Error while converting GFF file to GTF using AGAT

Question

[Genetics]

Hi I am trying to convert a gff file to gtf file which I want to use for STAR. I tried AGAT(latest version) to convet but it gives me a series of error(mailny tow types) .I have attached the error and alsobelow .Could you please help me to solve this error. What I have to add and which jason file I have to add?

ERROR FILE:

INPUT GFF3file:

M_inter_1389_PBcR_C01 ena_exon biological_region 647 1158 . - . external_name=BQ2448_39%3B FMSP01000003.1:exon:complement(647..1158);logic_name=ena_exon
M_inter_1389_PBcR_C01 ena_exon biological_region 1233 1696 . - . external_name=BQ2448_39%3B FMSP01000003.1:exon:complement(1233..1696);logic_name=ena_exon
M_inter_1389_PBcR_C01 ena_exon biological_region 1779 1963 . - . external_name=BQ2448_39%3B FMSP01000003.1:exon:complement(1779..1963);logic_name=ena_exon
M_inter_1389_PBcR_C01 ena_exon biological_region 2026 2067 . - . external_name=BQ2448_39%3B FMSP01000003.1:exon:complement(2026..2067);logic_name=ena_exon
M_inter_1389_PBcR_C01 ena_exon biological_region 2129 2331 . - . external_name=BQ2448_39%3B FMSP01000003.1:exon:complement(2129..2331);logic_name=ena_exon
M_inter_1389_PBcR_C01 ena_exon biological_region 2457 2499 . - . external_name=BQ2448_39%3B FMSP01000003.1:exon:complement(2457..2499);logic_name=ena_exon
M_inter_1389_PBcR_C01 ena_exon biological_region 2579 2897 . - . external_name=BQ2448_39%3B FMSP01000003.1:exon:complement(2579..2897);logic_name=ena_exon
M_inter_1389_PBcR_C01 ena_exon biological_region 3343 4159 . + . external_name=BQ2448_40%3B FMSP01000003.1:exon:3343..4159;logic_name=ena_exon
M_inter_1389_PBcR_C01 ena gene 3343 6920 . + .

[Ram]

I've fixed your title, formatted your post and fixed your tags. Next time, please put in more effort into presenting your problem better.

[Genetics]

Thank you

Answer 1

[Juke34]

Hi,

The first problem is "biological_region" feature does not have an ID => It's fine AGAT will add one automatically.

The second problem is "supercontig" not taken in account => AGAT will skip that feature and not report it into the output. If you wish to inform AGAT to keep that feature see: https://agat.readthedocs.io/en/latest/troubleshooting.html#agat-throws-features-out-because-the-feature-type-is-not-yet-taken-into-account
Modify the feature_levels.yaml file and add the supercontig as level1 feature with the standalone value.