Platform for Drug Discovery


Check statuses of pipelines


Table of contents


How to check the status of running pipelines


  1. After you run a pipeline, you can check the running status of the pipeline in the 'Analysis Status' view.
  2. Update status with 'Refresh' button
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    • If you want to check current status of running pipelines, click 'Refresh' button at the head of the 'Analysis Status' view.
    • Our system does not update the status list automatically for reducing the load on servers and these network traffic.
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    • After a few minutes you run a pipeline, the pipeline status will become 'Prog.'.
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    • Oops! The record about a pipeline is disappeared. I am sure I ran a pipeline few hours ago. What is this!?
    • Please not be surprised, the current list in the 'Analysis Status' displays pipelines running only.
    • If the pipeline is end correctly or incorrectly, the record will disappear.
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    • You can change a filter with a select box on the left of 'Filter by Status'. If you choose a blank, all pipeline statuses including the statuses of pipelines already ended are displayed on the list.
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    • If you open 'Analysis Status' tab just after login the Maser, all of pipelines are displayed on the list.
    • Note that the status list is shared with your group members. Most of users join in a lonely group, this is not concerned.

Pipeline and module status list


#StatusOn 'Analysis Status'On 'Pipeline Flow View'On 'Module Flow View'Description
1Unexpected
abort
Image Abort Image Image This status means this pipeline (or this module) encounters any trouble and stop running with abnormal end status.
2Cancel
by user
Image Cancel Image Image This status means this pipeline (or this module) is canceled by a user.
3Prepare
to cancel
Image CancellingIcon is the same
with progress
Icon is the same
with progress
This status means a controller prepare to cancel this pipeline (or this module).
Usually it takes a few minutes.
4Normal end Image End Image Image This status means this pipeline (or this module) end without detection of errors.
Please remember some pipelines with this 'End' status sometimes return an invalid result because of any trouble.
5Pipeline
progressing
Image Prog. Image Image This status means this pipeline (or this module) is running on the server or waiting for other jobs.
Most of pipelines finish in a few hours or days, but there are extremely time consuming pipelines which takes several weeks or a few months.
6Prepare
to run
Image Waiting Image Image This status means a controller prepare to run this pipeline (or this module).
Usually it takes a few minutes.


Status change


    • Image
    • This is the status transition image.

In a normal case

    • 'Waiting' status finishes in a few minutes and become 'Progress' status.
    • Processing time of a 'Progress' status depends on pipeline choice, input data size and crowding level of processing servers.
    • Many pipelines finish in a few hours or a few days.
    • Some pipelines listed below takes a few weeks or several months.
      • #Kind of pipelines
        1Trinity related pipelines
        4SNP related multi sample pipelines especially HaplotypeCaller of GATK
        2TopHat-Cufflinks pipeline with many samples
        3Bisulfite related many steps pipelines
        4Blast or Blat related pipelines
        5InterProScan related annotation pipelines
    • If you encounter unusually long processing time, please contact us.

In an abnormal case

    • Sometimes running pipeline stops with unexpected 'Abort'.
    • Rarely a pipeline with normal 'End' status produces no valid result or returns some invalid data.
    • In many cases, a program outputs warning messages or error messages in an execution log.
    • If you encounter a trouble, please see about the troubleshooting.

In a cancelled case

    • If you want to cancel the pipeline, please see how to cancel pipelines.
    • The canceled pipeline generates no output.
    • If a pipeline constitute of several steps of modules and some of these modules end correctly, these modules usually produce some intermediate results.
    • You can use these intermediates for further analysis.

Module level status


    • Some pipelines constitute of several modules.
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      • In this case a pipeline "BWA and GATK + GE (human (hg37d5) only, PE)" constitute of 10 modules of step.
      • Such long pipelines take a long time to process, so many users want to check how far this pipeline proceeds.
      • You can check the progress of each module in these views.
    • #Status of modulesIn Analysis Status(in the list)In 'Analysis Status - Progress' viewIn 'Analysis Status - Result' view
      State1Running_module_1
      Waiting_module_2
      Image Image Image
      State2End_module_1
      Running_module_2
      Same as above Image Image
      State3End_module_1
      End_module_2
      Image Image Image
    • In this case a pipeline 'BWA (SE) + GE' constitute of two modules 'BWA (SE)' and 'loadBAM2ge_db (single-end)'.
    • You can see the progress per module unit in 'Analysis Status Progress' view, 'Analysis Status - Result' view and 'Module Flow View' in a 'Project Detail'.
    • What is the difference between these views is described here.

Difference of each views


    • #View nameimage examplesdescription
      1In Analysis Status(in the list) Image You can see the several statuses of analysis histories at once.
      You can stop and delete pipeline in this view.
      Input and output data search is available.
      How to open this view is described here.
      2In 'Analysis Status - Progress' view Image On this view, module level progresses about one pipeline are displayed.
      You can check the running condition here.
      You can open execution logs about these modules from this.
      How to open this view is described here.
      3In 'Analysis Status - Result' view Image On this view, data including results and modules about one pipeline are displayed.
      You can open the result and run next step analysis.
      You can also check the running condition here.
      You can open execution logs about these modules from this.
      How to open this view is described here.
      4'Module Flow View'
      in 'Project - Detail'
      Image On this view, the whole history in this project is displayed at module level.
      You can open the result and run next step analysis.
      You can also check the running condition here.
      You can open execution logs about these modules from this.
      How to open this view is described here.
      5'Pipeline Flow View'
      in 'Project - Detail'
      Image On this view, the whole history including several pipelines
      in this project is displayed at pipeline level.
      You can open the result and run next step analysis.
      You open an executed pipeline explanation page from this.
      How to open this view is described here.

How to open views about a pipeline history


    How to open 'Project - Detail', 'Pipeline Flow View' and 'Module Flow View'.

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    • Click 'Project' tab and click a Project ID of a project you interested in.
    • You can see the 'Pipeline Flow View' in 'Project - Detail'.
    • If you click 'Module Flow View' button, a 'Module Flow View' is displayed.

    How to open 'Analysis Status', 'Analysis Status - Progress' and 'Analysis Status - Result'

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    • When you click 'Analysis Status' tab, the 'Analysis Status' view is displayed.
    • Click the request ID of an analysis status record you are interested in and open an 'Analysis Status - Progress' view on which you can check the progress of this pipeline at module levels.
    • You can open an 'Analysis Status - Result' view when you click a link described 'View Result' at the right head of an 'Analysis Status - Progress' view. On this page, you can check the result data, result reports or result views of this pipeline running.