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    Kevin
    @klkeys
    FWIW, I didn’t know what else to do, so I played “did you reboot the computer” by disabling and reenabling the ECS compute environment and suddenly things work again :eyes: I’m still curious to know what caused this error
    Paolo Di Tommaso
    @pditommaso
    never seen this before, if it's happening again worth investigating with AWS supprot what's the root cause
    Jeffrey Massung
    @massung
    Is there a way - from within a process block to determine if -with-tower was passed along or not?
    Jeffrey Massung
    @massung
    To be more precise, I guess I care whether or not it's being run locally. I'd like to use the containerOptions only if running locally
    Moritz E. Beber
    @Midnighter
    How about managing that with a profile?
    1 reply
    Paolo Di Tommaso
    @pditommaso
    indeed, that info is not exposed, pipeline should depend on tower execution
    Julianus Pfeuffer
    @jpfeuffer
    Hi! Is it currently possible to setup e.g. a SLURM compute environment in Tower if the head node is behind an SSH gateway/tunnel?
    (disclaimer: also shortly asked on nf-core Slack)
    James Fellows Yates
    @jfy133:matrix.org
    [m]

    I tried looking in the Nextflow documentation nor searching here, but I didn't see anything along these lines: is there some hidden/secret flag or something that allows you turn on/off sending run 'tracking' to an organisation (vs. your own personal account?)

    In other words: generally I want to monitor my runs in a workspace shared with other people in my department, but sometimes if I'm running a 'sensitive' project, I want to keep a given run so that I can monitor in my personal workspace. Is there such a functioanlity to switch this in on and off per run?

    1 reply
    Julianus Pfeuffer
    @jpfeuffer
    Another question that I have is if nf-tower (SLURM connector) can start the orchestrating nextflow job directly on the head node? I have two different clusters where the admins specifically want me to run long-running orchestrating jobs on the node directly.
    Paolo Di Tommaso
    @pditommaso
    nope, tower does not allow running in the login node
    Thomas Sandmann
    @thomas_sandmann_twitter
    Hi! I am using AWS S3 for the result directory - but the target bucket is owned by another AWS account. The bucket is set up to accept the files from the AWS account that runs nextflow, and the objects are written without a problem. But the objects are still owned by the nextflow account, e.g. not the owner of the destination bucket. It seems that AWS S3 support automatically assigning object ownership to the bucket owner (see: bucket-owner-full-control ) by specifying the "bucket-owner-full-control" ACL in the request. For example, in the AWS CLI this could be done by including the "--acl bucket-owner-full-control" command line argument. Is it possible to configure nextflow's s3 backend to include this option? Or perhaps there is an even better solution to deliver files into S3 buckets in another account? Many thanks!
    1 reply
    Marc Serret
    @MarcSerretCRG
    Hi everyone. I'm using the nf-tower API to retrieve the workflows to get the status (/workflow endpoint). My question is what determines the lenght of the response, the date range. Thanks you
    Paolo Di Tommaso
    @pditommaso
    the number of returned records is controlled via the max params. There's no data filter at this stage
    Marc Serret
    @MarcSerretCRG
    I see, thanks you
    G Fedewa
    @harper357
    I am having trouble launching pipelines when I select my organizations workspace. In other words, when I select a pipeline from my Launchpad, I select a different Workspace. It gives me the error "Http failure response for https://tower.nf/api/workflow/launch?workspaceId=<>: 403 Forbidden". Is there some setting I need to change/add to let me launch pipelines in different workspaces?
    Ido Tamir
    @idot
    Hello, since yesterday i get Unexpected response code 400 for request https://api.tower.nf/trace/create . I am now desperately trying to not use tower: I unset TOWER_ACCESS_TOKEN and don't use -with-tower ( version 21.04.1) but its always the same error
    Ido Tamir
    @idot
    Now it started and I get Unexpected response code 400 for request https://api.tower.nf/trace/MDfCwae87pju7/progress
    Error ID: 1e1h4Ib3Fd14YYvCOdQHLP
    Ido Tamir
    @idot
    Starting again I get Unexpected response code 400 for request https://api.tower.nf/trace/create and the workflow does not run at all
    Ido Tamir
    @idot
    tower seems to work again
    Ido Tamir
    @idot
    tower was active because i had it in ~/.nextflow/config
    Jeffrey Massung
    @massung

    I have a workflow I’m building for which some of the early processes take considerable CPU/memory to run, so I’m forced to run workflow on AWS (no biggie). So far, I’ve been slowly adding steps and relaunching the same pipeline with resume and it’s all working great.

    However, the time spent provisioning EC2 instances for later processes that don’t require much CPU/memory is frustrating. I could (in theory) just run those processes locally while I build out the rest of the workflow.

    Is it possible for me to do something like copy the work/scratch directory from S3 to my local work/ directory and -resume the workflow running locally? I’ve tried the naive way of doing it, but it won’t detect that the workflow has already successfully run some of the processes. Are there any logs/files I can just manually edit - or pass something on the CLI - to get it to do so?

