8182993c53f22a7e006a8c7fe868f1e0032d52b5.tar.gz | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: Building container as an unprivileged user. If you run this container as root | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: it may be missing some functionality. | |
| WARNING:toil.leader:1/O/job5Fne_P Building Singularity image... | |
| WARNING:toil.leader:1/O/job5Fne_P Singularity container built: ./busybox:latest.img | |
| WARNING:toil.leader:1/O/job5Fne_P Cleaning up... | |
| WARNING:toil.leader:1/O/job5Fne_P Done. Container is at: ./busybox:latest.img | |
| WARNING:toil.leader:1/O/job5Fne_P [job example.cwl] /tmp/tmp6Z25vF/f/6/out_tmpdirLVWsh8$ singularity \ | |
| WARNING:toil.leader:1/O/job5Fne_P --quiet \ | |
| WARNING:toil.leader:1/O/job5Fne_P exec \ | |
| WARNING:toil.leader:1/O/job5Fne_P --contain \ | |
| WARNING:toil.leader:1/O/job5Fne_P --pid \ | |
| WARNING:toil.leader:1/O/job5Fne_P --ipc \ | |
| WARNING:toil.leader:1/O/job5Fne_P --bind \ | |
| WARNING:toil.leader:1/O/job5Fne_P /tmp/tmp6Z25vF/f/6/out_tmpdirLVWsh8:/ZCMtlY:rw \ | |
| WARNING:toil.leader:1/O/job5Fne_P --bind \ | |
| WARNING:toil.leader:1/O/job5Fne_P /usr/people/pvh/toil/tmp:/tmp:rw \ | |
| WARNING:toil.leader:1/O/job5Fne_P --pwd \ | |
| WARNING:toil.leader:1/O/job5Fne_P /ZCMtlY \ | |
| WARNING:toil.leader:1/O/job5Fne_P /tmp/toil-cca549db-0a73-4c28-b1e8-8156c2ce2080-fdb23d803088485fa8951979ad4e693f/tmpJwp1iA/42fe7c5a-9aa5-474e-ad75-2b33295756c9/busybox:latest.img \ | |
| WARNING:toil.leader:1/O/job5Fne_P echo \ | |
| WARNING:toil.leader:1/O/job5Fne_P 'Hello world!' > /tmp/tmp6Z25vF/f/6/out_tmpdirLVWsh8/output.txt | |
| WARNING:toil.leader:1/O/job5Fne_P INFO:cwltool:[job example.cwl] /tmp/tmp6Z25vF/f/6/out_tmpdirLVWsh8$ singularity \ | |
| WARNING:toil.leader:1/O/job5Fne_P --quiet \ | |
| WARNING:toil.leader:1/O/job5Fne_P exec \ | |
| WARNING:toil.leader:1/O/job5Fne_P --contain \ | |
| WARNING:toil.leader:1/O/job5Fne_P --pid \ | |
| WARNING:toil.leader:1/O/job5Fne_P --ipc \ | |
| WARNING:toil.leader:1/O/job5Fne_P --bind \ | |
| WARNING:toil.leader:1/O/job5Fne_P /tmp/tmp6Z25vF/f/6/out_tmpdirLVWsh8:/ZCMtlY:rw \ | |
| WARNING:toil.leader:1/O/job5Fne_P --bind \ | |
| WARNING:toil.leader:1/O/job5Fne_P /usr/people/pvh/toil/tmp:/tmp:rw \ | |
| WARNING:toil.leader:1/O/job5Fne_P --pwd \ | |
| WARNING:toil.leader:1/O/job5Fne_P /ZCMtlY \ | |
| WARNING:toil.leader:1/O/job5Fne_P /tmp/toil-cca549db-0a73-4c28-b1e8-8156c2ce2080-fdb23d803088485fa8951979ad4e693f/tmpJwp1iA/42fe7c5a-9aa5-474e-ad75-2b33295756c9/busybox:latest.img \ | |
| WARNING:toil.leader:1/O/job5Fne_P echo \ | |
| WARNING:toil.leader:1/O/job5Fne_P 'Hello world!' > /tmp/tmp6Z25vF/f/6/out_tmpdirLVWsh8/output.txt | |
| WARNING:toil.leader:1/O/job5Fne_P ERROR : Failed to set loop flags on loop device: Resource temporarily unavailable | |
| WARNING:toil.leader:1/O/job5Fne_P ABORT : Retval = 255 | |
| WARNING:toil.leader:1/O/job5Fne_P [job example.cwl] completed permanentFail | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING:cwltool:[job example.cwl] completed permanentFail | |
| WARNING:toil.leader:1/O/job5Fne_P Traceback (most recent call last): | |
| WARNING:toil.leader:1/O/job5Fne_P File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/worker.py", line 331, in workerScript | |
| WARNING:toil.leader:1/O/job5Fne_P job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore) | |
| WARNING:toil.leader:1/O/job5Fne_P File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/job.py", line 1378, in _runner | |
| WARNING:toil.leader:1/O/job5Fne_P returnValues = self._run(jobGraph, fileStore) | |
| WARNING:toil.leader:1/O/job5Fne_P File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/job.py", line 1323, in _run | |
| WARNING:toil.leader:1/O/job5Fne_P return self.run(fileStore) | |
| WARNING:toil.leader:1/O/job5Fne_P File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 606, in run | |
| WARNING:toil.leader:1/O/job5Fne_P raise cwltool.errors.WorkflowException(status) | |
| WARNING:toil.leader:1/O/job5Fne_P WorkflowException: permanentFail | |
