Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 10.2.0
-
Labels:None
-
Story Points:1
-
Epic Link:
-
Sprint:Fall 7, Fall 5, Fall 6, Fall 7, Fall 8
Description
Situation: I've noticed an occasional error in the logs when loading GFF files in IGB. It's not currently well-understood how GFF files are being parsed in IGB which is making the debugging process for this issue difficult.
Task: Reproduce the error by following the instructions below, then investigate the IGB codebase to determine what's supposed to happen when a GFF file is parsed and loaded in IGB. For example, is the "##FASTA" section in a GFF file supposed to be parsed as the reference sequence when no genome is loaded in IGB? Please report your findings on this ticket.
- Open IGB
- Download prodigal_Lambda_phage_sequences.gff from Google Drive (may need permission - https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK?usp=drive_link)
- Without selecting a genome, drag and drop prodigal_Lambda_phage_sequences.gff into IGB.
Note: Files for testing are also available via the Loraine Lab Google Drive: https://drive.google.com/drive/folders/1MLsVItXNcskfiCAg62GFmxWc1-NR40Tx?usp=drive_link
Attachments
Issue Links
Activity
Ann Loraine - when I try to open the early access installer for Mac I'm seeing "IGB-macos-universal-main.dmg” is damaged and can’t be opened. You should move it to the Trash." Can you rebuild and redeploy the installer?
Update - I tried building installers from my branch and got the same error. I have a feeling this has to do with this warning in the build:
[WARNING] Certificate issued to Developer ID Application: Ann Loraine expired on Nov 20, 2025, 7:57 PM.
I created IGBF-4369 to address this issue. I will test this ticket using main branch jar.
PR is merged. New installers are build and deployed tp the early access section of the bioviz.org website. Ready for testing.
The situations tested above are all working and I have found no errors in the log. The only adjacent issue I found was that if the GFF file contains multiple FASTA files, the provided sequences are only loaded in IGB for the last FASTA in the file. I have created IGBF-4362 to investigate the issue.
Recommend pull request.
While loading the GFF files that contain #FASTA code, I observed a NullPointerException. Upon checking the code, I identified the cause of the exception. The issue occurs because, while reading each line in the GFF file, the code reads the end of the line as a empty string but in code it is checking for null, which is causing the NullPointerException.
The impact of this exception is that it prevents loading any tracks for files that contain #FASTA sections.
Tested on Mac using main branch jar.
Able to load GFF files with and without fasta section. No errors in log.
Closing ticket.