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JetBrains-Research / jbr

JBR Genome Browser
https://doi.org/10.1093/bioinformatics/btab376
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Support `*.gff3.gz` files as Genes annotations source #151

Open iromeo opened 3 years ago

iromeo commented 3 years ago

New CHM13 genome provides only *.gff3.gz files for genes annotations, see https://github.com/marbl/CHM13#v11. So we cannot configure genes markup for new genome in JBR

iromeo commented 3 years ago

image

Is result of opening new chm13t2t-v1.1 session after #150 workaround

iromeo commented 3 years ago

https://learn.gencore.bio.nyu.edu/ngs-file-formats/gff3-format/

iromeo commented 3 years ago

NB:

GFF3 file format is weird, e.g. here we have several transcripts with same ID ENST00000457736.1. Our GTF parser doesn't expect such usecase. We assume encode transcript is unique:

chr4    Liftoff transcript  9127305 9128897 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002011;Parent=LOFF_G0002011;transcript_id=LOFF_T0002506;transcript_name=USP17L11-1;ID=LOFF_T0002506;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9127305 9128897 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002011;transcript_id=LOFF_T0002506;transcript_name=USP17L11-0;Parent=LOFF_T0002506;ID=exon:LOFF_T0002506:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9127305 9128897 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002011;transcript_id=LOFF_T0002506;transcript_name=USP17L11-0;Parent=LOFF_T0002506;ID=CDS:LOFF_T0002506:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9132054 9133646 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002012;Parent=LOFF_G0002012;transcript_id=LOFF_T0002508;transcript_name=USP17L11-1;ID=LOFF_T0002508;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9132054 9133646 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002012;transcript_id=LOFF_T0002508;transcript_name=USP17L11-0;Parent=LOFF_T0002508;ID=exon:LOFF_T0002508:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9132054 9133646 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002012;transcript_id=LOFF_T0002508;transcript_name=USP17L11-0;Parent=LOFF_T0002508;ID=CDS:LOFF_T0002508:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9136804 9138396 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002013;Parent=LOFF_G0002013;transcript_id=LOFF_T0002510;transcript_name=USP17L11-1;ID=LOFF_T0002510;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9136804 9138396 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002013;transcript_id=LOFF_T0002510;transcript_name=USP17L11-0;Parent=LOFF_T0002510;ID=exon:LOFF_T0002510:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9136804 9138396 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002013;transcript_id=LOFF_T0002510;transcript_name=USP17L11-0;Parent=LOFF_T0002510;ID=CDS:LOFF_T0002510:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9141553 9143145 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002014;Parent=LOFF_G0002014;transcript_id=LOFF_T0002512;transcript_name=USP17L11-1;ID=LOFF_T0002512;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9141553 9143145 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002014;transcript_id=LOFF_T0002512;transcript_name=USP17L11-0;Parent=LOFF_T0002512;ID=exon:LOFF_T0002512:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9141553 9143145 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002014;transcript_id=LOFF_T0002512;transcript_name=USP17L11-0;Parent=LOFF_T0002512;ID=CDS:LOFF_T0002512:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9146303 9147895 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002015;Parent=LOFF_G0002015;transcript_id=LOFF_T0002514;transcript_name=USP17L11-1;ID=LOFF_T0002514;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9146303 9147895 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002015;transcript_id=LOFF_T0002514;transcript_name=USP17L11-0;Parent=LOFF_T0002514;ID=exon:LOFF_T0002514:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9146303 9147895 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002015;transcript_id=LOFF_T0002514;transcript_name=USP17L11-0;Parent=LOFF_T0002514;ID=CDS:LOFF_T0002514:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9151054 9152646 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002016;Parent=LOFF_G0002016;transcript_id=LOFF_T0002516;transcript_name=USP17L11-1;ID=LOFF_T0002516;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9151054 9152646 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002016;transcript_id=LOFF_T0002516;transcript_name=USP17L11-0;Parent=LOFF_T0002516;ID=exon:LOFF_T0002516:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9151054 9152646 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002016;transcript_id=LOFF_T0002516;transcript_name=USP17L11-0;Parent=LOFF_T0002516;ID=CDS:LOFF_T0002516:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9165302 9166894 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002019;Parent=LOFF_G0002019;transcript_id=LOFF_T0002521;transcript_name=USP17L11-1;ID=LOFF_T0002521;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9165302 9166894 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002019;transcript_id=LOFF_T0002521;transcript_name=USP17L11-0;Parent=LOFF_T0002521;ID=exon:LOFF_T0002521:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9165302 9166894 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002019;transcript_id=LOFF_T0002521;transcript_name=USP17L11-0;Parent=LOFF_T0002521;ID=CDS:LOFF_T0002521:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9170051 9171643 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002020;Parent=LOFF_G0002020;transcript_id=LOFF_T0002523;transcript_name=USP17L11-1;ID=LOFF_T0002523;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9170051 9171643 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002020;transcript_id=LOFF_T0002523;transcript_name=USP17L11-0;Parent=LOFF_T0002523;ID=exon:LOFF_T0002523:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9170051 