| WARNING:toil.leader:1/O/job5Fne_P ERROR:toil.worker:Exiting the worker because of a failed job on host cmc1-05-hpc.sanbi.ac.za | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P with ID 1/O/job5Fne_P to 1 | |
| INFO:toil.leader:Issued job 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P with job batch system ID: 1 and cores: 1, disk: 3.0 G, and memory: 2.0 G | |
| DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/tmp/tmp6Z25vF'. | |
| INFO:toil.worker:Redirecting logging to /tmp/toil-cca549db-0a73-4c28-b1e8-8156c2ce2080-fdb23d803088485fa8951979ad4e693f/tmpqNfajR/worker_log.txt | |
| INFO:toil.leader:Job ended successfully: 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P | |
| WARNING:toil.leader:The job seems to have left a log file, indicating failure: 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P | |
| WARNING:toil.leader:1/O/job5Fne_P INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- | |
| WARNING:toil.leader:1/O/job5Fne_P INFO:toil:Running Toil version 3.20.0-cf34ca3416697f2abc816b2538f20ee29ba16932. | |
| WARNING:toil.leader:1/O/job5Fne_P /usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: | |
| WARNING:toil.leader:1/O/job5Fne_P DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. | |
| WARNING:toil.leader:1/O/job5Fne_P Please upgrade your Python as the Python 2.7 version of cwltool won't be | |
| WARNING:toil.leader:1/O/job5Fne_P maintained after that date. | |
| WARNING:toil.leader:1/O/job5Fne_P | |
| WARNING:toil.leader:1/O/job5Fne_P """, category=CWLToolDeprecationWarning) | |
| WARNING:toil.leader:1/O/job5Fne_P ['singularity', 'pull', '--force', '--name', 'busybox:latest.img', 'docker://busybox:latest'] | |
| WARNING:toil.leader:1/O/job5Fne_P INFO:cwltool:['singularity', 'pull', '--force', '--name', 'busybox:latest.img', 'docker://busybox:latest'] | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: pull for Docker Hub is not guaranteed to produce the | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: same image on repeated pull. Use Singularity Registry | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: (shub://) to pull exactly equivalent images. | |
| WARNING:toil.leader:1/O/job5Fne_P Docker image path: index.docker.io/library/busybox:latest | |
| WARNING:toil.leader:1/O/job5Fne_P Cache folder set to /usr/people/pvh/.singularity/docker | |
| WARNING:toil.leader:1/O/job5Fne_P Importing: base Singularity environment | |
| WARNING:toil.leader:1/O/job5Fne_P Exploding layer: sha256:0f8c40e1270f10d085dda8ce12b7c5b17cd808f055df5a7222f54837ca0feae0.tar.gz | |
| WARNING:toil.leader:1/O/job5Fne_P Exploding layer: sha256:29ade4f96a9909940ce0251b8182993c53f22a7e006a8c7fe868f1e0032d52b5.tar.gz | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: Building container as an unprivileged user. If you run this container as root | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING: it may be missing some functionality. | |
| WARNING:toil.leader:1/O/job5Fne_P Building Singularity image... | |
| WARNING:toil.leader:1/O/job5Fne_P Singularity container built: ./busybox:latest.img | |
| WARNING:toil.leader:1/O/job5Fne_P Cleaning up... | |
| WARNING:toil.leader:1/O/job5Fne_P Done. Container is at: ./busybox:latest.img | |
| WARNING:toil.leader:1/O/job5Fne_P [job example.cwl] /tmp/tmp6Z25vF/9/9/out_tmpdir2sGhuT$ singularity \ | |
| WARNING:toil.leader:1/O/job5Fne_P --quiet \ | |
| WARNING:toil.leader:1/O/job5Fne_P exec \ | |
| WARNING:toil.leader:1/O/job5Fne_P --contain \ | |
| WARNING:toil.leader:1/O/job5Fne_P --pid \ | |
| WARNING:toil.leader:1/O/job5Fne_P --ipc \ | |
| WARNING:toil.leader:1/O/job5Fne_P --bind \ | |
| WARNING:toil.leader:1/O/job5Fne_P /tmp/tmp6Z25vF/9/9/out_tmpdir2sGhuT:/LBIhXZ:rw \ | |
| WARNING:toil.leader:1/O/job5Fne_P --bind \ | |
| WARNING:toil.leader:1/O/job5Fne_P /usr/people/pvh/toil/tmp:/tmp:rw \ | |
| WARNING:toil.leader:1/O/job5Fne_P --pwd \ | |
| WARNING:toil.leader:1/O/job5Fne_P /LBIhXZ \ | |
