Improve Moa error logging for ruff jobs

[cfljam@pgenome 15.BLASTX_USDA_GH32]$ pwd /data/moa/onion/70.CG_marker_design/40.CHO/GH32/15.BLASTX_USDA_GH32 [cfljam@pgenome 15.BLASTX_USDA_GH32]$ moa show db /data/moa/db/uniprot/10.uniprot.trembl/uniprot_trembl
eval 1e-10
gff_blasthit F
gff_source BLAST
input ../12.retrieve_USDA_GH32/.fasta
nohits 50
nothreads 2
outgff gff/.gff
output out/*.out
postcommand
precommand
program blastx
project
title Blast against Trembl PLants
[cfljam@pgenome 15.BLASTX_USDA_GH32]$ ls -l .. total 16
drwxrwxr-x 2 cfljam users 4096 May 24 13:27 00.raw_data_motifs
drwxrwxr-x 3 cfljam users 4096 May 25 12:51 11.fuzztran
drwxrwxr-x 3 cfljam users 4096 May 25 13:00 12.retrieve_USDA_GH32
drwxrwxr-x 5 cfljam users 4096 May 25 13:06 15.BLASTX_USDA_GH32
[cfljam@pgenome 15.BLASTX_USDA_GH32]$ ls -la total 20
drwxrwxr-x 5 cfljam users 4096 May 25 13:06 .
drwxrwxr-x 6 cfljam users 4096 May 25 13:02 ..
drwxrwxr-x 2 cfljam users 4096 May 25 13:06 gff
drwxrwxr-x 4 cfljam users 4096 May 25 13:07 .moa
drwxrwxr-x 2 cfljam users 4096 May 25 13:06 out
[cfljam@pgenome 15.BLASTX_USDA_GH32]$moa run

  File "/opt/moa10/lib/python/moa/backend/ruff.py", line 381, in executor
    raise ruffus.JobSignalledBreak
JobSignalledBreak:

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")
ruffus.ruffus_exceptions.JobSignalledBreak(


    ):
for moa.backend.ruff.executor.Job = [[[../12.retrieve_USDA_GH32/5225.singletons_GH32.fasta, uniprot_trembl]] -> [gff/5225.singletons_GH32.gff, out/5225.singletons_GH32.out], #!/bin/bash -e
    blastall -i ../12.retrieve_USDA_GH32/5225.singletons_GH32.fasta -p blastx \
            -e 1e-10 -m 7 -a 2 -d /data/moa/db/uniprot/10.uniprot.trembl/uniprot_trembl \
            -b 50 -v  50 -o out/5225.singletons_GH32.out

    cat out/5225.singletons_GH32.out | blast2gff -b F  \
        -s BLAST -d query > gff/5225.singletons_GH32.gff, {'program': 'blastx', 'postcommand': '', 'wd': '/data/moa/onion/70.CG_marker_design/40.CHO/GH32/15.BLASTX_USDA_GH32', 'precommand': '', 'db': '/data/moa/db/uniprot/10.uniprot.trembl/uniprot_trembl', 'job': <moa.job.Job object at 0x10facf50>, 'nothreads': '2', 'eval': '1e-10', 'input': '../12.retrieve_USDA_GH32/5225.singletons_GH32.fasta', 'outgff': 'gff/5225.singletons_GH32.gff', 'silent': None, 'default_command': 'run', 'moa_filesets': ['input', 'db', 'outgff', 'output'], 'title': 'Blast against Trembl PLants', 'project': '', 'gff_source': 'BLAST', 'nohits': '50', 'gff_blasthit': 'F', 'output': 'out/5225.singletons_GH32.out'}]

Traceback (most recent call last):
  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 381, in executor
    raise ruffus.JobSignalledBreak
JobSignalledBreak: