Ok. Thanks for your clarifications. So I will wait for your upcoming
distribution of Galaxy and redo the test.

Best,
Amine

2012/7/20 Jeremy Goecks <jeremy.goe...@emory.edu>

> Hmm, this appears to be an indexing error, but there are many potential
> causes so that doesn't narrow down the issue much.
>
> Because you're using galaxy-dist, the simplest thing to do is wait for our
> upcoming distribution (which should happen in the next couple days),
> upgrade and see if that fixes the problem. Trackster is under active
> development, so there are quite a few bug fixes and improvements that will
> be available with the next distribution.
>
> If you're still experiencing problems after upgrading, let us know and
> we'll keep trying to figure out what's going on.
>
> Best,
> J.
>
> On Jul 19, 2012, at 11:03 AM, Chebbi Mohamed Amine wrote:
>
> HI!
>
> I'am usig Galaxy-dist.
>
> SO I have done the test again, I did a simple scrolling to visualize by
> the Trackster the different  chromosome regions and then the galaxy crashed
> suddenly.
>
> Here Above what java script log looks :
>
> 22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5DFailed
> to load resource
>
> http://xxx.xxxxx.com/tracks/data?chrom=chr19&low=1449105&high=1449853&mode=Pack&resolution=1.8693312836279785&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5DFailedto
>  load resource
>
> However The paster.log looks more talking this time :
>
> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=2a8867ca0da68ac1&hda_ldda=hda&filter_cols=%5B%22Score%22%2C%22exon_number%22%2C%22frac%22%2C%22cov%22%2C%22conf_lo%22%2C%22FPKM%22%2C%22conf_hi%22%5D
> HTTP/1.1" 200 - "http://xxxx.xxxx.com/tracks/browser?id=df7a1f0c02a5b08e";
> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Auto&resolution=2.3339731285988483&dataset_id=18644201db609b11&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
> HTTP/1.1" 200 - "http://xxxx.xxxx.com/tracks/browser?id=df7a1f0c02a5b08e";
> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
> xx.xx.xxx.xxx - - [19/Jul/2012:16:46:33 +0200] "GET
> /tracks/data?chrom=chr19&low=1457332&high=1458266&mode=Pack&resolution=2.3339731285988483&dataset_id=7350596ac236c69d&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
> HTTP/1.1" 500 - "http://xxxx.xxxx.com/tracks/browser?id=df7a1f0c02a5b08e";
> "Mozilla/5.0 (X11; Linux i686) AppleWebKit/535.19 (KHTML, like Gecko)
> Ubuntu/12.04 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
> Error - <type 'exceptions.IOError'>: could not open index
> `/srv/Galaxy/Galaxy_test/database/files/_metadata_files/000/metadata_75.dat`
>
>
> 2012/7/19 Jeremy Goecks <jeremy.goe...@emory.edu>
>
>> JavaScript logs are found in the Web browser. For Safari/Chrome, see the
>> View --> Developer --> JavaScript console option; for Firefox, see Tools
>> --> Web Developer --> Web Console.
>>
>> The fact that the Paster log isn't showing errors is problematic. Are
>> there certain scenarios where Trackster/Galaxy is more likely to crash?
>> Finally, are you using galaxy-dist or galaxy-central?
>>
>> Best,
>> J.
>>
>>
>> On Jul 18, 2012, at 8:50 AM, Chebbi Mohamed Amine wrote:
>>
>>
>>
>> ---------- Forwarded message ----------
>> From: Chebbi Mohamed Amine <chebbimam...@gmail.com>
>> Date: 2012/7/18
>> Subject: Re: [galaxy-dev] Galaxy crach while visualization
>> To: Jeremy Goecks <jeremy.goe...@emory.edu>
>>
>>
>> Hello Jeremy!
>> Thanks for your response. Yes the paster.log is not complaining. Excuse
>> me where I can found the javascript log. In /var/log I haven't any file
>> related to javascript.log.
>> Thanks
>> Amine
>>
>>
>> 2012/7/17 Jeremy Goecks <jeremy.goe...@emory.edu>
>>
>>> Hello Amine,
>>>
>>> The paster log looks normal, and Postgre log is standard given the
>>> crash. Was there anything out of the ordinary that you can spot in the
>>> paster log and/or Javascript log in your Web browser?
>>>
>>> Thanks,
>>> J.
>>>
>>> On Jul 17, 2012, at 6:53 AM, Chebbi Mohamed Amine wrote:
>>>
>>> Hello Galaxy team !
>>>
>>> I have e strange problem whith my Galaxy trackster visualization . While
>>> viewing bookmarked regions in my visualisation the whole
>>> Galaxy process crashed and needed to be restarted, mainly when I use
>>> Chrome browser.
>>>
>>> Above the Paster.log :
>>>
>>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
>>> /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=f4b17be90d9b3c9d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>>> HTTP/1.1" 200 - "
>>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
>>> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
>>> /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
>>> HTTP/1.1" 200 - "
>>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
>>> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
>>> /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
>>> HTTP/1.1" 200 - "
>>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
>>> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
>>> /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D
>>> HTTP/1.1" 200 - "
>>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
>>> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
>>> /galaxy/tracks/data?chrom=chr19&low=1180427&high=1181609&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>>> HTTP/1.1" 200 - "
>>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
>>> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
>>> /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>>> HTTP/1.1" 200 - "
>>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4)
>>> AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET
>>> /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>>> HTTP/1.1" 200 - "
>>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
>>> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>>> xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:37 +0200] "GET
>>> /galaxy/tracks/data?chrom=chr19&low=814128&high=815310&mode=Auto&resolution=2.954022988505747&dataset_id=7710e7c5028b7c3b&hda_ldda=hda&filter_cols=%5B%22Score%22%5D
>>> HTTP/1.1" 200 - "
>>> http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output";
>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML,
>>> like Gecko) Chrome/20.0.1132.47 Safari/536.11"
>>>
>>> PostgreSQL saw the crach :
>>>
>>> 2012-07-12 12:56:40 CEST LOG:  could not receive data from client:
>>> Connection reset by peer
>>> 2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
>>> 2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
>>> 2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:00:46.907
>>> user=user database=database host=server port=33106
>>> 2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
>>> 2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
>>> 2012-07-12 12:56:40 CEST LOG:  unexpected EOF on client connection
>>> 2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:03:45.206
>>> user=user database=database host=server port=42867
>>> 2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:06:43.257
>>> user=user database=database host=server port=56383
>>> 2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:04:22.120
>>> user=user database=database host=server port=42663
>>> 2012-07-12 12:56:40 CEST LOG:  disconnection: session time: 0:04:22.596
>>> user=user database=database host=server port=42656
>>>
>>>
>>> Thanks
>>> Amine
>>> ___________________________________________________________
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>>>
>>
>>
>>
>
>
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