Bwa And Bowtie Not Working

Question: Bwa And Bowtie Not Working

5.8 years ago by

Dear Sir/Madam Greetings, This is to inform you that i am the user of galaxy user with an user id naveedbio@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: naveedbio@yahoo.com PReduce, Reuse, Recycle, Respect - Think before you print.

bwa alignment bowtie • 882 views

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modified 5.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.8 years ago by naveed ahmed • 10

5.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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