9171643 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002020;transcript_id=LOFF_T0002523;transcript_name=USP17L11-0;Parent=LOFF_T0002523;ID=CDS:LOFF_T0002523:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9174798 9176390 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002021;Parent=LOFF_G0002021;transcript_id=LOFF_T0002525;transcript_name=USP17L11-1;ID=LOFF_T0002525;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9174798 9176390 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002021;transcript_id=LOFF_T0002525;transcript_name=USP17L11-0;Parent=LOFF_T0002525;ID=exon:LOFF_T0002525:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9174798 9176390 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002021;transcript_id=LOFF_T0002525;transcript_name=USP17L11-0;Parent=LOFF_T0002525;ID=CDS:LOFF_T0002525:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9184299 9185891 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002023;Parent=LOFF_G0002023;transcript_id=LOFF_T0002528;transcript_name=USP17L11-1;ID=LOFF_T0002528;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9184299 9185891 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002023;transcript_id=LOFF_T0002528;transcript_name=USP17L11-0;Parent=LOFF_T0002528;ID=exon:LOFF_T0002528:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9184299 9185891 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002023;transcript_id=LOFF_T0002528;transcript_name=USP17L11-0;Parent=LOFF_T0002528;ID=CDS:LOFF_T0002528:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9189049 9190641 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002024;Parent=LOFF_G0002024;transcript_id=LOFF_T0002530;transcript_name=USP17L11-1;ID=LOFF_T0002530;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9189049 9190641 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002024;transcript_id=LOFF_T0002530;transcript_name=USP17L11-0;Parent=LOFF_T0002530;ID=exon:LOFF_T0002530:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9189049 9190641 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002024;transcript_id=LOFF_T0002530;transcript_name=USP17L11-0;Parent=LOFF_T0002530;ID=CDS:LOFF_T0002530:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9193800 9195392 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002025;Parent=LOFF_G0002025;transcript_id=LOFF_T0002532;transcript_name=USP17L11-1;ID=LOFF_T0002532;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9193800 9195392 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002025;transcript_id=LOFF_T0002532;transcript_name=USP17L11-0;Parent=LOFF_T0002532;ID=exon:LOFF_T0002532:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9193800 9195392 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002025;transcript_id=LOFF_T0002532;transcript_name=USP17L11-0;Parent=LOFF_T0002532;ID=CDS:LOFF_T0002532:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9198551 9200143 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002026;Parent=LOFF_G0002026;transcript_id=LOFF_T0002534;transcript_name=USP17L11-1;ID=LOFF_T0002534;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9198551 9200143 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002026;transcript_id=LOFF_T0002534;transcript_name=USP17L11-0;Parent=LOFF_T0002534;ID=exon:LOFF_T0002534:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9198551 9200143 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.2;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=True;gene_id=LOFF_G0002026;transcript_id=LOFF_T0002534;transcript_name=USP17L11-0;Parent=LOFF_T0002534;ID=CDS:LOFF_T0002534:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=paralog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff transcript  9227046 9228638 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;Parent=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-1;ID=LOFF_T0002541;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff start_codon 9227046 9227048 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-0;Parent=LOFF_T0002541;ID=start_codon:LOFF_T0002541;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff exon    9227046 9228638 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-0;Parent=LOFF_T0002541;ID=exon:LOFF_T0002541:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff CDS 9227046 9228638 .   +   0   gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-0;Parent=LOFF_T0002541;ID=CDS:LOFF_T0002541:0;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A
chr4    Liftoff stop_codon  9228636 9228638 .   +   .   gene_name=USP17L11;source_gene=ENSG00000233136.3;gene_biotype=protein_coding;transcript_biotype=protein_coding;source_transcript=ENST00000457736.1;Name=USP17L11;source_gene_common_name=USP17L11;extra_paralog=False;gene_id=LOFF_G0002032;transcript_id=LOFF_T0002541;transcript_name=USP17L11-0;Parent=LOFF_T0002541;ID=stop_codon:LOFF_T0002541;alignment_id=N/A;alternative_source_transcripts=N/A;paralogy=N/A;unfiltered_paralogy=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;exon_annotation_support=N/A;intron_annotation_support=N/A;transcript_class=ortholog;transcript_modes=Liftoff;valid_start=N/A;valid_stop=N/A;proper_orf=N/A

Leads to error like:

[9 Jul 2021 01:37:37] ERROR PathExtensions Processing genes: recalculating /Users/romeo/.jbr_browser/genomes/chm13t2t-v1.1/chm13t2t-v1.1.gene_annotation.v4.gff3.json.gz: [FAILED] after 17.61 s
Caused by: ERROR IllegalStateException [START_CODON] We assume 'start_codon' (9227045) starts in CDS 5'end (9127304) but is false here. Gene: ENST00000457736.1
org.jetbrains.bio.genome.GtfReader.readTranscripts(Ensembl.kt:92)
org.jetbrains.bio.genome.Transcripts$loadTranscripts$1$transcripts$1.invoke(Transcripts.kt:287)
org.jetbrains.bio.genome.Transcripts$loadTranscripts$1$transcripts$1.invoke(Transcripts.kt:219)
org.jetbrains.bio.util.LoggerExtensionsKt.time(LoggerExtensions.kt:18)
...