FALCON error while running

Question

[s.kyungyong64]

Hi, all. I am trying to run FALCON on my Mac, but there seems to be problems...

:FALCON_2_trial $ fc_run.py fc_run.cfg
[9620]$('lfs setstripe -c 12 /Users/Desktop/Heinz/FALCON_2_trial')
sh: lfs: command not found
[9620]WARNING: Call 'lfs setstripe -c 12 /Users/Desktop/Heinz/FALCON_2_trial' returned 32512.

I am not so sure what module this is. The only thing I found was lfs in Lustre. Is this right? would it be necessary to install this? Then, the log continues

[INFO]Setup logging from file "None".
[INFO]fc_run started with configuration fc_run.cfg
[WARNING]In simple_pwatcher_bridge, pwatcher_impl=<module 'pwatcher.fs_based' from '/Users/Desktop/software/FALCON-integrate/pypeFLOW/pwatcher/fs_based.pyc'>
[INFO]In simple_pwatcher_bridge, pwatcher_impl=<module 'pwatcher.fs_based' from '/Users/StaskawiczLab/Desktop/Meng/software/FALCON-integrate/pypeFLOW/pwatcher/fs_based.pyc'>
[INFO]job_type='local', job_queue='default', sge_option='-pe smp 4', use_tmpdir=False, squash=True
[INFO]Num unsatisfied: 1, graph: 1
[INFO]About to submit: Node(1-preads_ovl/preads-fofn-abs)
[INFO]starting job Job(jobid='Pe71cab57624da1', cmd='/bin/bash run.sh', rundir='/Users/Desktop/Heinz/FALCON_2_trial/1-preads_ovl/preads-fofn-abs', options={'job_queue': 'default', 'sge_option': '-pe smp 4', 'job_type': 'local'})
[INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Pe71cab57624da1', cmd='/bin/bash run.sh', rundir='/Users/Desktop/Heinz/FALCON_2_trial/1-preads_ovl/preads-fofn-abs', options={'job_queue': 'default', 'sge_option': '-pe smp 4', 'job_type': 'local'}), lang_exe='/bin/bash'))

[INFO]recently_satisfied: set([Node(1-preads_ovl/preads-fofn-abs)])
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 0
[INFO]Num unsatisfied: 1, graph: 2
[INFO]About to submit: Node(1-preads_ovl)
[INFO]starting job Job(jobid='Pbaa415c7e588ec', cmd='/bin/bash run.sh', rundir='/Users/Desktop/Heinz/FALCON_2_trial/1-preads_ovl', options={'job_queue': 'default', 'sge_option': '-pe smp 4', 'job_type': 'local'})
[INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Pbaa415c7e588ec', cmd='/bin/bash run.sh', rundir='/Users/Desktop/Heinz/FALCON_2_trial/1-preads_ovl', options={'job_queue': 'default', 'sge_option': '-pe smp 4', 'job_type': 'local'}), lang_exe='/bin/bash'))
[INFO]sleep 0.1s
[INFO]sleep 0.2s

[INFO]recently_satisfied: set([])
[INFO]Num satisfied in this iteration: 0
[INFO]Num still unsatisfied: 1
[ERROR]Some tasks are recently_done but not satisfied: set([Node(1-preads_ovl)])
[ERROR]ready: set([])
submitted: set([])
Traceback (most recent call last):
  File "/Users/Desktop/software/FALCON-integrate/fc_env/bin/fc_run.py", line 8, in <module>
    execfile(__file__)
  File "/Users/Desktop/software/FALCON-integrate/FALCON/src/py_scripts/fc_run.py", line 5, in <module>
    main(sys.argv)
  File "/Users/Desktop/software/FALCON-integrate/FALCON/falcon_kit/mains/run1.py", line 466, in main
    main1(argv[0], args.config, args.logger)
  File "/Users/Desktop/software/FALCON-integrate/FALCON/falcon_kit/mains/run1.py", line 137, in main1
    input_fofn_plf=input_fofn_plf,
  File "/Users/Desktop/software/FALCON-integrate/FALCON/falcon_kit/mains/run1.py", line 346, in run
    wf.refreshTargets([pdb_build_done])
  File "/Users/Desktop/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py", line 226, in refreshTargets
    self._refreshTargets(updateFreq, exitOnFailure)
  File "/Users/Desktop/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py", line 292, in _refreshTargets
    raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: set([Node(1-preads_ovl)])

And this is the error in all.log

2017-06-27 21:46:18,298 - pwatcher.fs_based - DEBUG - Unable to remove heartbeat '/Users/StaskawiczLab/Desktop/Kyungyong/Heinz/FALCON_2_trial/mypwatcher/heartbeats/heartbeat-Pe71cab57624da1' when sentinal was found in exit-sentinels listdir.
Traceback (most recent call last):
  File "/Users/StaskawiczLab/Desktop/Meng/software/FALCON-integrate/pypeFLOW/pwatcher/fs_based.py", line 565, in get_status
    os.remove(heartbeat_path)
OSError: [Errno 2] No such file or directory: '/Users/StaskawiczLab/Desktop/Kyungyong/Heinz/FALCON_2_trial/mypwatcher/heartbeats/heartbeat-Pe71cab57624da1'

2017-06-27 21:46:18,298 - pwatcher.fs_based - DEBUG - Status EXIT 256 for heartbeat:heartbeat-Pe71cab57624da1
2017-06-27 21:46:18,298 - pypeflow.simple_pwatcher_bridge - ERROR - Task Node(1-preads_ovl/preads-fofn-abs) failed with exit-code=256
2017-06-27 21:46:18,298 - pypeflow.simple_pwatcher_bridge - DEBUG - recently_done: [(Node(1-preads_ovl/preads-fofn-abs), False)]
2017-06-27 21:46:18,298 - pypeflow.simple_pwatcher_bridge - DEBUG - Num done in this iteration: 1
2017-06-27 21:46:18,298 - pypeflow.simple_pwatcher_bridge - INFO - recently_satisfied: set([])
2017-06-27 21:46:18,298 - pypeflow.simple_pwatcher_bridge - INFO - Num satisfied in this iteration: 0
2017-06-27 21:46:18,299 - pypeflow.simple_pwatcher_bridge - INFO - Num still unsatisfied: 1
2017-06-27 21:46:18,299 - pypeflow.simple_pwatcher_bridge - ERROR - Some tasks are recently_done but not satisfied: set([Node(1-preads_ovl/preads-fofn-abs)])
2017-06-27 21:46:18,299 - pypeflow.simple_pwatcher_bridge - ERROR - ready: set([])
submitted: set([])
2017-06-27 21:46:18,299 - pwatcher.fs_based - DEBUG - delete(which='known', jobids=<0>)
2017-06-27 21:46:18,299 - pwatcher.fs_based - DEBUG - Deleting jobs for jobids from known ([])
2017-06-27 21:46:18,299 - pwatcher.fs_based - DEBUG - Failed to kill job for heartbeat 'heartbeat-Pe71cab57624da1': IOError(2, 'No such file or directory')
2017-06-27 21:46:18,299 - pwatcher.fs_based - DEBUG - Cannot remove heartbeat: OSError(2, 'No such file or directory')
2017-06-27 21:46:18,299 - pypeflow.simple_pwatcher_bridge - DEBUG - In notifyTerminate(), result of delete:None

Do you guys have any idea why this is happening? Thank you in advance!

[shikhar]

I am having the same problem. Did you manage to solve it?

[s.kyungyong64]

It seems lfs isn't required. I guess my problem was the PATH variable as Kevin said. I set up virtualenv and the paths. Everything worked out fine.

[Kevin Blighe]

Can you check that it is indeed the PATH variable that's the problem, and then perhaps indicate that in a comment below? This will help others who have the same issue (I noticed a few others across the World Wide Web that had problems like this).

To add a directory to path, use:

export PATH="/MyPrograms/FALCON/bin/:$PATH"

[1348988193]

I have similar problem.But run-time error appear at Raw sub-reads overlapping for error correction.Can you help me?Thanks a lot.

I run the test by virtualenv named 'fc_env'.Also I add the PATH variable.

"export PATH=$PATH:/root/FALCON-integrate/fc_env/bin" (fc_env) root@iZwz9gfo7g3450iygsp5zpZ:~/FALCON-integrate/FALCON/examples/test# fc_run.py fc_run.cfg

[output]

[1333]$(u'lfs setstripe -c 12 /root/FALCON-integrate/FALCON/examples/test') sh: 1: lfs: not found

[1333]WARNING: Call u'lfs setstripe -c 12 /root/FALCON-integrate/FALCON/examples/test' returned 32512.

ERROR …… …… [ERROR]Task Node(0-rawreads) failed with exit-code=1 [INFO]recently_satisfied: set([])

[INFO]Num satisfied in this iteration: 0

[INFO]Num still unsatisfied: 2 [ERROR]Some tasks are recently_done but not satisfied: set([Node(0-rawreads)])

[ERROR]ready: set([]) submitted: set([])

Answer 1

[Kevin Blighe]

It looks like an issue related to the fact that your FALCON scripts/executables are not in the PATH variable.

See this notice from the developers:

If FALCON calls a function that is missing, an error message is returned. It is likely then that the FALCON scripts are not yet added to the Matlab Path. The easiest solution is to browse to the FALCON pipeline folder and type “FalconInstall” on the command window in order to add scripts and all folders including examples to the Path. Alternatively, the users can also manually right-click on the FALCON folder and choose Add to Path -> Selected Folders and Subfolders. Typically the users should not encounter this issue if the users run the driver script or use the GUI version. Nevertheless, one might still face this problem if one chooses to specifically call a single FALCON function from another script or the command window.

[source: https://github.com/sysbiolux/FALCON/wiki/The-FALCON-scripts-and-examples-are-not-added-to-the-path]