Dear sir or madam,
I am using galaxy public server and I am trying to build a custom genome using the function "custom Builds" in "user" section. I specified the Name, Key and uploaded the genome fasta file also the chromosome length file. But when I click "submit", galaxy gave an error information like that: "" *Server Error:* An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) "" I don't know where to find the error logs and how to turn debug on. Could you tell me how to fix the problem and upload the custom builds? Thanks a lot!
Pengfei
Yeah, Hope we could find the answer from Galaxy team soon :-)
Pengfei
On Thu, Feb 16, 2012 at 11:00 PM, Noa Sher noa.sher@gmail.com wrote:
I also had exactly the same problem yesterday - glad to see that maybe it wasn't just me.
Happy for help!
Noa
On 16/02/2012 22:24, Pengfei Yu wrote:
Dear sir or madam,
I am using galaxy public server and I am trying to build a custom genome using the function "custom Builds" in "user" section. I specified the Name, Key and uploaded the genome fasta file also the chromosome length file. But when I click "submit", galaxy gave an error information like that: "" *Server Error:* An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) "" I don't know where to find the error logs and how to turn debug on. Could you tell me how to fix the problem and upload the custom builds? Thanks a lot!
Pengfei
Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301
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 Pengfei and Noa,
I suspect this was a temporary problem related to software issues that we encountered yesterday. Please try again and let us know if you're still having problems.
Also, note that either a FASTA dataset or a Len file is needed, but not both. Using a FASTA dataset enables viewing genome data in Trackster.
Best, J.
On Feb 17, 2012, at 12:00 AM, Noa Sher wrote:
I also had exactly the same problem yesterday - glad to see that maybe it wasn't just me. Happy for help! Noa
On 16/02/2012 22:24, Pengfei Yu wrote:
Dear sir or madam,
I am using galaxy public server and I am trying to build a custom genome using the function "custom Builds" in "user" section. I specified the Name, Key and uploaded the genome fasta file also the chromosome length file. But when I click "submit", galaxy gave an error information like that: "" Server Error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) "" I don't know where to find the error logs and how to turn debug on. Could you tell me how to fix the problem and upload the custom builds? Thanks a lot!
Pengfei
Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301
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:
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 Jeremy,
Thanks for the help! I can upload fasta data for custom builds (name:'NCI-H209-hg18'; key:'NCI-H209-V1') now. but when I try to use a bed file specific for this custom builds to fetch sequences from this custom genome, it gives error information that no sequences are available for 'NCI-H209-v1'. I might do something wrong, do you know what would be the reason?
Thanks! Pengfei
On Fri, Feb 17, 2012 at 7:40 AM, Jeremy Goecks jeremy.goecks@emory.eduwrote:
Hi Pengfei and Noa,
I suspect this was a temporary problem related to software issues that we encountered yesterday. Please try again and let us know if you're still having problems.
Also, note that either a FASTA dataset or a Len file is needed, but not both. Using a FASTA dataset enables viewing genome data in Trackster.
Best, J.
On Feb 17, 2012, at 12:00 AM, Noa Sher wrote:
I also had exactly the same problem yesterday - glad to see that maybe it wasn't just me. Happy for help! Noa
On 16/02/2012 22:24, Pengfei Yu wrote:
Dear sir or madam,
I am using galaxy public server and I am trying to build a custom genome using the function "custom Builds" in "user" section. I specified the Name, Key and uploaded the genome fasta file also the chromosome length file. But when I click "submit", galaxy gave an error information like that: "" *Server Error:* An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) "" I don't know where to find the error logs and how to turn debug on. Could you tell me how to fix the problem and upload the custom builds? Thanks a lot!
Pengfei
Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301
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:
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:
Hi Pengfei,
The "User -> Custom Builds:" form is used to set up genomes for use with Trackster. To use custom reference genomes with tools from the left tool panel, only the fasta dataset in the history is needed. It sounds like you already have loaded this, but if not, do this before following the steps below, using FTP to load if the genome is large: http://wiki.g2.bx.psu.edu/FTPUpload
These are the steps to extract sequences with a custom genome:
1 - starting with the tool "Fetch Sequences -> Extract Genomic DNA" 2 - set "Fetch sequences for intervals in:" to be the BED file of coordinates 3 - set "Source for Genomic Data:" to be "History" 4 - the form will refresh to reveal a new menu option, set "Using reference file:" to be the dataset from your history that is the fasta version of your reference genome 5 - set "Output data type:" to be "FASTA"
It is important that the chromosome/scaffold names in the BED file are identical to the identifiers in the FASTA reference genome dataset. If there are mismatches, an error will result and corrections to the IDs should be made.
Hopefully this helps, but if you continue to have problems, please send in a bug report (using the green bug icon) from the red failed Extract job and we can provide feedback.
Best,
Jen Galaxy team
On 2/17/12 8:25 AM, Pengfei Yu wrote:
Hi Jeremy,
Thanks for the help! I can upload fasta data for custom builds (name:'NCI-H209-hg18'; key:'NCI-H209-V1') now. but when I try to use a bed file specific for this custom builds to fetch sequences from this custom genome, it gives error information that no sequences are available for 'NCI-H209-v1'. I might do something wrong, do you know what would be the reason?
Thanks! Pengfei
On Fri, Feb 17, 2012 at 7:40 AM, Jeremy Goecks <jeremy.goecks@emory.edu mailto:jeremy.goecks@emory.edu> wrote:
Hi Pengfei and Noa, I suspect this was a temporary problem related to software issues that we encountered yesterday. Please try again and let us know if you're still having problems. Also, note that either a FASTA dataset or a Len file is needed, but not both. Using a FASTA dataset enables viewing genome data in Trackster. Best, J. On Feb 17, 2012, at 12:00 AM, Noa Sher wrote:I also had exactly the same problem yesterday - glad to see that maybe it wasn't just me. Happy for help! Noa On 16/02/2012 22:24, Pengfei Yu wrote:Dear sir or madam, I am using galaxy public server and I am trying to build a custom genome using the function "custom Builds" in "user" section. I specified the Name, Key and uploaded the genome fasta file also the chromosome length file. But when I click "submit", galaxy gave an error information like that: "" *Server Error:* An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) "" I don't know where to find the error logs and how to turn debug on. Could you tell me how to fix the problem and upload the custom builds? Thanks a lot! Pengfei -- Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone:217-898-6301 <tel:217-898-6301> ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.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/___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.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/-- Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301
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:
Hello Pengfei, Noa,
Galaxy was experiencing intermittent cluster failures yesterday. Please run your jobs again. I was able to create a test build a few minutes ago without a problem at the public Main instance.
We are very sorry for the inconvenience,
Jen Galaxy team
On 2/16/12 12:24 PM, Pengfei Yu wrote:
Dear sir or madam,
I am using galaxy public server and I am trying to build a custom genome using the function "custom Builds" in "user" section. I specified the Name, Key and uploaded the genome fasta file also the chromosome length file. But when I click "submit", galaxy gave an error information like that: "" *Server Error:* An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) "" I don't know where to find the error logs and how to turn debug on. Could you tell me how to fix the problem and upload the custom builds? Thanks a lot!
Pengfei
Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301 tel:217-898-6301
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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Jennifer Jackson -
Jeremy Goecks -
Noa Sher -
Pengfei Yu