{"action":"created","comment":{"url":"https://api.github.com/repos/pb-cdunn/FALCON-examples/pulls/comments/55318774","id":55318774,"diff_hunk":"@@ -16,16 +16,13 @@ lambda-creads.1.fasta:\n lambda-hgap-3.creads.fasta:\n \tcp -f /lustre/hpcprod/cdunn/data/lambda/hgap-3.corrected.fasta $@\n synth0.pb.fasta:\n-\twget https://www.dropbox.com/s/a80t8ll29gvt883/cx.pb.fasta.gz\n-\tgunzip -c cx.pb.fasta.gz >| $@\n+\twget https://www.dropbox.com/s/a80t8ll29gvt883/cx.pb.fasta.gz | zcat > $@","path":"git-sym.makefile","position":6,"original_position":6,"commit_id":"fe99ccbf1aff6153edbb81455a26e3ba1e3b6431","original_commit_id":"fe99ccbf1aff6153edbb81455a26e3ba1e3b6431","user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"body":"Doesn't this one need `-O -` too?","created_at":"2016-03-08T05:41:51Z","updated_at":"2016-03-08T05:41:51Z","html_url":"https://github.com/pb-cdunn/FALCON-examples/pull/2#discussion_r55318774","pull_request_url":"https://api.github.com/repos/pb-cdunn/FALCON-examples/pulls/2","_links":{"self":{"href":"https://api.github.com/repos/pb-cdunn/FALCON-examples/pulls/comments/55318774"},"html":{"href":"https://github.com/pb-cdunn/FALCON-examples/pull/2#discussion_r55318774"},"pull_request":{"href":"https://api.github.com/repos/pb-cdunn/FALCON-examples/pulls/2"}}},"pull_request":{"url":"https://api.github.com/repos/pb-cdunn/FALCON-examples/pulls/2","id":62013236,"html_url":"https://github.com/pb-cdunn/FALCON-examples/pull/2","diff_url":"https://github.com/pb-cdunn/FALCON-examples/pull/2.diff","patch_url":"https://github.com/pb-cdunn/FALCON-examples/pull/2.patch","issue_url":"https://api.github.com/repos/pb-cdunn/FALCON-examples/issues/2","number":2,"state":"open","locked":false,"title":"avoid intermediate gzip files","user":{"login":"bwlang","id":61636,"avatar_url":"https://avatars.githubusercontent.com/u/61636?v=3","gravatar_id":"","url":"https://api.github.com/users/bwlang","html_url":"https://github.com/bwlang","followers_url":"https://api.github.com/users/bwlang/followers","following_url":"https://api.github.com/users/bwlang/following{/other_user}","gists_url":"https://api.github.com/users/bwlang/gists{/gist_id}","starred_url":"https://api.github.com/users/bwlang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bwlang/subscriptions","organizations_url":"https://api.github.com/users/bwlang/orgs","repos_url":"https://api.github.com/users/bwlang/repos","events_url":"https://api.github.com/users/bwlang/events{/privacy}","received_events_url":"https://api.github.com/users/bwlang/received_events","type":"User","site_admin":false},"body":"fixes a problem with dropbox urls that seem to be redirecting, so the filenames get changed causing missing files\r\n\r\nTests are still not working well in my hands (symlinks are in the wrong places), but this a step forward.\r\n\r\nremaining problems...\r\n```\r\n[ERROR] Contents of '/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh.log':\r\ntrap 'touch /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/rdb_build_done.exit' EXIT\r\n+ trap 'touch /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/rdb_build_done.exit' EXIT\r\ncd /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads\r\n+ cd /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads\r\nhostname\r\n+ hostname\r\nlogin-0-1.local\r\ndate\r\n+ date\r\nMon Mar  7 20:55:56 EST 2016\r\nfasta2DB -v raw_reads -f/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/input.fofn\r\n+ fasta2DB -v raw_reads -f/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/input.fofn\r\nSkipping '/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/data/synth0.fasta', file is empty!\r\nUpdating block partition ...\r\nLB=$(cat raw_reads.db | awk '$1 == \"blocks\" {print $3}')\r\ncat raw_reads.db | awk '$1 == \"blocks\" {print $3}')\r\ncat raw_reads.db | awk '$1 == \"blocks\" {print $3}'\r\n++ awk '$1 == \"blocks\" {print $3}'\r\n+ LB=-4\r\nHPCdaligner -v -dal4 -t16 -h1 -e.70 -l1 -s1000 -H1 raw_reads -3-$LB > /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/run_jobs.sh\r\n+ HPCdaligner -v -dal4 -t16 -h1 -e.70 -l1 -s1000 -H1 raw_reads -3--4\r\nHPCdaligner: -3 is an illegal option\r\ntouch /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/rdb_build_done.exit\r\n+ touch /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/rdb_build_done.exit\r\nTraceback (most recent call last):\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 67, in _run_script_local\r\n    system(cmd, check=True)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 24, in system\r\n    raise Exception(msg)\r\nException: Call 'bash /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh 1> /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh.log 2>&1' returned 256.\r\n[ERROR] PypeTaskBase failed:\r\n{'__class__.__name__': 'PypeThreadTaskBase',\r\n '_status': 'TaskInitialized',\r\n 'inputDataObjs': {'input_fofn': PypeLocalFile('file://localhost/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/input.fofn', '/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/input.fofn')},\r\n 'mutableDataObjs': {},\r\n 'outputDataObjs': {'rdb_build_done': PypeLocalFile('file://localhost/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/rdb_build_done', '/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/rdb_build_done'),\r\n                    'run_jobs': PypeLocalFile('file://localhost/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/run_jobs.sh', '/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/run_jobs.sh')},\r\n 'parameters': {'config': {'cns_concurrent_jobs': 8,\r\n                           'falcon_sense_option': '--output_multi --min_idt 0.70 --min_cov 1 --local_match_count_threshold 100 --max_n_read 20000 --n_core 0 --output_dformat',\r\n                           'falcon_sense_skip_contained': False,\r\n                           'input_fofn_fn': 'input.fofn',\r\n                           'input_type': 'raw',\r\n                           'install_prefix': '/mnt/home/langhorst/src/FALCON-integrate/fc_env',\r\n                           'job_type': 'local',\r\n                           'length_cutoff': 1,\r\n                           