MissingInputFile thrown, pipeline hangs, never exits or proceeds

[GoogleCodeExporter]

What steps will reproduce the problem?
0. Using the current 2.3 codebase:

1.Run a pipeline step using  @transform (ie: 
@transform([align_to_viral,align_to_bacterial],suffix(".cat"),".qc")

2.Make sure the input files do not exist (no *.cat files are passed)

3. run pipeline

What is the expected output? What do you see instead?
MissingInputFileError is expected, and I assumed the pipeline would log an 
error and proceed, or exit completely.
Instead, the pipeline hangs after reporting the error... never returns to the 
command line prompt.

What version of the product are you using? On what operating system?
2.3 (checked out Jan 4 2012)

Please provide any additional information below.

Below is the output prior to the hang(which never exits AFAICT):::

Task enters queue = summarize_alignment_results

    Job  = [UNMAPPED___P5E1R1_BL1_TS002.2cat -> UNMAPPED___P5E1R1_BL1_TS002.2.qc] Missing file [UNMAPPED___P5E1R1_BL1_TS002.2cat] 
Traceback (most recent call last):
  File "../check_unmapped_reads.py", line 63, in <module>
    pipeline_run([three], verbose = 3, multiprocess = 2 )
  File "/usr/local/lib/python2.7/dist-packages/ruffus-2.3b-py2.7.egg/ruffus/task.py", line 2941, in pipeline_run
QC
    fill_queue_with_job_parameters(job_parameters, parameter_q, multiprocess, logger, verbose)
  File "/usr/local/lib/python2.7/dist-packages/ruffus-2.3b-py2.7.egg/ruffus/task.py", line 2662, in fill_queue_with_job_parameters
    for param in job_parameters:
  File "/usr/local/lib/python2.7/dist-packages/ruffus-2.3b-py2.7.egg/ruffus/task.py", line 2601, in parameter_generator
    raise errt
ruffus.ruffus_exceptions.RethrownJobError: 

    Exceptions generating parameters for

    def summarize_alignment_results(...):

Original exception:

    Exception #1
      'ruffus.ruffus_exceptions.MissingInputFileError(    

        No way to run job: Input file ['UNMAPPED___P5E1R1_BL1_TS002.2cat'] does not exist)' raised in ...
       Task = def summarize_alignment_results(...):

    Traceback (most recent call last):
      File "/usr/local/lib/python2.7/dist-packages/ruffus-2.3b-py2.7.egg/ruffus/task.py", line 2535, in parameter_generator
        check_input_files_exist (*param)
      File "/usr/local/lib/python2.7/dist-packages/ruffus-2.3b-py2.7.egg/ruffus/file_name_parameters.py", line 232, in check_input_files_exist
        "Input file ['%s'] does not exist" % f)
    MissingInputFileError:     

        No way to run job: Input file ['UNMAPPED___P5E1R1_BL1_TS002.2cat'] does not exist

Original issue reported on code.google.com by john.ma...@locusdev.net on 10 Jan 2012 at 10:52

[GoogleCodeExporter]

ADDITIONAL INFO::  The above behaviour is only present when multiprocess=2+.
When set to multiprocess=1 the pipeline exits to the shell after throwing the 
error.

Original comment by john.ma...@locusdev.net on 10 Jan 2012 at 11:00

[GoogleCodeExporter]

Bug fixes in v 2.4 to pipeline run in thread and queue handling should have 
resolved this.

Original comment by bunbu...@gmail.com on 16 Dec 2013 at 6:36

• Changed state: Fixed