Files Submission

How to Submit Files

Hint

• See ENA assembly submission file types documentation for the types of files that can be submitted in COPO for assembly submissions.

• See ENA read submission file types documentation for the types of files that can be submitted in COPO for read submissions.

See also

• How to Delete Files

• How to check if data files for metadata submissions have been processed after upload to ENA

• Files FAQ

• How to Submit Reads

• How to Submit Assemblies

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Accessing the Files’ Web Page

The Files’ web page can be accessed from the Components button associated with a profile [1].

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Use Components’ Button to Navigate to Files’ Web Page

Click the button associated with a profile. Then, click the from the popup menu displayed as shown below:

Genomics Profile Components: Files component button

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Submit Files from your Local (Computer) System

Note

The total maximum file size that can be uploaded from your local (computer) system is around 2 GB. If you have a file larger than 2 GB or have multiple files whose combined total size exceeds 2 GB, please submit the file(s) via the terminal.

1. Click the button on the Files web page to add a new file by browsing your local file system

   

   Files web page: ‘Add new file by browsing local file system’ button

   
   

2. An Upload File dialogue is displayed. Click the Upload button to choose a file from your local system.

   

   Files submission: Upload File dialogue

   
   

3. The new file(s) will be displayed on the Files web page after a successful submission.

   

   Files submission: Files’ web page displaying the uploaded file(s)

   
   
   

   Hint

   To add more files from your local system, click the button (once files have been submitted to the profile) as an alternative to clicking the button.

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Submit Files via the Terminal

1. Click the button on the Files web page to add a new file from a cluster via the terminal.

   

   Files web page: ‘Add new file via terminal’ button

   
   

2. A Move Data dialogue is displayed. Follow the instructions displayed then, click the Process button to submit the file(s) to the profile.

   

   Files submission: Move Data dialogue

   

   Input $ ls - F1 command in the terminal

   
   

   

   Move Data dialogue: Input the filename(s) returned after having ran the $ ls - F1 command in the terminal. Then, click the Process button.

   
   

   

   Move Data dialogue: Command outputted after having clicked command in the Process button. Download the command displayed.

   The downloaded file will have unknown or download as the file name depending on the browser you are using.

   
   

   

   Paste the copied command in the terminal

   Alternatively, you can make the downloaded file executable then, run the file in the directory where the files are located:

   
   

   
   

3. The new file(s) will be displayed on the Files web page after a successful file submission via the terminal i.e. after the command has been executed successfully in the terminal.

   

   Files submission: Files’ web page displaying the uploaded file(s)

   
   
   

   Hint

   To add more files via the terminal, click the button (once files have been submitted to the profile) as an alternative to clicking the button.

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How to Delete Files

Click the desired file from the list of files displayed on the Files’ web page. Then, click the Delete button (located in the top-right corner of the table) as shown below:

File deletion: Click the “Delete” button to remove the highlighted file from the profile

File deletion: File has been deleted

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Checking ENA File Processing Status

Note

A reads, annotations or assembly submission must be completed before the file(s) can be uploaded to ENA (European Nucleotide Archive).

After completing a reads, annotations or assembly submission and associating file(s) with it in COPO during the submission process, the file(s) are submitted to ENA (European Nucleotide Archive).

The upload status from COPO to ENA is displayed in the ENA FILE UPLOAD STATUS column. This status shows whether the file(s) have been successfully uploaded to ENA after submission.

The file processing status of the file(s) uploaded to the ENA can be checked in the column, ENA FILE PROCESSING STATUS, on the reads, sequence annotations or assembly web page. This status indicates that ENA is verifying and validating the submitted file(s).

The ENA FILE PROCESSING STATUS column is highlighted with a red rectangle border in the image below:

Hint

• Rows with a status of File archived: PUBLIC or File archived : PRIVATE or in a green colour indicate that the file(s) have been successfully submitted to ENA.

• Rows with a status of Invalid file integrity: PRIVATE or in a red colour indicate that the file(s) failed to be submitted to ENA.

• According to ENA, accessions that follow the format, ERZxxxxxxx refer to a private accession number that is not visible outside ENA.

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Footnotes

[1]

Also known as COPO profile. See: COPO profile or work profile.