'length_cutoff_pr': 1,\r\n                           'openending': False,\r\n                           'overlap_filtering_setting': '--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0',\r\n                           'ovlp_DBsplit_option': '-x5 -s50 -a',\r\n                           'ovlp_HPCdaligner_option': '-v -dal4 -t32 -h1 -e.99 -l1 -s1000',\r\n                           'ovlp_concurrent_jobs': 32,\r\n                           'pa_DBsplit_option': '-x5 -s1 -u16 -a',\r\n                           'pa_HPCdaligner_option': '-v -dal4 -t16 -h1 -e.70 -l1 -s1000',\r\n                           'pa_concurrent_jobs': 32,\r\n                           'sge_option_cns': '-pe smp 8 -q production',\r\n                           'sge_option_da': '-pe smp 8 -q production',\r\n                           'sge_option_fc': '-pe smp 24 -q production',\r\n                           'sge_option_la': '-pe smp 2 -q production',\r\n                           'sge_option_pda': '-pe smp 8 -q production',\r\n                           'sge_option_pla': '-pe smp 2 -q production',\r\n                           'target': 'assembly',\r\n                           'use_tmpdir': False},\r\n                'work_dir': '/mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads'}}\r\nTraceback (most recent call last):\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 341, in __call__\r\n    return self.runInThisThread(*argv, **kwargv)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 362, in runInThisThread\r\n    self.run(*argv, **kwargv)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 276, in run\r\n    rtn = self._runTask(self, *argv, **kwargv)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 190, in _runTask\r\n    return self._taskFun(self)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 157, in task_build_rdb\r\n    run_script(job_data, job_type = config[\"job_type\"])\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 97, in run_script\r\n    rc = _run_script(job_data)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 67, in _run_script_local\r\n    system(cmd, check=True)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 24, in system\r\n    raise Exception(msg)\r\nException: Call 'bash /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh 1> /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh.log 2>&1' returned 256.\r\nException in thread Thread-1:\r\nTraceback (most recent call last):\r\n  File \"/mnt/galaxy/data/galaxy/sw/lib/python2.7/threading.py\", line 801, in __bootstrap_inner\r\n    self.run()\r\n  File \"/mnt/galaxy/data/galaxy/sw/lib/python2.7/threading.py\", line 754, in run\r\n    self.__target(*self.__args, **self.__kwargs)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 341, in __call__\r\n    return self.runInThisThread(*argv, **kwargv)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 362, in runInThisThread\r\n    self.run(*argv, **kwargv)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 276, in run\r\n    rtn = self._runTask(self, *argv, **kwargv)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 190, in _runTask\r\n    return self._taskFun(self)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 157, in task_build_rdb\r\n    run_script(job_data, job_type = config[\"job_type\"])\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 97, in run_script\r\n    rc = _run_script(job_data)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 67, in _run_script_local\r\n    system(cmd, check=True)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 24, in system\r\n    raise Exception(msg)\r\nException: Call 'bash /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh 1> /mnt/home/langhorst/src/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh.log 2>&1' returned 256.\r\n\r\n[INFO] Failure ('fail'). Joining 'task:///mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py/task_build_rdb'...\r\n[ERROR] Any exception caught in RefreshTargets() indicates an unrecoverable error. Shutting down...\r\nTraceback (most recent call last):\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py\", line 519, in refreshTargets\r\n    rtn = self._refreshTargets(task2thread, objs = objs, callback = callback, updateFreq = updateFreq, exitOnFailure = exitOnFailure)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py\", line 732, in _refreshTargets\r\n    raise TaskFailureError(\"Counted %d failures.\" %failedJobCount)\r\nTaskFailureError: 'Counted 1 failures.'\r\n\r\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\r\n! Please wait for all threads / processes to terminate !\r\n! Also, maybe use 'ps' or 'qstat' to check all threads,!\r\n! processes and/or jobs are terminated cleanly.        !\r\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\r\n[WARNING] #tasks=1, #alive=0\r\nTraceback (most recent call last):\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/bin/fc_run.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('falcon-kit==0.4.0', 'fc_run.py')\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pkg_resources/__init__.py\", line 729, in run_script\r\n    self.require(requires)[0].run_script(script_name, ns)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pkg_resources/__init__.py\", line 1642, in run_script\r\n    exec(code, namespace, namespace)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/fc_run.py\", line 5, in <module>\r\n    main(sys.argv)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 646, in main\r\n    main1(*argv)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 501, in main1\r\n    wf.refreshTargets([rdb_build_done])\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py\", line 519, in refreshTargets\r\n    rtn = self._refreshTargets(task2thread, objs = objs, callback = callback, updateFreq = updateFreq, exitOnFailure = exitOnFailure)\r\n  File \"/mnt/home/langhorst/src/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py\", line 732, in _refreshTargets\r\n    raise TaskFailureError(\"Counted %d failures.\" %failedJobCount)\r\npypeflow.controller.TaskFailureError: 'Counted 1 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