    Paolo Di Tommaso
    @pditommaso
    Ec2 provisioning time is something we can do little
    however, best practice for building NF pipelines consists of doing in your local computer with a small test dataset and then deploy on AWS
    this is crucial for testing and troubleshooting
    Combiz Khozoie
    @combiz
    Hi, is there a way to obtain a tabulated version of the nf-tower cloud cost estimates for all tasks? It's possible to see the 'cost' field when clicking on a single task; however, we need to aggregate the predicted costs for hundreds of tasks.
    Paolo Di Tommaso
    @pditommaso
    Hi, currently it's only possible via workflow/tasks API endpoint
    Combiz Khozoie
    @combiz
    Perfect, thanks
    Combiz Khozoie
    @combiz
    Does this endpoint paginate the results? I seem to obtain only the first 10 tasks. (https://tower.nf/openapi/index.html#get-/workflow/-workflowId-/tasks)
    Combiz Khozoie
    @combiz
    Filed an issue.. seqeralabs/nf-tower#325
    rmeinl
    @rmeinl
    Hey! I'm looking to run a workflow in nf-tower that accesses a Postgres DB. When I run it locally I store the credentials in the nextflow config. Is there a way to securely store them somewhere in nf-tower to initiate my workflow?
    Danilo Imparato
    @daniloimparato

    Hi all!

    Super hyped to be trying tower. The user experience has been impressive so far. 🚀

    However, I could not get even a single workflow to execute on the Google Life Sciences backend.

    I have set up this very minimal example below. Can someone please enlighten me what might be wrong?

    #!/usr/bin/env nextflow
    
    nextflow.enable.dsl=2
    
    process echo_remote_file_content {
    
      container = "docker.io/taniguti/wf-cas9:latest"   // this does not work :(
      // container = "docker.io/docker/whalesay:latest" // this works!! both images are public
    
      input: path remote_file
    
      output: stdout emit: cat
    
      script: "cat $remote_file"
    }
    
    workflow {
      echo_remote_file_content(params.remote_file)
      println echo_remote_file_content.out.cat.view()
    }

    This is the error report:

    Error executing process > 'echo_remote_file_content'
    
    Caused by:
      Process `echo_remote_file_content` terminated with an error exit status (9)
    
    Command executed:
      cat str.txt
    
    Command exit status:
      9
    
    Command output:
      (empty)
    
    Command error:
      Execution failed: generic::failed_precondition: while running "nf-6f1c929e312542a7ee1699175d05f753-main": unexpected exit status 1 was not ignored
    
    Work dir:
      gs://sensitive-bucket-name/scratch/1uc7mIoqwEIZV0/6f/1c929e312542a7ee1699175d05f753
    
    Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
    Paolo Di Tommaso
    @pditommaso
    hello please open an issue including the "Nextflow console output" and "Nextflow log file" (you can find in the Exection logs panel)
    Danilo Imparato
    @daniloimparato
    Done, thanks! @pditommaso
    Vlad Kiselev
    @wikiselev

    Hi All, I am trying to start a pipeline using NF-tower on AWS batch, however the head job (nextflow itself) fails to start... I get:

    Status reason
    Task failed to start

    And also

    CannotStartContainerError: Error response from daemon: OCI runtime create failed: runc did not terminate successfully: unknown

    The image that it is trying to start is:

    public.ecr.aws/seqera-labs/tower/nf-launcher:21.08.0-edge

    Has anyone had this before?

    Vlad Kiselev
    @wikiselev

    there was several fails as described before, and now at the latest attempt it managed to start but this is the log from the nextflow container:

    /usr/local/bin/nf-launcher.sh: line 25: /usr/bin/tee: Cannot allocate memory
    /usr/local/bin/nf-launcher.sh: line 71:    12 Killed                  aws s3 sync --only-show-errors "$NXF_WORK/$cache_path" "$cache_path"
    Failed to launch the Java virtual machine
    NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:
     JAVA_CMD: /usr/lib/jvm/java-11-amazon-corretto/bin/java
     NXF_OPTS: 
    /usr/local/bin/nf-launcher.sh: line 43:    30 Killed                  [[ "$NXF_WORK" == s3://* ]]

    obviously something is very wrong, but I feel I've checked everything and not sure where else to look...

    Arghhh, ok, please ignore all of the above - I specified 8MB of RAM instead of 8Gb!..
    Paolo Di Tommaso
    @pditommaso
    :smile:
    Vlad Kiselev
    @wikiselev
    Is that normal that the hosted tower server has API request problems. Seeing a lot of Oops... Unable to process request - Error ID: Ac7sDnGIoR0r7IKFYLkbR both on the website and in NF logs
    Vlad Kiselev
    @wikiselev
    And also this: Http failure response for https://tower.nf/api/orgs: 502 Bad Gateway, can't really use it at the moment
    Combiz Khozoie
    @combiz
    I'm finding that the tasks API (https://tower.nf/openapi/index.html#get-/workflow/-workflowId-/tasks) is returning info for a previous run of the same data (-resume was not used). Any ideas?
    Yes, @wikiselev, same here. Hopefully back up soon!
    Thankfully downtime is v. rare, the first time I've seen it, so definitely not normal. :)
    Vlad Kiselev
    @wikiselev
    good to know! I used for the first time yesterday and was super excited, but can't do anything today :-)
    probably an API service requires a restart
    Paolo Di Tommaso
    @pditommaso
    um, let me check
    @wikiselev give another try please
    1 reply