Assistance Needed with MAJIQ Build Error

[ashwaq...@gmail.com]

Dear MAJIQ Support Team,

I hope this email finds you well. I am reaching out to seek assistance with an issue I encountered while running MAJIQ. Below are the details:

1. Issue Description:

   • I am attempting to build splice graphs using majiq build with a custom GFF3 file (Homo_sapiens.GRCh38.113_fixed.gff3) on Biowulf. Despite validating the file using gt gff3validator(which confirmed it is a valid GFF3), I receive the following error when running the command:

     Error, transcript (record.type=transcript) doesn't have an attribute recognized for inferring transcript_id (ID) or transcript parent (Parent).

   • The specific command I used is:

     majiq build -c /path/to/majiq_build_config.ini -o ./build/ -j 30 /path/to/Homo_sapiens.GRCh38.113_fixed.gff3

2. Steps Taken:

   • I have edited the GFF3 file to include ID= for transcript identifiers and Parent= for exon-parent relationships.
   • The file passed validation using gt gff3validator.

3. Environment Details:

   • Platform: Biowulf
   • MAJIQ Version: 2.4
   • Custom GFF3 file generated from Ensembl’s GTF using gffread.

4. Additional Context:

   • I’ve reviewed the documentation and ensured the build configuration is correct, including paths to BAM files and the GFF3 file.

Could you please advise if there’s an additional step required to prepare the GFF3 file or if I am missing any specific formatting for MAJIQ? I would greatly appreciate your guidance in resolving this issue.

Thank you very much for your time and support!

Best regards,
Ashwaq

[San Jewell]

Hi Ashwaq,

Would you be able to provide a link to the exact gff3 file where it's hosted? It's possible there is a strange situation that we have not encountered before while parsing other gff3 files, and I'd better be able to do a test run and determine where the problem occurs in depth.

Thanks!

-San