"BAM does not exist at" Error
Locked
 
|
Hello everyone,
What does the following error in the apache log file mean? Could not open database: /var/lib/gbrowse2/databases/strawberry/Embryo/Embryo_4_1/Embryo_4_1_filtered_Aligned.sort.bam does not exist at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44. Thank you, ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Hi Omar, I hate to ask the obvious, but does the file /var/lib/gbrowse2/databases/strawberry/Embryo/Embryo_4_1/Embryo_4_1_filtered_Aligned.sort.bam exist? And is it readable by the webserver? Scott On Fri, Dec 13, 2013 at 12:13 PM, Omar Darwish <[hidden email]> wrote:
------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: "BAM does not exist at" Error
|
|
Hi Scot, It was working before, then stopped. Here is the output of (ls -l /var/lib/gbrowse2/databases/strawberry/Embryo/Embryo_4_1):
-rwxrwxrwx. 1 root root 596995781 Feb 13 2013 Embryo_4_1_filtered_Aligned.sort.bam
-rwxrwxrwx. 1 root root 434008 Feb 13 2013 Embryo_4_1_filtered_Aligned.sort.bam.bai Thank you On Wed, Dec 18, 2013 at 12:07 AM, Scott Cain <[hidden email]> wrote:
Regards, Omar
------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Hi Omar, The owned by root thing makes me a little uncomfortable, but should be fine. What about upstream directories? Does the apache user have permission to read and change into them?
Scott On Wed, Dec 18, 2013 at 12:20 AM, Omar Darwish <[hidden email]> wrote:
------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: "BAM does not exist at" Error
|
|
Hi Scott, I changed the whole path ownership and group to apache, with the same permissions as above. Still same problem. I can try any command you suggest.
Thanks! On Wed, Dec 18, 2013 at 12:29 AM, Scott Cain <[hidden email]> wrote:
Regards, Omar
------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Weird. Now we get into black magic. Try renaming (mv) the file and it's parent directory to another name and update your conf to use the new name. If that doesn't do it, I am really tapped out :-/ On Wed, Dec 18, 2013 at 11:34 AM, Omar Darwish <[hidden email]> wrote:
------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: "BAM does not exist at" Error
|
|
Thanks Scott, I tried your suggestion, same problem !!! On Wed, Dec 18, 2013 at 1:01 PM, Scott Cain <[hidden email]> wrote:
Regards, Omar
------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
«
Return to GBrowse
|
1 view|%1 views
| Free forum by Nabble | Edit this page |