{"action":"opened","issue":{"url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/1","repository_url":"https://api.github.com/repos/gconcepcion/pb-assembly","labels_url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/1/comments","events_url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/1/events","html_url":"https://github.com/gconcepcion/pb-assembly/issues/1","id":357809733,"node_id":"MDU6SXNzdWUzNTc4MDk3MzM=","number":1,"title":"Error with Quiver polishing of unzipped haplotypes on test data","user":{"login":"cbergman","id":24303,"node_id":"MDQ6VXNlcjI0MzAz","avatar_url":"https://avatars3.githubusercontent.com/u/24303?v=4","gravatar_id":"","url":"https://api.github.com/users/cbergman","html_url":"https://github.com/cbergman","followers_url":"https://api.github.com/users/cbergman/followers","following_url":"https://api.github.com/users/cbergman/following{/other_user}","gists_url":"https://api.github.com/users/cbergman/gists{/gist_id}","starred_url":"https://api.github.com/users/cbergman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cbergman/subscriptions","organizations_url":"https://api.github.com/users/cbergman/orgs","repos_url":"https://api.github.com/users/cbergman/repos","events_url":"https://api.github.com/users/cbergman/events{/privacy}","received_events_url":"https://api.github.com/users/cbergman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-06T20:15:24Z","updated_at":"2018-09-06T20:15:24Z","closed_at":null,"author_association":"NONE","body":"I have been trying to get your bioconda falcon/falcon-unzip install to work on CentOS and had partial success with the Example test case. Following the instructions in the Readme, I can get falcon to run to completion and falcon-unzip to generate the expected alternate haplotypes. However, I consistently get an error at the quiver step. I have tried several clean installs of the conda environment and the test data repositories on 2 different machines, one using Centos 6 on a directly attached disk and one on Centos 7 using a lustre filesystem. The behavior is identical on both systems. No `4-quiver/cns-output` directory is generated.\r\n\r\nThe results of my test run are as follows:\r\n```\r\n(FALCON) [cbergman@genome] $ ls -lrt 3-unzip/\r\ntotal 480\r\ndrwxr-xr-x. 8 cbergman bergmanlab   4096 Sep  6 15:41 reads\r\ndrwxr-xr-x. 6 cbergman bergmanlab   4096 Sep  6 15:41 0-phasing\r\ndrwxr-xr-x. 3 cbergman bergmanlab   4096 Sep  6 15:41 1-hasm\r\ndrwxr-xr-x. 6 cbergman bergmanlab   4096 Sep  6 15:41 2-htigs\r\n-rw-r--r--. 1 cbergman bergmanlab   1394 Sep  6 15:41 template.sh\r\n-rw-r--r--. 1 cbergman bergmanlab    581 Sep  6 15:41 task.sh\r\n-rw-r--r--. 1 cbergman bergmanlab    593 Sep  6 15:41 task.json\r\n-rw-r--r--. 1 cbergman bergmanlab    207 Sep  6 15:41 run.sh\r\n-rwxr-xr-x. 1 cbergman bergmanlab    254 Sep  6 15:41 run-Pa16d27079404fc.bash\r\n-rw-r--r--. 1 cbergman bergmanlab   1671 Sep  6 15:41 user_script.sh\r\n-rw-r--r--. 1 cbergman bergmanlab 188573 Sep  6 15:41 all_h_ctg.fa\r\n-rw-r--r--. 