Hi,
I'm running IGVtools (http://toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools) tile tool in Galaxy on a WIG file but it's failing with exit code 1 and producing no output file. On the other hand, IGVtools count and sort run successfully in Galaxy on their respective inputs.
Also, IGVtools tile tool runs successfully by itself from the command line on the same input WIG file from the same user account that runs this Galaxy instance.
Standard out and error from running tile in Galaxy are below. I was wondering if anyone had a similar problem with IGVtools in their Galaxy instance.
Thanks, Ilya
stdout:
Tile. File = input_file.wig Max zoom = 7 Probe file = None Window functions: mean IGV directory: /n/galaxy/home/galaxy_scc/igv INFO [2012-11-27 00:14:07,942] [GenomeManager.java:118] [main] Genome loaded
Processing chromosome chr19 .........10.0% .........20.0% .........30.0% .........40.0% .........50.0% ..INFO [2012-11-27 00:14:12,778] [Preprocessor.java:179] [main] Ignoring data from non-existent locus. Probe = null Locus = chr19:61342442-61342477. chr19 length = 61342430 Group idx: 1 100.0%
stderr:
cp: cannot stat `/n/galaxy/www/galaxy_scc_dev/galaxy-central-hbc-20121101220520/database/jo b_working_directory/000/100/output.tdf': No such file or directory