[galaxy-user] bed file error
Dear Galaxy users, I made a bed file from BAM for some farther analysis. Original BAM file could be nicely displayed in UCSC browser as well as in trackster. However, resulting bed file cannot be taken into UCSC-web page just stops loading without any message. Trackster returns message: Dataset cannot be displayed due to an error When I press view error button the page says Killed. Is there any way to fix this? Best Aleks ___ 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/
[galaxy-user] bwa and bowtie not working
Dear Sir/Madam Greetings, This is to inform you that i am the user of galaxy user with an user id naveed...@yahoo.com where as when i run NGS Mapping, for my sample with BWA or Bowtie illumina, it keep on job waiting for more than 24-48hrs, even though the time pass the application is not working. I tried with other samples even though the problem is persisting. Concerning this i request you to let me how to solve this problem. your return confirmation would be highly appreciable... with warm regards Naveed Ahmed Syed email: naveed...@yahoo.com PReduce, Reuse, Recycle, Respect - Think before you print. ___ 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/
Re: [galaxy-user] bwa and bowtie not working
Hello Naveed, The public Main Galaxy instance at https://main.g2.bx.psu.edu (usegalaxy.org) has been very busy for the last week or so. NGS jobs, such as BWA/Bowtie mapping jobs, are among those that have the longest queue times. The best strategy is to launch the most important jobs first, then leave them completely alone in the grey waiting to run state until they execute and complete. Stopping/restarting a job effectively loses your prior placement in the queue and moves the job to the end. Jobs are distributed evenly among all users. To keep this fair, and prevent misuse, when more than one account is detected for a user, all accounts are deleted. This monitoring occurs at regular, frequent intervals: http://main.g2.bx.psu.edu/static/terms.html http://wiki.galaxyproject.org/Main#User_data_and_job_quotas If your work is very urgent, then a local or cloud instance is recommended. Another public Galaxy site could also be an option if it has the tools you need, but each is different and you will need to review/test if they fit your needs. This wiki has links with more information about all of these options: http://wiki.galaxyproject.org/Big%20Picture/Choices I included a bit more information here than usual, since I know that many users are also experiencing delays, and this reply will likely be helpful for them as well. I can let you know that we are aware that this situation is not ideal and also that we are actively working on a strategy to better accommodate peak usage going forward. The public Main instance will never be able to handle all of everyone's analysis needs (world wide!), no single system ever could, but some improvements are possible and will be deployed in the near term. Take care, Jen Galaxy team On 1/24/13 5:42 AM, naveed ahmed wrote: Dear Sir/Madam Greetings, This is to inform you that i am the user of galaxy user with an user id naveed...@yahoo.com where as when i run NGS Mapping, for my sample with BWA or Bowtie illumina, it keep on job waiting for more than 24-48hrs, even though the time pass the application is not working. I tried with other samples even though the problem is persisting. Concerning this i request you to let me how to solve this problem. your return confirmation would be highly appreciable... with warm regards *Naveed Ahmed Syed * * *email: naveed...@yahoo.com * *PReduce, Reuse, Recycle, Respect - Think before you print**.* * ___ 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training 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/
Re: [galaxy-user] bed file error
Hi Aleks, The Trackster error is curious, I am not aware of any limits on the main Public Galaxy instance at https://main.g2.bx.psu.edu (usegalaxy.org). Double checking format and metadata assignments is probably a good idea. BED format is described here https://main.g2.bx.psu.edu/ and can be modified for a dataset through tools in the group 'Text Manipulation' and by clicking on the pencil icon (metadata assignments). Once format is determined to be OK, it may still be that the BED file is too large to display at UCSC in this format. Try converting to bigBED. The tool Convert Formats - BED-to-bigBed converter can be used. Best, Jen Galaxy team On 1/24/13 4:42 AM, ＳＣＨＥＩＮ ＡＬＥＫＳ wrote: Dear Galaxy users, I made a bed file from BAM for some farther analysis. Original BAM file could be nicely displayed in UCSC browser as well as in trackster. However, resulting bed file cannot be taken into UCSC-web page just stops loading without any message. Trackster returns message: Dataset cannot be displayed due to an error When I press view error button the page says Killed. Is there any way to fix this? Best Aleks ___ 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training 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/
[galaxy-user] can't download big files
Hello everyone, We have galaxy-dist-17d57db9a7c0 installed on our Mandriva 2009 64bit. There are 2 big fasta files, file A is 4.4G and file B is 3.3G which I tried to download without success. I've used browser download,including mozilla,IE and Chrome,also from suggestion by Jennifer: linux command: wget and curl -O.None of them work. For file A,the downloaded file size is always 450M(9% of total size),no matter which way ( mentionedabove )I use, For file B,the downloaded file size is 0 byte. Following is the error report by :curl -O curl: (18) transfer closed with 4294967296 bytes remaining to read Any help will be very appreciated. Allan ___ 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/
[galaxy-user] Problem Joining Two Datasets
Good Afternoon, I have been having problems with my Galaxy account. The upload issue I was having has been fixed, but now I can't seem to join two datasets. I have checked both text files that I want to join to ensure they have common columns, but there are no options available when I try the drop-down menu to select a sheet to join. I also get an error message stating Either you are not allowed to view this history or the owner of this history has not made it accessible when I first try to view one of my other saved histories, but then the files eventually appear for that saved history. Thanks, Kim ___ 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/
