Re: [galaxy-dev] galaxy-dev Digest, Vol 77, Issue 31
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" <isytchev@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%isytchev@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
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" <johns198@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" <isytchev@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%isytchev@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
Ilya, I fixed the igvtools_tile.xml tool config and pushed it to the toolshed. Thanks for finding and reporting the problem. JJ On 11/27/12 3:18 PM, Sytchev, Ilya wrote:
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" <johns198@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" <isytchev@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%isytchev@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
The error is gone, thank you very much! What was the problem? Ilya On 11/27/12 5:34 PM, "Jim Johnson" <johns198@umn.edu> wrote:
Ilya, I fixed the igvtools_tile.xml tool config and pushed it to the toolshed. Thanks for finding and reporting the problem. JJ
On 11/27/12 3:18 PM, Sytchev, Ilya wrote:
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" <johns198@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" <isytchev@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%isytchev@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/databas e/ jo b_working_directory/000/100/output.tdf': No such file or directory
participants (2)
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Jim Johnson -
Sytchev, Ilya