[galaxy-user] Galaxy Main - Files not Found, Server Error
Hello, I am getting a resource not found error when I try to view data on the Galaxy Main Server. For some of my FASTQ Groomed files I get: The resource could not be found. File Not Found (/galaxy/main_pool/pool7/files/006/764/dataset_6764692.dat). [[Note the number before .dat changes depending on the file requested for viewing]] For some of my Map with Bowtie for Illumina files I get: Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. If you want to contact us about this error, please reference the following GURU MEDITATION: #dc57d31266564204baf90d698880401a I also have two mapping processes that have not been processed since Friday afternoon (It is Monday Morning as of this post). Any help on this matter would be great Thank you very much for your help. Nathan ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Galaxy Main - Files not Found, Server Error
Hello Nathan, The view history issue has been resolved. However, there were known failures over the weekend. These jobs should be re-run. The NGS cluster is down at this moment due to a datacenter problem, but is expected to be restored shortly. Queued jobs will process when back up as normal. Our apologies for the inconvenience, Jen Galaxy team On 9/23/13 6:02 AM, Yardley, Nathan wrote: Hello, I am getting a resource not found error when I try to view data on the Galaxy Main Server. For some of my FASTQ Groomed files I get: The resource could not be found. File Not Found (/galaxy/main_pool/pool7/files/006/764/dataset_6764692.dat). [[Note the number before .dat changes depending on the file requested for viewing]] For some of my Map with Bowtie for Illumina files I get: Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. If you want to contact us about this error, please reference the following GURU MEDITATION: #dc57d31266564204baf90d698880401a I also have two mapping processes that have not been processed since Friday afternoon (It is Monday Morning as of this post). Any help on this matter would be great Thank you very much for your help. Nathan ___ 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: 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 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] non-coding RNA annotation
Hello, If you are using the Tuxedo suite of tools, then iGenomes is one good resource. The NCBI files represent RefSeq, and RefSeq includes non-coding transcripts. NM_ = coding transcript with defined p_id, tss_id, gene_name NR_ = non-coding transcript with defined tss_id, gene_name The mm9 version of the iGenomes GTF file is already on the public Main Galaxy server at: Shared Data - Data Libraries - iGenomes More about the source is here, and is also where you can obtain mm10 (download tar locally to your computer, then just upload the genes.gtf file as a dataset): http://cufflinks.cbcb.umd.edu/igenomes.html If using other software, you have many other good choices. Most will have user groups that suggested the best fit for the tool. Reviewing the 'Gene and Gene Prediction' tracks at UCSC (http://genome.ucsc.edu) will give you an idea of those that contain non-coding, predicted, etc. transcripts. Biomart is also a great resource where Ensembl and other annotation in GTF or BED format can be reviewed and retrieved. Thanks, Jen Galaxy team On 9/22/13 7:45 PM, Hoang, Thanh wrote: Hi all, I am analyzing my small RNA sequencing data on mouse tissue. Does anyone know where to download annotation file for non-coding RNA? Thanks Thanh ___ 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: 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 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] History will not load?
Hello Maria, The issue has been resolved. Our apologies for the inconvenience, Jen Galaxy team On 9/22/13 11:55 AM, Maria Hoffman wrote: Hello, I have been having trouble with Galaxy since yesterday. I have been trying to run cuffdiff which has been waiting to run since Friday afternoon and now my history will not even load (red error message shows up). Any incite would be much appreciated. Maria ___ 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: 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 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
