Majiq Build error

[ARITRA DEB]

Hello, I was trying the Majiq build command for the first time. I at first created the .bam files using STAR considering 'hg19.ncbiRefSeq.gtf' and 'hg19.fa' as reference. Then I downloaded the used the 'hg19.ncbiRefSeq.gff3' for Majiq build command. Then I got this following error:

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2024-12-01 00:29:58,144 (PID:2957018) - INFO - Majiq Build v2.5.8.dev1+g9eebd1fc
2024-12-01 00:29:58,154 (PID:2957018) - INFO - Command: /users/3056262/gridware/share/python/3.10.5/bin/majiq build -c ./settings.ini /users/3056262/sharedscratch/annotation/human/refseq_hg19/hg19.ncbiRefSeq.gff3 -o ./majiq -j 8
2024-12-01 00:29:59,115 (PID:2957018) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2024-12-01 00:29:59,115 (PID:2957018) - INFO - ╠╡ ACADEMIC License applied                                     ║
2024-12-01 00:29:59,115 (PID:2957018) - INFO - ║  Name: Official Majiq Academic-only License                   ║
2024-12-01 00:29:59,115 (PID:2957018) - INFO - ║  File: majiq_license_academic_official.lic                    ║
2024-12-01 00:29:59,116 (PID:2957018) - INFO - ║  Expiration Date: Never                                       ║
2024-12-01 00:29:59,116 (PID:2957018) - INFO - ║                                                               ║
2024-12-01 00:29:59,116 (PID:2957018) - INFO - ╠╡ The academic license is for non-commercial purposes by       ║
2024-12-01 00:29:59,116 (PID:2957018) - INFO - ╠╡ individuals at an academic or not for profit institution.    ║
2024-12-01 00:29:59,116 (PID:2957018) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2024-12-01 00:29:59,459 (PID:2957018) - INFO - Parsing GFF3
Unable to unpack attribute transcript_id "NR_046018.2" not in GFF3 style
Traceback (most recent call last):
  File "/users/3056262/gridware/share/python/3.10.5/bin/majiq", line 8, in <module>
    sys.exit(main())
  File "/users/3056262/gridware/share/python/3.10.5/lib/python3.10/site-packages/rna_majiq/run_majiq.py", line 641, in main
    args.func(args)
  File "rna_majiq/src/build.pyx", line 649, in rna_majiq.src.build.build
  File "/users/3056262/gridware/share/python/3.10.5/lib/python3.10/site-packages/rna_majiq/src/basic_pipeline.py", line 13, in pipeline_run
    return pipeline.run()
  File "rna_majiq/src/build.pyx", line 657, in rna_majiq.src.build.Builder.run
  File "rna_majiq/src/build.pyx", line 671, in rna_majiq.src.build.Builder.builder
  File "rna_majiq/src/build.pyx", line 570, in rna_majiq.src.build._core_build
  File "rna_majiq/src/io.pyx", line 53, in rna_majiq.src.io.read_gff
  File "/users/3056262/gridware/share/python/3.10.5/lib/python3.10/site-packages/rna_majiq/src/gff.py", line 78, in parse_gff3
    "attributes": __parse_gff_attributes(parts[8]),
  File "/users/3056262/gridware/share/python/3.10.5/lib/python3.10/site-packages/rna_majiq/src/gff.py", line 38, in __parse_gff_attributes
    raise e
  File "/users/3056262/gridware/share/python/3.10.5/lib/python3.10/site-packages/rna_majiq/src/gff.py", line 35, in __parse_gff_attributes
    key, value = attribute.split("=")
ValueError: not enough values to unpack (expected 2, got 1)

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Please help me how to solve this problem. I also tried that gtf2gff3.pl but that's also not working maybe due to the lack of proper .cfg file.

[San Jewell]

Hello,

So it looks like there is some problem in the formatting of the gff3 file here. Can you link the place you got the gff3 file from so that I can try to reproduce this error?

Thanks,

-San