{"action":"created","issue":{"url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/2","repository_url":"https://api.github.com/repos/gconcepcion/pb-assembly","labels_url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/2/comments","events_url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/2/events","html_url":"https://github.com/gconcepcion/pb-assembly/issues/2","id":358524558,"node_id":"MDU6SXNzdWUzNTg1MjQ1NTg=","number":2,"title":" FALCON doesn't work on test data (CENTOS)","user":{"login":"a-velt","id":23554476,"node_id":"MDQ6VXNlcjIzNTU0NDc2","avatar_url":"https://avatars0.githubusercontent.com/u/23554476?v=4","gravatar_id":"","url":"https://api.github.com/users/a-velt","html_url":"https://github.com/a-velt","followers_url":"https://api.github.com/users/a-velt/followers","following_url":"https://api.github.com/users/a-velt/following{/other_user}","gists_url":"https://api.github.com/users/a-velt/gists{/gist_id}","starred_url":"https://api.github.com/users/a-velt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/a-velt/subscriptions","organizations_url":"https://api.github.com/users/a-velt/orgs","repos_url":"https://api.github.com/users/a-velt/repos","events_url":"https://api.github.com/users/a-velt/events{/privacy}","received_events_url":"https://api.github.com/users/a-velt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-10T08:46:15Z","updated_at":"2018-09-10T15:46:23Z","closed_at":null,"author_association":"NONE","body":"Hi all,\r\n\r\nI installed the latest version of FALCON with your instructions, on my CENTOS server. I created a new conda environment and I used this conda to install FALCON with the command : _conda install pb-assembly_. This installation worked perfectly.\r\n\r\nThen, I recovered the test data, and launched Falcon with your instructions : \r\n\r\n```\r\ngit clone https://github.com/cdunn2001/git-sym.git\r\ngit clone https://github.com/pb-cdunn/FALCON-examples.git\r\ncd FALCON-examples\r\n../git-sym/git-sym update run/greg200k-sv2\r\ncd run/greg200k-sv2\r\nfc_run fc_run.cfg\r\n```\r\n\r\nAnd I got the following error : \r\n\r\n> falcon-kit 1.2.2\r\n> pypeflow 2.0.4\r\n> [INFO]Setup logging from file \"None\".\r\n> [INFO]$ lfs setstripe -c 12 /cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2 >\r\n> [INFO]Apparently '/cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2' is not in lustre filesystem, which is fine.\r\n> [INFO]fc_run started with configuration fc_run.cfg\r\n> [WARNING]Unexpected keys in input config: set(['ovlp_HPCTANmask_option'])\r\n> [WARNING]Please supply a default for \"njobs\" (aka concurrency) in section [job.defaults]. For now, we will use 8\r\n> [INFO]cfg=\r\n> {\r\n>   \"General\": {\r\n>     \"LA4Falcon_preload\": false,\r\n>     \"avoid_text_file_busy\": true,\r\n>     \"bestn\": 12,\r\n>     \"dazcon\": false,\r\n>     \"falcon_sense_greedy\": false,\r\n>     \"falcon_sense_option\": \"--output-multi --min-cov-aln 4 --min-idt 0.70 --min-cov 4 --max-n-read 200 --n-core 8\",\r\n>     \"falcon_sense_skip_contained\": false,\r\n>     \"fc_ovlp_to_graph_option\": \" --min_len 1\",\r\n>     \"genome_size\": \"200000\",\r\n>     \"input_fofn\": \"input.fofn\",\r\n>     \"input_type\": \"raw\",\r\n>     \"length_cutoff\": \"1000\",\r\n>     \"length_cutoff_pr\": \"1\",\r\n>     \"overlap_filtering_setting\": \"--max-diff 120 --max-cov 120 --min-cov 2 --n-core 8\",\r\n>     \"ovlp_DBsplit_option\": \"-s100\",\r\n>     \"ovlp_HPCTANmask_option\": \"-l500\",\r\n>     \"ovlp_HPCdaligner_option\": \"-v -B128 -M24\",\r\n>     \"ovlp_daligner_option\": \"-e.9 -l2500 -k24 -h1024 -w6 -s100\",\r\n>     \"pa_DBdust_option\": \"\",\r\n>     \"pa_DBsplit_option\": \"-a -x500 -s4\",\r\n>     \"pa_HPCTANmask_option\": \"-l500\",\r\n>     \"pa_HPCdaligner_option\": \"-v -B128 -M24\",\r\n>     \"pa_REPmask_code\": \"0,300;0,300;0,300\",\r\n>     \"pa_daligner_option\": \"-e.8 -l3200 -k18 -h480  -w8 -s100\",\r\n>     \"pa_dazcon_option\": \"-j 4 -x -l 500\",\r\n>     \"pa_fasta_filter_option\": \"streamed-median\",\r\n>     \"seed_coverage\": 20,\r\n>     \"skip_checks\": false,\r\n>     \"target\": \"assembly\"\r\n>   },\r\n>   \"job.defaults\": {\r\n>     \"NPROC\": \"4\",\r\n>     \"job_type\": \"string\",\r\n>     \"njobs\": 8,\r\n>     \"pwatcher_type\": \"blocking\",\r\n>     \"submit\": \"bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}\",\r\n>     \"use_tmpdir\": false\r\n>   },\r\n>   \"job.step.asm\": {\r\n>     \"NPROC\": \"32\"\r\n>   },\r\n>   \"job.step.cns\": {\r\n>     \"NPROC\": \"8\"\r\n>   },\r\n>   \"job.step.da\": {},\r\n>   \"job.step.la\": {},\r\n>   \"job.step.pda\": {},\r\n>   \"job.step.pla\": {}\r\n> }\r\n> [INFO]In simple_pwatcher_bridge, pwatcher_impl=<module 'pwatcher.blocking' from '/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/pwatcher/blocking.pyc'>\r\n> [INFO]job_type='string', (default)job_defaults={'pwatcher_type': 'blocking', 'use_tmpdir': False, 'job_type': 'string', 'submit': 'bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}', 'NPROC': '4', 'njobs': 8}, use_tmpdir=False, squash=True, job_name_style=0\r\n> [INFO]Setting max_jobs to 8; was None\r\n> [INFO]Num unsatisfied: 2, graph: 2\r\n> [INFO]About to submit: Node(0-rawreads/build)\r\n> [INFO]Popen: 'bash -C /cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/pwatcher/mains/job_start.sh >| /cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2/0-rawreads/build/run-P47d6213d776274.bash.stdout 2>| /cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2/0-rawreads/build/run-P47d6213d776274.bash.stderr'\r\n> [INFO](slept for another 0.0s -- another 1 loop iterations)\r\n> [INFO](slept for another 0.3s -- another 2 loop iterations)\r\n> [ERROR]Task Node(0-rawreads/build) failed with exit-code=1\r\n> [ERROR]Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])\r\n> [ERROR]ready: set([])\r\n>         submitted: set([])\r\n> [ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.\r\n> Traceback (most recent call last):\r\n>   File \"/cm/shared/apps/FALCON_10-09-2018/bin/fc_run\", line 11, in <module>\r\n>     load_entry_point('falcon-kit==1.2.2', 'console_scripts', 'fc_run')()\r\n>   File \"/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/falcon_kit/mains/run1.py\", line 724, in main\r\n>     main1(argv[0], args.config, args.logger)\r\n>   File \"/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/falcon_kit/mains/run1.py\", line 76, in main1\r\n>     input_fofn_fn=input_fofn_fn,\r\n>   File \"/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/falcon_kit/mains/run1.py\", line 242, in run\r\n>     dist=Dist(NPROC=4, MB=4000, job_dict=config['job.step.da']),\r\n>   File \"/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/falcon_kit/pype.py\", line 106, in gen_parallel_tasks\r\n>     wf.refreshTargets()\r\n>   File \"/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py\", line 277, in refreshTargets\r\n>     self._refreshTargets(updateFreq, exitOnFailure)\r\n>   File \"/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py\", line 361, in _refreshTargets\r\n>     raise Exception(msg)\r\n> Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])\r\n\r\nHave you an idea about that ? \r\n\r\nBest,\r\nAmandine"},"comment":{"url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/comments/419961186","html_url":"https://github.com/gconcepcion/pb-assembly/issues/2#issuecomment-419961186","issue_url":"https://api.github.com/repos/gconcepcion/pb-assembly/issues/2","id":419961186,"node_id":"MDEyOklzc3VlQ29tbWVudDQxOTk2MTE4Ng==","user":{"login":"gconcepcion","id":4172670,"node_id":"MDQ6VXNlcjQxNzI2NzA=","avatar_url":"https://avatars1.githubusercontent.com/u/4172670?v=4","gravatar_id":"","url":"https://api.github.com/users/gconcepcion","html_url":"https://github.com/gconcepcion","followers_url":"https://api.github.com/users/gconcepcion/followers","following_url":"https://api.github.com/users/gconcepcion/following{/other_user}","gists_url":"https://api.github.com/users/gconcepcion/gists{/gist_id}","starred_url":"https://api.github.com/users/gconcepcion/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gconcepcion/subscriptions","organizations_url":"https://api.github.com/users/gconcepcion/orgs","repos_url":"https://api.github.com/users/gconcepcion/repos","events_url":"https://api.github.com/users/gconcepcion/events{/privacy}","received_events_url":"https://api.github.com/users/gconcepcion/received_events","type":"User","site_admin":false},"created_at":"2018-09-10T15:46:23Z","updated_at":"2018-09-10T15:46:23Z","author_association":"OWNER","body":"The very first step building the database failed. \r\n\r\nI need to see the contents of:\r\n\r\n`/cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2/0-rawreads/build/run-P47d6213d776274.bash.stderr`"}}
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