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%5DFailed > to 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 >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >> > >
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