| WARNING:toil.leader:1/O/job5Fne_P /tmp/toil-cca549db-0a73-4c28-b1e8-8156c2ce2080-fdb23d803088485fa8951979ad4e693f/tmpqNfajR/80d1c3e2-674c-4110-ba5e-f62b95b15d99/busybox:latest.img \ | |
| WARNING:toil.leader:1/O/job5Fne_P echo \ | |
| WARNING:toil.leader:1/O/job5Fne_P 'Hello world!' > /tmp/tmp6Z25vF/9/9/out_tmpdir2sGhuT/output.txt | |
| WARNING:toil.leader:1/O/job5Fne_P INFO:cwltool:[job example.cwl] /tmp/tmp6Z25vF/9/9/out_tmpdir2sGhuT$ singularity \ | |
| WARNING:toil.leader:1/O/job5Fne_P --quiet \ | |
| WARNING:toil.leader:1/O/job5Fne_P exec \ | |
| WARNING:toil.leader:1/O/job5Fne_P --contain \ | |
| WARNING:toil.leader:1/O/job5Fne_P --pid \ | |
| WARNING:toil.leader:1/O/job5Fne_P --ipc \ | |
| WARNING:toil.leader:1/O/job5Fne_P --bind \ | |
| WARNING:toil.leader:1/O/job5Fne_P /tmp/tmp6Z25vF/9/9/out_tmpdir2sGhuT:/LBIhXZ:rw \ | |
| WARNING:toil.leader:1/O/job5Fne_P --bind \ | |
| WARNING:toil.leader:1/O/job5Fne_P /usr/people/pvh/toil/tmp:/tmp:rw \ | |
| WARNING:toil.leader:1/O/job5Fne_P --pwd \ | |
| WARNING:toil.leader:1/O/job5Fne_P /LBIhXZ \ | |
| WARNING:toil.leader:1/O/job5Fne_P /tmp/toil-cca549db-0a73-4c28-b1e8-8156c2ce2080-fdb23d803088485fa8951979ad4e693f/tmpqNfajR/80d1c3e2-674c-4110-ba5e-f62b95b15d99/busybox:latest.img \ | |
| WARNING:toil.leader:1/O/job5Fne_P echo \ | |
| WARNING:toil.leader:1/O/job5Fne_P 'Hello world!' > /tmp/tmp6Z25vF/9/9/out_tmpdir2sGhuT/output.txt | |
| WARNING:toil.leader:1/O/job5Fne_P ERROR : Failed to set loop flags on loop device: Resource temporarily unavailable | |
| WARNING:toil.leader:1/O/job5Fne_P ABORT : Retval = 255 | |
| WARNING:toil.leader:1/O/job5Fne_P [job example.cwl] completed permanentFail | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING:cwltool:[job example.cwl] completed permanentFail | |
| WARNING:toil.leader:1/O/job5Fne_P Traceback (most recent call last): | |
| WARNING:toil.leader:1/O/job5Fne_P File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/worker.py", line 331, in workerScript | |
| WARNING:toil.leader:1/O/job5Fne_P job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore) | |
| WARNING:toil.leader:1/O/job5Fne_P File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/job.py", line 1378, in _runner | |
| WARNING:toil.leader:1/O/job5Fne_P returnValues = self._run(jobGraph, fileStore) | |
| WARNING:toil.leader:1/O/job5Fne_P File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/job.py", line 1323, in _run | |
| WARNING:toil.leader:1/O/job5Fne_P return self.run(fileStore) | |
| WARNING:toil.leader:1/O/job5Fne_P File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 606, in run | |
| WARNING:toil.leader:1/O/job5Fne_P raise cwltool.errors.WorkflowException(status) | |
| WARNING:toil.leader:1/O/job5Fne_P WorkflowException: permanentFail | |
| WARNING:toil.leader:1/O/job5Fne_P ERROR:toil.worker:Exiting the worker because of a failed job on host cmc1-05-hpc.sanbi.ac.za | |
| WARNING:toil.leader:1/O/job5Fne_P WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P with ID 1/O/job5Fne_P to 0 | |
| WARNING:toil.leader:Job 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P with ID 1/O/job5Fne_P is completely failed | |
| INFO:toil.leader:Finished toil run with 1 failed jobs. | |
| INFO:toil.leader:Failed jobs at end of the run: 'file:///usr/people/pvh/toil/example.cwl' echo 1/O/job5Fne_P | |
| Traceback (most recent call last): | |
| File "/usr/people/pvh/miniconda3/envs/toil/bin/toil-cwl-runner", line 12, in <module> | |
| sys.exit(main()) | |
| File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 1276, in main | |
| outobj = toil.start(wf1) | |
| File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/common.py", line 781, in start | |
| return self._runMainLoop(rootJobGraph) | |
| File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/common.py", line 1054, in _runMainLoop | |
| jobCache=self._jobCache).run() | |
| File "/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/toil/leader.py", line 246, in run | |
| raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) | |
| toil.leader.FailedJobsException |
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