1 cbergman bergmanlab      0 Sep  6 15:41 hasm_done\r\n-rw-r--r--. 1 cbergman bergmanlab 203182 Sep  6 15:41 all_p_ctg.fa\r\n-rw-r--r--. 1 cbergman bergmanlab   7709 Sep  6 15:41 all_p_ctg_edges\r\n-rw-r--r--. 1 cbergman bergmanlab     79 Sep  6 15:41 all_h_ctg.paf\r\n-rw-r--r--. 1 cbergman bergmanlab     17 Sep  6 15:41 all_h_ctg_ids\r\n-rw-r--r--. 1 cbergman bergmanlab   8190 Sep  6 15:41 all_h_ctg_edges\r\n-rw-r--r--. 1 cbergman bergmanlab  16329 Sep  6 15:41 all_phased_reads\r\n-rw-r--r--. 1 cbergman bergmanlab      0 Sep  6 15:41 run.sh.done\r\n-rw-r--r--. 1 cbergman bergmanlab   3419 Sep  6 15:41 run-Pa16d27079404fc.bash.stdout\r\n-rw-r--r--. 1 cbergman bergmanlab   7451 Sep  6 15:41 run-Pa16d27079404fc.bash.stderr\r\n(FALCON) [cbergman@genome] $ ls -lrt 4-quiver/\r\ntotal 48\r\ndrwxr-xr-x. 2 cbergman bergmanlab 4096 Sep  6 15:41 track-reads\r\ndrwxr-xr-x. 2 cbergman bergmanlab 4096 Sep  6 15:41 select-reads\r\ndrwxr-xr-x. 4 cbergman bergmanlab 4096 Sep  6 15:41 merge-reads\r\ndrwxr-xr-x. 2 cbergman bergmanlab 4096 Sep  6 15:41 segregate-split\r\ndrwxr-xr-x. 4 cbergman bergmanlab 4096 Sep  6 15:41 segregate-chunks\r\ndrwxr-xr-x. 4 cbergman bergmanlab 4096 Sep  6 15:41 segregate-run\r\ndrwxr-xr-x. 2 cbergman bergmanlab 4096 Sep  6 15:42 segregate-gathered\r\ndrwxr-xr-x. 2 cbergman bergmanlab 4096 Sep  6 15:42 segregated-bam\r\ndrwxr-xr-x. 3 cbergman bergmanlab 4096 Sep  6 15:42 quiver-split\r\ndrwxr-xr-x. 3 cbergman bergmanlab 4096 Sep  6 15:42 cns-gather\r\ndrwxr-xr-x. 4 cbergman bergmanlab 4096 Sep  6 15:42 quiver-chunks\r\ndrwxr-xr-x. 4 cbergman bergmanlab 4096 Sep  6 15:42 quiver-run\r\n```\r\n- the errors output to the terminal are as follows:\r\n```\r\n[INFO](slept for another 0.4s -- another 3 loop iterations)\r\n[INFO](slept for another 1.4s -- another 4 loop iterations)\r\n[INFO](slept for another 4.0s -- another 5 loop iterations)\r\n[ERROR]Task Node(4-quiver/quiver-run/000000Fp01_00001) failed with exit-code=1\r\n[ERROR]Task Node(4-quiver/quiver-run/000000Fp01) failed with exit-code=1\r\n[ERROR]Some tasks are recently_done but not satisfied: set([Node(4-quiver/quiver-run/000000Fp01), Node(4-quiver/quiver-run/000000Fp01_00001)])\r\n[ERROR]ready: set([])\r\n\tsubmitted: set([])\r\n[ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.\r\nTraceback (most recent call last):\r\n  File \"/home/cbergman/miniconda3/envs/FALCON/bin/fc_unzip.py\", line 11, in <module>\r\n    load_entry_point('falcon-unzip==1.1.2', 'console_scripts', 'fc_unzip.py')()\r\n  File \"/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_unzip/mains/start_unzip.py\", line 29, in main\r\n    unzip.run(**vars(args))\r\n  File \"/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_unzip/unzip.py\", line 126, in run\r\n    unzip_all(config)\r\n  File \"/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_unzip/unzip.py\", line 28, in unzip_all\r\n    tasks_unzip.run_workflow(wf, config, rule_writer)\r\n  File \"/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_unzip/tasks/unzip.py\", line 708, in