I'm currently trying to connect ergatis and workflow with the SGE.
My test pipeline is an exact copy of the pipeline described in the "pipeline creation tutorial" (formatdb and blastall).
The problem occurred during the blastall run. After the job is distributed on the cluster the job runs, finishes and creates all output_data except the bsml.list, raw.list and btab.list.
The program doesn't finish and runs on and on and on...
The entry.log contains the following:
I~~~ wrapper script starting job
I~~~ Job Process id is 15233
F~~~623~~~106~~~Mon Sep 13 12:01:02 CEST 2010~~~command finished~~~0
The stdout and stderr of ergatis contains the following:
The Workflow is invoked. View Workflow Monitor to check the progress.
log4j:WARN No appenders could be found for logger (org.tigr.antware.shared.util.AppConfig).
log4j:WARN Please initialize the log4j system properly.
WARN 12:01:02:957 [Thread: (1) Monitor Command 623] Command taskFinished:1065 Task 0 finished but it was never started...
The SGE command qacct tells me the job finished without an error.
It is obvious that the process officially never started but the data is there. Furthermore the program seems to think it didn't finish.