Here's a link to one of the WIG files I am using:
https://www.dropbox.com/s/rv201lawduflr7j/Galaxy12-scc.wig.zip
I'd appreciate any pointers.

Thanks,
Ilya


On 11/27/12 3:57 PM, "Jim Johnson" <johns...@umn.edu> wrote:

>
>
>
>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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