"BAM does not exist at" Error

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"BAM does not exist at" Error

Omar Darwish
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,

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Re: "BAM does not exist at" Error

Scott Cain
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:
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,



--
------------------------------------------------------------------------
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!
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Re: "BAM does not exist at" Error

Omar Darwish
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:
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:
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,



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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
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Re: "BAM does not exist at" Error

Scott Cain
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:
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:
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:
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,



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Regards,
Omar



--
------------------------------------------------------------------------
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
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Re: "BAM does not exist at" Error

Omar Darwish
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:
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:
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:
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:
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,



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Regards,
Omar



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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
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Re: "BAM does not exist at" Error

Scott Cain
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:
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:
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:
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:
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:
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,



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Regards,
Omar



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Regards,
Omar



--
------------------------------------------------------------------------
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
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Re: "BAM does not exist at" Error

Omar Darwish
Thanks Scott, I tried your suggestion, same problem !!!


On Wed, Dec 18, 2013 at 1:01 PM, Scott Cain <[hidden email]> wrote:
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:
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:
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:
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:
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:
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,



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Regards,
Omar



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Regards,
Omar



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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
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