Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error:
hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe
This is followed by a number of lines of the same error code. I am not sure what is happening. Can you please elaborate?
Thanks, Varun
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What is the type of the file from GEO? Any additional information you provide will help debug this.
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 1:53 PM, Kilaru, Varun vkilaru@emory.edu wrote:
Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error:
hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe
This is followed by a number of lines of the same error code. I am not sure what is happening. Can you please elaborate?
Thanks, Varun
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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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Hi Professor James Taylor,
Good day. I am using a .wig file and the zipped file is attached to this email. Thanks a lot for your help in debugging this.
Thanks, Varun ________________________________________ From: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: Friday, February 01, 2013 2:40 PM To: Kilaru, Varun Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error using Trackster
What is the type of the file from GEO? Any additional information you provide will help debug this.
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 1:53 PM, Kilaru, Varun vkilaru@emory.edu wrote:
Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error:
hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe
This is followed by a number of lines of the same error code. I am not sure what is happening. Can you please elaborate?
Thanks, Varun
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Professor James Taylor,
Good day. Its a .wig file I downloaded from GEO. I tried to upload the zipped version to a previous mail but it is pending moderator approval. I downloaded the file from this link: http://www.ncbi.nlm.nih.gov/epigenomics/19516/ and did not make any changes to the file. Thanks a lot for helping me debug this.
Thanks so much, Varun ________________________________________ From: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: Friday, February 01, 2013 2:40 PM To: Kilaru, Varun Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error using Trackster
What is the type of the file from GEO? Any additional information you provide will help debug this.
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 1:53 PM, Kilaru, Varun vkilaru@emory.edu wrote:
Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error:
hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe
This is followed by a number of lines of the same error code. I am not sure what is happening. Can you please elaborate?
Thanks, Varun
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Okay. In Galaxy, what genome build (dbkey) is selected for the dataset?
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 3:09 PM, Kilaru, Varun vkilaru@emory.edu wrote:
Hi Professor James Taylor,
Good day. Its a .wig file I downloaded from GEO. I tried to upload the zipped version to a previous mail but it is pending moderator approval. I downloaded the file from this link: http://www.ncbi.nlm.nih.gov/epigenomics/19516/ and did not make any changes to the file. Thanks a lot for helping me debug this.
Thanks so much, Varun ________________________________________ From: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: Friday, February 01, 2013 2:40 PM To: Kilaru, Varun Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error using Trackster
What is the type of the file from GEO? Any additional information you provide will help debug this.
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 1:53 PM, Kilaru, Varun vkilaru@emory.edu wrote:
Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error:
hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe
This is followed by a number of lines of the same error code. I am not sure what is happening. Can you please elaborate?
Thanks, Varun
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Professor James Taylor,
Good day. This issue is resolved thanks to your foresight. I forgot to give a dbkey to this one dataset and hence it failed to open. Everything is working fine now.
Thanks so much once again, Varun ________________________________________ From: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: Friday, February 01, 2013 3:36 PM To: Kilaru, Varun Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error using Trackster
Okay. In Galaxy, what genome build (dbkey) is selected for the dataset?
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 3:09 PM, Kilaru, Varun vkilaru@emory.edu wrote:
Hi Professor James Taylor,
Good day. Its a .wig file I downloaded from GEO. I tried to upload the zipped version to a previous mail but it is pending moderator approval. I downloaded the file from this link: http://www.ncbi.nlm.nih.gov/epigenomics/19516/ and did not make any changes to the file. Thanks a lot for helping me debug this.
Thanks so much, Varun ________________________________________ From: james@taylorlab.org [james@taylorlab.org] on behalf of James Taylor [james@jamestaylor.org] Sent: Friday, February 01, 2013 2:40 PM To: Kilaru, Varun Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error using Trackster
What is the type of the file from GEO? Any additional information you provide will help debug this.
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 1, 2013 at 1:53 PM, Kilaru, Varun vkilaru@emory.edu wrote:
Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error:
hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe
This is followed by a number of lines of the same error code. I am not sure what is happening. Can you please elaborate?
Thanks, Varun
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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:
galaxy-user@lists.galaxyproject.org
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James Taylor -
Kilaru, Varun