Error On Custom Builds On Public Galaxy Server

Question: Error On Custom Builds On Public Galaxy Server

6.8 years ago by

Pengfei Yu • 30 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

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modified 6.8 years ago by Jeremy Goecks • 2.2k • written 6.8 years ago by Pengfei Yu • 30

6.8 years ago by

Pengfei Yu • 30

Pengfei Yu • 30 wrote:

Yeah, Hope we could find the answer from Galaxy team soon :-) Pengfei -- Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301

ADD COMMENT • link written 6.8 years ago by Pengfei Yu • 30

6.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 6.8 years ago by Jennifer Hillman Jackson ♦ 25k

6.8 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k 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.

ADD COMMENT • link written 6.8 years ago by Jeremy Goecks • 2.2k

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 -- Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301

ADD REPLY • link written 6.8 years ago by Pengfei Yu • 30

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD REPLY • link written 6.8 years ago by Jennifer Hillman Jackson ♦ 25k

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