inconsistent BAM-to-SAM behavior

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inconsistent BAM-to-SAM behavior

Jennifer Jackson
Hi Mike,

I am moving this over to the [hidden email] mailing list as it concerns a local install. This is the best way to make contact with others working with the same type of Galaxy.
https://wiki.galaxyproject.org/MailingLists

A few things to provide more context that will help with troubleshooting:

1 - Are you running the most current version of Galaxy?
      https://wiki.galaxyproject.org/DevNewsBriefs (Nov 4, 2013)

2 - The local has some of the initial production server changes made?
      initial install: http://getgalaxy.org
      next steps are under: https://wiki.galaxyproject.org/Admin
      in particular: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

3 - You installed SAMTools from the Tool Shed? The config is correct? And are running the latest version?
      https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
      https://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
      https://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

4 - When you run the same dataset(s) through on the public Main Galaxy instance at http://usegalaxy.org, is it successful or does it fail?

I wasn't sure if you meant that the same file will fail and then pass, or if some fail and some pass. If you could clarify that, it would help. It could mean the difference between a processing problem (pointing to a config or other issue) and a simple memory problem (where allocating more could help). Please keep all replies on the mailing list with a cc.

Thanks!

Jen
Galaxy team

On 12/10/13 12:07 PM, Michael Mason wrote:
Hi,

I have run some top hap output through the samtools BAM-to-SAM wrapper. It creates the SAM file about 50% of the time. The rest of the time it makes an empty file. In this case if I just rerun it often works. I was wondering if anyone else has seen this behavior. I am using a cloud server and think  I might need to change some settings. This causes my workflow to fail for many libraries so I also interested in any workarounds anyone has figured out.
Thanks in advance for any help.
Cheers
Mike
-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
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:
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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
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Re: inconsistent BAM-to-SAM behavior

Michael Mason
Thanks for the response Jen!

Answers to your questions below. 

  1. It should be the newest version of Galaxy
  2.  We did make production server changes but I'll check the admin part again
  3. This might be the problem.  I tried to install package_samtools_0_1_19 but it failed, then I installed package_samtools_0_1_18 which succeeded, and lastly I installed bam_to_sam
  4. I have not tried the main galaxy instance yet. 
I did mean the "same" file. I just turned off autoscaling to simplify things. 
I'll get back to after: unistalling  package_samtools_0_118 and bam_to_sam and then just installing bam_to_sam and reviewing the how our production server is set up.
Thanks 
Mike

From: Jennifer Jackson <[hidden email]>
Date: Tuesday, December 10, 2013 3:03 PM
To: Michael Mason <[hidden email]>, Galaxy Dev <[hidden email]>
Subject: inconsistent BAM-to-SAM behavior

Hi Mike,

I am moving this over to the [hidden email] mailing list as it concerns a local install. This is the best way to make contact with others working with the same type of Galaxy.
https://wiki.galaxyproject.org/MailingLists

A few things to provide more context that will help with troubleshooting:

1 - Are you running the most current version of Galaxy?
      https://wiki.galaxyproject.org/DevNewsBriefs (Nov 4, 2013)

2 - The local has some of the initial production server changes made?
      initial install: http://getgalaxy.org
      next steps are under: https://wiki.galaxyproject.org/Admin
      in particular: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

3 - You installed SAMTools from the Tool Shed? The config is correct? And are running the latest version?
      https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
      https://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
      https://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

4 - When you run the same dataset(s) through on the public Main Galaxy instance at http://usegalaxy.org, is it successful or does it fail?

I wasn't sure if you meant that the same file will fail and then pass, or if some fail and some pass. If you could clarify that, it would help. It could mean the difference between a processing problem (pointing to a config or other issue) and a simple memory problem (where allocating more could help). Please keep all replies on the mailing list with a cc.

Thanks!

Jen
Galaxy team

On 12/10/13 12:07 PM, Michael Mason wrote:
Hi,

I have run some top hap output through the samtools BAM-to-SAM wrapper. It creates the SAM file about 50% of the time. The rest of the time it makes an empty file. In this case if I just rerun it often works. I was wondering if anyone else has seen this behavior. I am using a cloud server and think  I might need to change some settings. This causes my workflow to fail for many libraries so I also interested in any workarounds anyone has figured out.
Thanks in advance for any help.
Cheers
Mike
-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

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Re: inconsistent BAM-to-SAM behavior

Jennifer Jackson
In reply to this post by Jennifer Jackson
Repost: Mike, please reply to the list threaded question to help us track and to permit the entire Galaxy community to learn and contribute to Q/A. Thanks!
-----

Thanks for the response Jen!

Answers to your questions below. 

  1. It should be the newest version of Galaxy
  2.  We did make production server changes but I'll check the admin part again
  3. This might be the problem.  I tried to install package_samtools_0_1_19 but it failed, then I installed package_samtools_0_1_18 which succeeded, and lastly I installed bam_to_sam
  4. I have not tried the main galaxy instance yet. 
I did mean the "same" file. I just turned off autoscaling to simplify things. 
I'll get back to after: unistalling  package_samtools_0_118 and bam_to_sam and then just installing bam_to_sam and reviewing the how our production server is set up.
Thanks 
Mike



On 12/10/13 3:03 PM, Jennifer Jackson wrote:
Hi Mike,

I am moving this over to the [hidden email] mailing list as it concerns a local install. This is the best way to make contact with others working with the same type of Galaxy.
https://wiki.galaxyproject.org/MailingLists

A few things to provide more context that will help with troubleshooting:

1 - Are you running the most current version of Galaxy?
      https://wiki.galaxyproject.org/DevNewsBriefs (Nov 4, 2013)

2 - The local has some of the initial production server changes made?
      initial install: http://getgalaxy.org
      next steps are under: https://wiki.galaxyproject.org/Admin
      in particular: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

3 - You installed SAMTools from the Tool Shed? The config is correct? And are running the latest version?
      https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
      https://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
      https://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

4 - When you run the same dataset(s) through on the public Main Galaxy instance at http://usegalaxy.org, is it successful or does it fail?

I wasn't sure if you meant that the same file will fail and then pass, or if some fail and some pass. If you could clarify that, it would help. It could mean the difference between a processing problem (pointing to a config or other issue) and a simple memory problem (where allocating more could help). Please keep all replies on the mailing list with a cc.

Thanks!

Jen
Galaxy team

On 12/10/13 12:07 PM, Michael Mason wrote:
Hi,

I have run some top hap output through the samtools BAM-to-SAM wrapper. It creates the SAM file about 50% of the time. The rest of the time it makes an empty file. In this case if I just rerun it often works. I was wondering if anyone else has seen this behavior. I am using a cloud server and think  I might need to change some settings. This causes my workflow to fail for many libraries so I also interested in any workarounds anyone has figured out.
Thanks in advance for any help.
Cheers
Mike
-- 
Jennifer Hillman-Jackson
http://galaxyproject.org


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org