pangenome run: urgent fix needed

[d-j-e]

Original error report from Jane:
(great report, wrong github)

The following error occurred in the collateRepStats job in RedDog 4.7:

Traceback (most recent call last):
File "/usr/local/python/2.7.5-gcc/bin/rubra", line 9, in
load_entry_point('Rubra==0.1.5', 'console_scripts', 'rubra')()
File "/usr/local/python/2.7.5-gcc/lib/python2.7/site-packages/rubra/rubra.py", line 66, in main
gnu_make_maximal_rebuild_mode=rebuildMode)
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 2680, in pipeline_run
ruffus.ruffus_exceptions.RethrownJobError:

Exceptions running jobs for

'def RedDog.collateRepStats(...):'

Original exception:

Exception #1
exceptions.UnboundLocalError(local variable 'stage_count' referenced before assignment):
for RedDog.collateRepStats.Job = [False -> allPlasmids_forMapping_CP003091_RepStats.txt, allPlasmids_forMapping, NG-6269_00_1059_lib14853_rep_cover.txt, CP003091, allPlasmids_forMapping_CP003091.collateRepStats.Success]

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 "RedDog.py", line 890, in collateRepStats
stage_count += 1
UnboundLocalError: local variable 'stage_count' referenced before assignment

Config file and log files here: /vlsci/VR0082/shared/jane/RedDog
Output file here: /vlsci/VR0082/shared/data/salmonella/kentucky/mapping/allPlasmids_RedDog47_270614/

[d-j-e]

if you are running a pangenome run of the pipeline, you will need to delete one line (line 890) in the following code in RedDog.py:

@follows(deriveRepStats)
@files(inputByCoreRep)
def collateRepStats(input, output, refName, exampleRepCover, repliconName, flagFile):
    stage_count += 1
    runStageCheck('collateRepStats', flagFile, refName, exampleRepCover, repliconName, sdOutgroupMultiplier, runType)
stage_count += len(core_replicons)

line 890 is 'stage_count += 1' - delete this line then save the file and you will be good to go

This fix will be implemented properly in v0.4.8 which enters testing this afternoon

[d-j-e]

Fix implemented in v0.4.8