Moamoa Moa → v1.1

.moa/log directory was not writable - should give a reasonable error message when this happens

Note that it dies in a flurry of ruffus measages etc but moa err is empty

[cfljam@pgenome 11.fuzztran]$ pwd /data/moa/onion/70.CG_marker_design/40.CHO/GH32/11.fuzztran [cfljam@pgenome 11.fuzztran]$ moa show input /data/moa/db/onion/80.USDAARS/.fasta
output ./.gff
postcommand
precommand
process fuzztran -sequence -pattern "HXX[PV]X(4)[LIVMA]NDPN[GA]" -outfile -frame 6 -rformat2 gff3
project
title scan for GH32 active site motif in USDA Assemblies
[cfljam@pgenome 11.fuzztran]$ moa set process process:
$ fuzztran -sequence {{input}} -pattern "HXX[PV]X(4)[LIVMA]NDPN[GA]" -outfile {{output}} -frame 6 -rformat2 gff3 [cfljam@pgenome 11.fuzztran]$ moa run . . .

   return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
  File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 447, in job_wrapper_io_files
    ret_val = user_defined_work_func(*param)
  File "/opt/moa10/lib/python/moa/backend/ruff.py", line 379, in executor
    rc = moa.actor.simpleRunner(jobData['wd'],  [tf.name], silent=jobData['silent'])
  File "/opt/moa10/lib/python/moa/actor.py", line 38, in simpleRunner
    SOUT = open(os.path.join(outDir, 'stdout'), 'a')
IOError: [Errno 2] No such file or directory: '/data/moa/onion/70.CG_marker_design/40.CHO/GH32/11.fuzztran/.moa/out/20110525T112914/stdout'

Warning: Encountered a run error?
Traceback (most recent call last):
File "/opt/moa10/bin/moa", line 318, in

run_1()

File "/opt/moa10/bin/moa", line 292, in run_1

run_2()

File "/opt/moa10/bin/moa", line 246, in run_2

run_3(wd)

File "/opt/moa10/bin/moa", line 201, in run_3

silent = sysConf.options.silent)

File "/opt/moa10/lib/python/moa/job.py", line 250, in execute

execNow, verbose = verbose, silent=silent)

File "/opt/moa10/lib/python/moa/backend/ruff.py", line 241, in execute

logger = ruffus.black_hole_logger,

File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 2680, in pipeline_run ruffus.ruffus_exceptions.RethrownJobError:

Exceptions running jobs for

'def moa.backend.ruff.executor(...):'

Original exception:

Exception [#1](/projects/73665/tickets/1 "Ticket #1")
exceptions.IOError([Errno 2] No such file or directory: '/data/moa/onion/70.CG_marker_design/40.CHO/GH32/11.fuzztran/.moa/out/20110525T112914/stdout'):
for moa.backend.ruff.executor.Job = [[[OH1.singletons.fasta]] -> [./OH1.singletons.gff], #!/bin/bash -e

fuzztran -sequence /data/moa/db/onion/80.USDAARS/OH1.singletons.fasta  -pattern 'HXX[PV]X(4)[LIVMA]NDPN[GA]' -outfile ./OH1.singletons.gff -frame 6  -rformat2 gff3, {'default_command': 'run', 'wd': '/data/moa/onion/70.CG_marker_design/40.CHO/GH32/11.fuzztran', 'moa_filesets': ['input', 'output'], 'title': 'scan for GH32 active site motif in USDA Assemblies', 'process': 'fuzztran -sequence {{input}}  -pattern 'HXX[PV]X(4)[LIVMA]NDPN[GA]' -outfile {{output}} -frame 6  -rformat2 gff3', 'postcommand': '', 'project': '', 'precommand': '', 'input': '/data/moa/db/onion/80.USDAARS/OH1.singletons.fasta', 'output': './OH1.singletons.gff', 'silent': None}]

Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 524, in run_pooled_job_without_exceptions
    return t_job_result(task_name, JOB_COMPLETED, job_name, return_value, None)
  File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
    self.gen.throw(type, value, traceback)
  File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 232, in do_nothing_semaphore
    yield
  File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 517, in run_pooled_job_without_exceptions
    return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
  File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 447, in job_wrapper_io_files
    ret_val = user_defined_work_func(*param)
  File "/opt/moa10/lib/python/moa/backend/ruff.py", line 379, in executor
    rc = moa.actor.simpleRunner(jobData['wd'],  [tf.name], silent=jobData['silent'])
  File "/opt/moa10/lib/python/moa/actor.py", line 38, in simpleRunner
    SOUT = open(os.path.join(outDir, 'stdout'), 'a')
IOError: [Errno 2] No such file or directory: '/data/moa/onion/70.CG_marker_design/40.CHO/GH32/11.fuzztran/.moa/out/20110525T112914/stdout'

[cfljam@pgenome 11.fuzztran]$ moa err

[cfljam@pgenome 11.fuzztran]$