[Swift-user] Problems with mappers on Beagle

[Lorenzo Pesce]

Hi --
We are trying to run a swift script that would run a set of java scripts. 
We are attempting to use swift 0.94xxxx, the version Mike installed on Beagle.

I am afraid that I am not understanding how swift sees filesystems. Basically what we want to run is something like this

/rootdir
/rootdir/workdir
/rootdir/datadir

swift is run in workdir, looks for input files in datadir and builds the same directory structure in workdir.

All files are Direct.

I am a worried that I incorrectly set absolute/relative paths. Currently the input file is set as a string, that was for debugging purposes and we would like to leave it as a file with Direct.

Location: /lustre/beagle/pittjj/SwiftRun

screen shot: 

lpesce at login5:/lustre/beagle/pittjj/SwiftRun> cat gatk_post.swift_2012-11-06_11:14:20
Swift trunk swift-r6003 cog-r3497

RunID: 20121106-1714-4tymbt3c
Progress:  time: Tue, 06 Nov 2012 17:14:23 +0000
Execution failed:
	Illegal extra argument `Dirs[0]:string = TCGA-AR-A24T-01A-11R-A169-07.accepted_hits - Closed' to _g_a_t_kpost @ gatk_post.kml, line: 186


Thanks

Lorenzo