Status Terminology

ā€‹

On the ENCODE Portal, statuses are used to indicate the processing phase of a specific object. In general only objects that have been assigned a status of 'released', 'revoked', or 'archived' can be viewed by the general public. Objects that have been assigned a status of 'deleted' or 'replaced' can not be viewed by the general public and can only be viewed by admins.


 

Experiment statuses

 

 
  • started - This assay has been started.  There is at least one replicate with submitted FASTQs. 
  • submitted - This assay has all of its associated fastq’s submitted to the DCC.
  • ready for review - The submitting laboratory has submitted all data associated with this assay and feels that it is ready to be reviewed. In order to transition to "ready for review" from "submitted", the submitting laboratory changes the status to signal to the DCC that this assay is a candidate for release.
  • released - This assay is released to the public. In order to transition to "released" from "ready for review" there should be no red audits, the submitting lab and the data wrangler should be satisfied with the metadata and all orange audits should be explained.
  • archived - This assay was not revoked for being faulty, however, in most cases there is more current data available using more current methods.  These experiments should have superseded_by value for the experiment that replaces them.  Ideally, the reason for archiving will be found in the submitter_comments.
  • revoked - This assay was deemed erroroneous or significantly below standards after it had been released. A revoked experiment should have its associated files and libraries revoked as well.  Ideally, the reason for revoking will be found in the submitter_comments.
  • replaced - This assay has been merged with another experiment and the experiments should now share accessions.  This is usually the case when multiple objects were created for the same experiment.  This state is special because the accession of a "replaced" object is available for reuse and should be given to the new merged experiment as an alternate_accession.
  • deleted - This assay was removed before it was released. Information may possibly be found in the notes field.

 

File statuses

 

 
  • uploading - The file is uploading to the Amazon S3 bucket and awaiting format and uniqueness checks.
  • upload failed - The file failed to upload to the Amazon S3 bucket.
  • content error - The file failed format check or uniqueness checks.
  • in progress - The file has successfully uploaded and passed format and uniqueness checks.
  • replaced - This file object is merged with another.  Either the files are duplicates in (content) md5sum or the format was found faulty and replaced with a remedied file.  Replaced is a special status because it allowes the accession to be reused.  The replacing file should now have this accession in alternate_accessions.
  • deleted - This file was removed before it was released.
  • released - This file is released to the public. 
  • archived - This file is considered superfluous or outdated.  There is nothing wrong with the file, but it is considered an extra to the experiment.
  • revoked - This file was deemed erroroneous or significantly below standards after it had been released. A revoked file should have some reason for revoking in the notes field.                         

 

Internal statuses

 

 

  • unreviewed - Experiment metadata and data have not yet been evaluated.
  • unrunnable - The data do not meet the criteria (format, quality, etc.) to be run through the appropriate pipeline.
  • no available pipeline - The ENCODE Consortium does not currently have a uniform processing pipeline for this data type.
  • requires lab review - Metadata and data have been reviewed and the experiment requires attention from the submitting lab before processing.
  • pipeline ready - Metadata and data have been reviewed and the experiment is considered ready for processing through the appropriate pipeline.
  • processing - Data is currently running through the appropriate pipeline.
  • pipeline error - Pipeline run was started but failed for a specific reason which is noted in pipeline_error_detail.
  • pipeline completed - Data was successfully run through the appropriate pipeline to completion.
  • release ready - The ENCODE DCC has approved this data for release.

Permissions statuses

 


 

Basic Object Statuses

 

 
 
 

Updated: January 2018