Cannot clone a workspace

Hi,

I try to clone my workspace so I can import configurations but I get an error Code: 504. Also another error is "Server UnavailableFireCloud service is temporarily unavailable". I would greatly appreciate your advice.
Thank you!

Best Answers

  • kribiokribio
    Accepted Answer

    thank you for your advice and help, Sushma! The issue is fixed.

    I need to get access to a set of method configuration for CNV/SNP/indel analysis (please see the attached file). Could you please provide me access to them?
    gatk/CNV_Somatic_Pair_Workflow (pair)
    gatk/CNV_Somatic_Panel_Workflow (sample_set)
    gatk/mutect2-gatk4 (pair)
    gatk/mutect2-normal-normal (sample-set)
    gatk/mutect2-pon (sample-set)

  • SChaluvadiSChaluvadi admin
    Accepted Answer

    @kribio I believe that the methods that you listed are already publicly available for you to export to your workspace. If you search the name of the method that you want in the Method Repository, you should see them and when you export them to your workspace you should have the option to choose the snapshot of the configuration. Please let me know if this is not the intention of your question and I can try to help you further.

  • SChaluvadiSChaluvadi admin
    Accepted Answer

    @kribio I hope you were able to import the methods to your workspace. Since we haven't heard from you, this ticket will be closed - as always feel free to reply back with any new questions!

Answers

  • kribiokribio Member

    Would be a problem with my billing account "nci-kgiannikou-bi-org" ?

  • kribiokribio Member

    Hi,

    I have another workspace entitled "broad-genomics-delivery/Kwiatkowski_Angiomyolipomas" and I have access only as a reader. It seems that you are the workspace owner is "[email protected]". Would be possible please to provide me access as an owner so I can clone the workspace and import the method configurations?
    Thank you!

    Best,
    Krinio

  • abaumannabaumann Broad DSDEMember, Broadie ✭✭✭

    You don't need owner access in order to clone - just reader or above. What you do need however is access to a project to clone into. When you try to clone, does it show a list of projects to clone into or do you see none (or maybe a grayed out Clone button)?

  • kribiokribio Member

    I have access to workspace/project, but as I said above when I try to clone it. I cannot. I get an Request Timed out error Code: 504. Also another error is "Server UnavailableFireCloud service is temporarily unavailable".

  • kribiokribio Member

    I have two worspaces. The one does not have large amount of data, the other one has a larger dataset but still not that huge. I would greatly appreciate your feedback!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @kribio - Can you double check to see if the workspace finished cloning despite the 504 error - sometimes it will have finished cloning despite the timeout. If this is not the case and it was unsuccessful in cloning, it looks like the workspace broad-genomics-delivery/Kwiatkowski_Angiomyolipomas has a very large amount of metadata potentially resulting in the 504 error. A workaround for this could be to download all the metadata from the workspace as a tsv and then upload it into an empty workspace in smaller chunks. This would do a similar action to cloning but you might lose some components like workspace associated method configurations. Since you are doing the upload in smaller pieces, there is a smaller chance of a timeout.

  • kribiokribio Member
    edited October 2018

    @SChaluvadi When I use another project name entitled "workshop-cptac" which seems to be another billing account, I can properly clone the workspace. But when I use my billing account "nci-kgiannikou-bi-org", I get the above mentioned errors and I cannot clone the workspace. I do not have large amount of metadata. The issue seems to be related to my billing account.
    Please advise.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @kribio We see a lot of errors from google that say "The project to be billed is associated with an absent billing account.". Can you double check the billing account details to make sure that has been set up correctly. The request times out because we keep retrying the failures, which are unable to succeed and eventually lead to the 504 error.

  • kribiokribio Member

    @SChaluvadi it seems that we set up another billing account/e-mail acount which was never activated. All my files (bam files etc) are in a workspace set up with another e-mail account. How could I fix this issue? With whom should I talk? Thank you!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @kribio - If I understand correctly, you would like to change the billing account associated with the workspace that contains all your files to a new billing account (the one that was previously not activated). If this is the case, here is a tutorial that lists the steps on how to do that under the "How do I assign my new billing account to my existing workspaces?". Please let me know if this is not what you are trying to do and I can further assist you!

