Error in DepthOfCoverage (GATK) tool
Hello, I'm facing an issue with "Depth Of Coverage" tool when it runs on refGene and target BED file. The error message is: File "cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py", line 402, in respond NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics' I noticed that the issue is only when the "Advanced GATK options" is enabled to set target BED file. The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue? Best, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD
Hi Raj, Thanks for reporting, this issue has been resolved in changeset 6778:35be930b21be. Please let us know if you encounter further issues. Thanks for using Galaxy, Dan On Mar 1, 2012, at 3:30 AM, Praveen Raj Somarajan wrote:
Hello,
I'm facing an issue with "Depth Of Coverage" tool when it runs on refGene and target BED file. The error message is:
File "cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py", line 402, in respond NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics'
I noticed that the issue is only when the "Advanced GATK options" is enabled to set target BED file.
The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue?
Best,
Raj
This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.
OCIMUMBIO SOLUTIONS (P) LTD ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Hello Dan, But, I am currently using the latest update of Galaxy (as 'hg incoming' says 'no changes'). Just to clarify one thing: which repository should I clone - https://bitbucket.org/galaxy/galaxy-dist/ (mentioned in GetGalaxy.org) OR http://www.bx.psu.edu/hg/galaxy/ (mentioned in NewsBrief website). I use the first one to update Galaxy. I tried to pull the below changeset, but it says 'invalid revision'. Please suggest. Best, Raj From: Daniel Blankenberg [mailto:dan@bx.psu.edu] Sent: Thursday, March 01, 2012 8:45 PM To: Praveen Raj Somarajan Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error in DepthOfCoverage (GATK) tool Hi Raj, Thanks for reporting, this issue has been resolved in changeset 6778:35be930b21be. Please let us know if you encounter further issues. Thanks for using Galaxy, Dan On Mar 1, 2012, at 3:30 AM, Praveen Raj Somarajan wrote: Hello, I'm facing an issue with "Depth Of Coverage" tool when it runs on refGene and target BED file. The error message is: File "cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py", line 402, in respond NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics' I noticed that the issue is only when the "Advanced GATK options" is enabled to set target BED file. The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue? Best, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http://usegalaxy.org>. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD
Hi Raj, This is currently available in -central (https://bitbucket.org/galaxy/galaxy-central), but will be available in the next dist release. You can pull directly from central, apply the changes manually, or wait for the next dist release. Thanks for using Galaxy, Dan On Mar 2, 2012, at 2:20 AM, Praveen Raj Somarajan wrote:
Hello Dan,
But, I am currently using the latest update of Galaxy (as 'hg incoming' says 'no changes'). Just to clarify one thing: which repository should I clone - https://bitbucket.org/galaxy/galaxy-dist/ (mentioned in GetGalaxy.org) OR http://www.bx.psu.edu/hg/galaxy/ (mentioned in NewsBrief website). I use the first one to update Galaxy. I tried to pull the below changeset, but it says 'invalid revision'.
Please suggest.
Best,
Raj
From: Daniel Blankenberg [mailto:dan@bx.psu.edu] Sent: Thursday, March 01, 2012 8:45 PM To: Praveen Raj Somarajan Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error in DepthOfCoverage (GATK) tool
Hi Raj,
Thanks for reporting, this issue has been resolved in changeset 6778:35be930b21be. Please let us know if you encounter further issues.
Thanks for using Galaxy,
Dan
On Mar 1, 2012, at 3:30 AM, Praveen Raj Somarajan wrote:
Hello,
I'm facing an issue with "Depth Of Coverage" tool when it runs on refGene and target BED file. The error message is:
File "cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py", line 402, in respond NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics'
I noticed that the issue is only when the "Advanced GATK options" is enabled to set target BED file.
The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue?
Best,
Raj
This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.
OCIMUMBIO SOLUTIONS (P) LTD ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.
OCIMUMBIO SOLUTIONS (P) LTD
participants (2)
-
Daniel Blankenberg -
Praveen Raj Somarajan