run_workflow\r\n    job_dict=config['job.step.unzip.quiver'],\r\n  File \"/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_kit/pype.py\", line 192, in gen_parallel_tasks\r\n    wf.refreshTargets()\r\n  File \"/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py\", line 277, in refreshTargets\r\n    self._refreshTargets(updateFreq, exitOnFailure)\r\n  File \"/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py\", line 361, in _refreshTargets\r\n    raise Exception(msg)\r\nException: Some tasks are recently_done but not satisfied: set([Node(4-quiver/quiver-run/000000Fp01), Node(4-quiver/quiver-run/000000Fp01_00001)])\r\n```\r\n- the errors in the all.log file are as follows:\r\n```\r\n(FALCON) [cbergman@genome] $ tail -n 20 all.log\r\n2018-09-06 19:55:34,598 - pypeflow.simple_pwatcher_bridge:324 - DEBUG - N in queue: 2 (max_jobs=8)\r\n2018-09-06 19:55:34,599 - pwatcher.blocking:463 - DEBUG - query(which='list', jobids=<2>)\r\n2018-09-06 19:55:36,099 - pypeflow.simple_pwatcher_bridge:324 - DEBUG - N in queue: 2 (max_jobs=8)\r\n2018-09-06 19:55:36,100 - pwatcher.blocking:463 - DEBUG - query(which='list', jobids=<2>)\r\n2018-09-06 19:55:36,540 - pwatcher.blocking:235 - DEBUG - rc: 1\r\n2018-09-06 19:55:36,540 - pwatcher.blocking:87 - DEBUG - Thread notify_exited(P1f23d83c72cc91->1).\r\n2018-09-06 19:55:37,495 - pwatcher.blocking:235 - DEBUG - rc: 1\r\n2018-09-06 19:55:37,495 - pwatcher.blocking:87 - DEBUG - Thread notify_exited(P2f4330e72933ab->1).\r\n2018-09-06 19:55:37,702 - pypeflow.simple_pwatcher_bridge:324 - DEBUG - N in queue: 2 (max_jobs=8)\r\n2018-09-06 19:55:37,702 - pwatcher.blocking:463 - DEBUG - query(which='list', jobids=<2>)\r\n2018-09-06 19:55:37,702 - pypeflow.simple_pwatcher_bridge:94 - ERROR - Task Node(4-quiver/quiver-run/000000Fp01_00001) failed with exit-code=1\r\n2018-09-06 19:55:37,702 - pypeflow.simple_pwatcher_bridge:94 - ERROR - Task Node(4-quiver/quiver-run/000000Fp01) failed with exit-code=1\r\n2018-09-06 19:55:37,702 - pypeflow.simple_pwatcher_bridge:342 - DEBUG - recently_done: [(Node(4-quiver/quiver-run/000000Fp01), False), (Node(4-quiver/quiver-run/000000Fp01_00001), False)]\r\n2018-09-06 19:55:37,703 - pypeflow.simple_pwatcher_bridge:343 - DEBUG - Num done in this iteration: 2\r\n2018-09-06 19:55:37,703 - pypeflow.simple_pwatcher_bridge:357 - ERROR - Some tasks are recently_done but not satisfied: set([Node(4-quiver/quiver-run/000000Fp01), Node(4-quiver/quiver-run/000000Fp01_00001)])\r\n2018-09-06 19:55:37,703 - pypeflow.simple_pwatcher_bridge:358 - ERROR - ready: set([])\r\n\tsubmitted: set([])\r\n2018-09-06 19:55:37,703 - pwatcher.blocking:467 - DEBUG - delete(which='known', jobids=<0>)\r\n2018-09-06 19:55:37,703 - pwatcher.blocking:431 - ERROR - Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.\r\n2018-09-06 19:55:37,703 - pypeflow.simple_pwatcher_bridge:189 - DEBUG - In notifyTerminate(), result of delete:None\r\n```\r\n\r\nAny ideas what might be causing this?\r\n\r\nThanks in advance!"}}
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