Error in Parallelizing same task with different inputs

[lonsbio]

From jasre...@gmail.com on 2012-05-11T06:39:33Z

I am trying Bpipe for one of our in-house software. The program runs fine when I run a single version of the "exec" command but when I try and run the same command by changing one input parameter and parallelizing the two shell commands, I get an error :

org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
script_from_command_line: 4: expecting anything but ''\n''; got it anyway @ line 4, column 192.

1 error

Any help would be appreciated.

Thanks
Jess

Original issue: http://code.google.com/p/bpipe/issues/detail?id=24

[lonsbio]

From jasre...@gmail.com on 2012-05-10T13:55:42Z

I just fixed that one by using 3 double quotes, but now there is another error. Since I dont use the input from the previous stage to the next stage, I get this error :

bpipe.PipelineStage INFO |3:52:30 Stage stage_one returned null as default inputs for next stage
bpipe.PipelineStage INFO |3:52:30 Removing inferred outputs matching [.bai$, .log$]
bpipe.PipelineStage INFO |3:52:30 Inferring nextInputs from inputs bpipe.PipelineContext@2c8c7d6.@input
bpipe.PipelineContext INFO |3:52:30 Setting output [] on context 46712790 in thread 1
bpipe.PipelineCategory INFO |3:52:30 multiply on input [] with pattern *
bpipe.PipelineStage INFO |3:52:30 Retaining pre-existing files [] from outputs
bpipe.Pipeline INFO |3:52:30 Pipeline segment failed (2): The pattern provided '*' did not match any of the files provided as input []
Pipeline failed!

[lonsbio]

From ssade...@gmail.com on 2012-05-19T23:31:26Z

I don't fully understand the pipeline well enough here to follow this up. Might be best to follow up by posting to the Google Group and we can figure out if its a bug or not.

NB: a few people have been confused by getting this error because they expect the input pattern to match files in the local directory automatically; however it only actually matches files you provide in the 'bpipe run' command. So even if you use a pattern you still need to provide the files for it to match ...

bpipe run yourpipeline <files....> <=== only these files are considered for matching the input.

[lonsbio]

From ssade...@gmail.com on 2012-05-19T23:31:45Z

Labels: -Type-Defect Type-Other