Ilya,

Could you send me a failing input file, and I'll try to find out what is 
failing?
Thanks,
JJ


------------------------------

Message: 6
Date: Tue, 27 Nov 2012 07:22:30 +0000
From: "Sytchev, Ilya" <isytc...@hsph.harvard.edu>
To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] No output from IGVtools tile
Message-ID: <ccd9d465.30c7%isytc...@hsph.harvard.edu>
Content-Type: text/plain; charset="us-ascii"

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



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