Error in Parallelizing same task with different inputs

[ssadedin]

Error in Parallelizing same task with different inputs

[lonsbio]

From [email protected] 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 [email protected] 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 [email protected] on 2012-05-19T23:31:45Z

Labels: -Type-Defect Type-Other