  • kribiokribio Member

    Hi @SChaluvadi , what I want to do is to keep the current workspace and activate the e-mail account associated with this workspace that contains all your files as a new billing account.

  • kribiokribio Member

    @SChaluvadi thank you for all information provided! it seems that the only way is to make a new Google billing account since I do not have administrator privileges and the system doesn’t not allow me to change payments contacts for the previous account.

  • kribiokribio Member
    Accepted Answer

    thank you for your advice and help, Sushma! The issue is fixed.

    I need to get access to a set of method configuration for CNV/SNP/indel analysis (please see the attached file). Could you please provide me access to them?
    gatk/CNV_Somatic_Pair_Workflow (pair)
    gatk/CNV_Somatic_Panel_Workflow (sample_set)
    gatk/mutect2-gatk4 (pair)
    gatk/mutect2-normal-normal (sample-set)
    gatk/mutect2-pon (sample-set)

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    Accepted Answer

    @kribio I believe that the methods that you listed are already publicly available for you to export to your workspace. If you search the name of the method that you want in the Method Repository, you should see them and when you export them to your workspace you should have the option to choose the snapshot of the configuration. Please let me know if this is not the intention of your question and I can try to help you further.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    Accepted Answer

    @kribio I hope you were able to import the methods to your workspace. Since we haven't heard from you, this ticket will be closed - as always feel free to reply back with any new questions!

  • kribiokribio Member

    @ Schaluvadi yes, the issue to import the methods to my workspace was solved. Thank you! I try now to review the variant calls in IGV. I try to import the URL path into IGV (copy and paste from my workspace in Firecloud), but I get the error "You must log in to access the files". I have connected to Broad through VPN and my firecloud worspace is accessible ( I am the owner), but still I get the same error and I cannot review the variants. Any advice? Much appreciate it!

  • kribiokribio Member

    @kribio said:
    @ Schaluvadi yes, the issue to import the methods to my workspace was solved. Thank you! I try now to review the variant calls in IGV. I try to import the URL path into IGV (copy and paste from my workspace in Firecloud), but I get the error "You must log in to access the files". I have connected to Broad through VPN and my firecloud worspace is accessible ( I am the owner), but still I get the same error and I cannot review the variants. Any advice? Much appreciate it!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @kribio My apologies! I don't know how I missed your questions but I will look into it and get back to you asap!

  • kribiokribio Member
    edited December 2018

    Thank you @SChaluvadi! Much appreciate it! Best

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    edited December 2018

    @kribio Can you confirm that you are entering the path to the filr with the "gs://" prefix? If this is the case, can you share the URL that you are attempting to load into IGV? Can you also confirm that the file you are trying to load lives in a Google bucket associated with your workspace? Or is it an external bucket that is not associated with your workspace?

  • kribiokribio Member
    edited December 2018

    An example of the path I try to upload in IGV is here: "gs://fc-27297f76-71ac-4d76-b3dc-cf8bd2b61f06/Kwiatkowski_PeComa_Cohort_WES/RP-1181/Exome/965-2307-T/v3/965-2307-T.bam".
    It seems to be right but it shows up in IGV..

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @kribio I will take another look and see if we can figure out why this is not working.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    edited December 2018

    @kribio Are you using IGV within FC or is it an external instance of IGV? If it is external can you re-login with Google inside the IGV?

    Post edited by SChaluvadi on
  • kribiokribio Member

    It is external connection. I have installed IGV on my Mac. It does not work...

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @kribio Thanks for being patient while we troubleshoot. Can you follow the Setup steps in this link to make sure that your local instance of IGV has "Google Access" checked and then test to see if you can load your BAM file from your cloud storage?

  • kribiokribio Member

    Thank you @SChaluvadi !The issue is fixed! Best wishes for a happy holiday season

Sign In or Register to comment.