Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/8e8d9bf3f9ddeb142b51efc10e9b4a/fi_workdir/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/55af4273a9f47ed10ab82cf8fd49fd/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/55af4273a9f47ed10ab82cf8fd49fd/.command.run ==> STAGING COMPLETE (3 inputs) Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file ------------------------------------------------------------------------------ | Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0 | | https://github.com/NBISweden/AGAT | | National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se | ------------------------------------------------------------------------------ ------ Start parsing ------ -------------------------- parse options and metadata -------------------------- => Accessing the feature_levels YAML file Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file => Attribute used to group features when no Parent/ID relationship exists (i.e common tag): * locus_tag * gene_id => merge_loci option deactivated => Machine information: This script is being run by perl v5.32.1 Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/ Operating system being used: linux => Accessing Ontology No ontology accessible from the gff file header! We use the SOFA ontology distributed with AGAT: /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo: 4 root terms, and 2596 total terms, and 1516 leaf terms Filtering ontology: We found 1861 terms that are sequence_feature or is_a child of it. --------------------------------- parsing file --------------------------------- => Number of line in file: 2700 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 2700 => Number of feature type (3rd column): 2 * Level1: 0 => * level2: 0 => * level3: 2 => CDS exon * unknown: 0 => =>Check because only level3 features: * Number of feature with Parent attribute:0 * Number of feature with a common attribute:2700 => Some common attributes and some Parent attributes missing. /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want... see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl). => Version of the Bioperl GFF parser selected by AGAT: 2 ------ End parsing (done in 1 second) ------ ------ Start checks ------ ---------------------------- Check1: feature types ----------------------------- ----------------------------------- ontology ----------------------------------- All feature types in agreement with the Ontology. ------------------------------------- agat ------------------------------------- AGAT can deal with all the encountered feature types (3rd column) ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check2: duplicates ------------------------------ None found ------------------------------ done in 0 seconds ------------------------------- -------------------------- Check3: sequential bucket --------------------------- Nothing to check as sequential bucket! ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check4: l2 linked to l3 ---------------------------- L1 and L2 created: DIS3L2--PTMA HAVANA gene 1001 36018 . + . FI_gene_label "DIS3L2^ENSG00000144535.20" ; ID "DIS3L2--PTMA^DIS3L2^ENSG00000144535.20" ; ccdsid "CCDS58752.1" ; exon_id "ENSE00001795680.1" ; exon_number 2 ; gene_id "DIS3L2--PTMA^DIS3L2^ENSG00000144535.20" ; gene_name DIS3L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153385.3" ; havana_transcript "OTTHUMT00000330974.1" ; hgnc_id "HGNC:28648" ; level 2 ; orig_coord_info "chr2,232014928,232014979,+" ; protein_id "ENSP00000273009.6" ; tag basic CCDS ; transcript_id "DIS3L2--PTMA^ENST00000273009.10" ; transcript_name "DIS3L2-201" ; transcript_support_level 2 ; transcript_type protein_coding DIS3L2--PTMA HAVANA mRNA 1001 36018 . + . FI_gene_label "DIS3L2^ENSG00000144535.20" ; ID "DIS3L2--PTMA^ENST00000273009.10" ; Parent "DIS3L2--PTMA^DIS3L2^ENSG00000144535.20" ; ccdsid "CCDS58752.1" ; exon_id "ENSE00001795680.1" ; exon_number 2 ; gene_id "DIS3L2--PTMA^DIS3L2^ENSG00000144535.20" ; gene_name DIS3L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153385.3" ; havana_transcript "OTTHUMT00000330974.1" ; hgnc_id "HGNC:28648" ; level 2 ; orig_coord_info "chr2,232014928,232014979,+" ; protein_id "ENSP00000273009.6" ; tag basic CCDS ; transcript_id "DIS3L2--PTMA^ENST00000273009.10" ; transcript_name "DIS3L2-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: DIS3L2--PTMA HAVANA gene 40640 45631 . + . FI_gene_label "PTMA^ENSG00000187514.17" ; ID "DIS3L2--PTMA^PTMA^ENSG00000187514.17" ; ccdsid "CCDS42833.1" ; exon_id "ENSE00001901103.1" ; exon_number 1 ; gene_id "DIS3L2--PTMA^PTMA^ENSG00000187514.17" ; gene_name PTMA ; gene_type protein_coding ; havana_gene "OTTHUMG00000153810.3" ; havana_transcript "OTTHUMT00000332553.1" ; hgnc_id "HGNC:9623" ; level 2 ; orig_coord_info "chr2,231708707,231708751,+" ; protein_id "ENSP00000344547.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "DIS3L2--PTMA^ENST00000341369.11" ; transcript_name "PTMA-201" ; transcript_support_level 1 ; transcript_type protein_coding DIS3L2--PTMA HAVANA mRNA 40640 45631 . + . FI_gene_label "PTMA^ENSG00000187514.17" ; ID "DIS3L2--PTMA^ENST00000341369.11" ; Parent "DIS3L2--PTMA^PTMA^ENSG00000187514.17" ; ccdsid "CCDS42833.1" ; exon_id "ENSE00001901103.1" ; exon_number 1 ; gene_id "DIS3L2--PTMA^PTMA^ENSG00000187514.17" ; gene_name PTMA ; gene_type protein_coding ; havana_gene "OTTHUMG00000153810.3" ; havana_transcript "OTTHUMT00000332553.1" ; hgnc_id "HGNC:9623" ; level 2 ; orig_coord_info "chr2,231708707,231708751,+" ; protein_id "ENSP00000344547.7" ; tag basic appris_alternative_1 CCDS ; transcript_id "DIS3L2--PTMA^ENST00000341369.11" ; transcript_name "PTMA-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: EIF2AK1--DGKB HAVANA gene 1001 19804 . + . FI_gene_label "EIF2AK1^ENSG00000086232.13" ; ID "EIF2AK1--DGKB^EIF2AK1^ENSG00000086232.13" ; ccdsid "CCDS5345.1" ; exon_id "ENSE00001634941.3" ; exon_number 1 ; gene_id "EIF2AK1--DGKB^EIF2AK1^ENSG00000086232.13" ; gene_name EIF2AK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090689.15" ; havana_transcript "OTTHUMT00000207373.4" ; hgnc_id "HGNC:24921" ; level 2 ; orig_coord_info "chr7,6058966,6059083,-" ; protein_id "ENSP00000199389.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2AK1--DGKB^ENST00000199389.11" ; transcript_name "EIF2AK1-201" ; transcript_support_level 1 ; transcript_type protein_coding EIF2AK1--DGKB HAVANA mRNA 1001 19804 . + . FI_gene_label "EIF2AK1^ENSG00000086232.13" ; ID "EIF2AK1--DGKB^ENST00000199389.11" ; Parent "EIF2AK1--DGKB^EIF2AK1^ENSG00000086232.13" ; ccdsid "CCDS5345.1" ; exon_id "ENSE00001634941.3" ; exon_number 1 ; gene_id "EIF2AK1--DGKB^EIF2AK1^ENSG00000086232.13" ; gene_name EIF2AK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090689.15" ; havana_transcript "OTTHUMT00000207373.4" ; hgnc_id "HGNC:24921" ; level 2 ; orig_coord_info "chr7,6058966,6059083,-" ; protein_id "ENSP00000199389.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2AK1--DGKB^ENST00000199389.11" ; transcript_name "EIF2AK1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: EIF2AK1--DGKB ENSEMBL gene 25662 59507 . + . FI_gene_label "DGKB^ENSG00000136267.14" ; ID "EIF2AK1--DGKB^DGKB^ENSG00000136267.14" ; ccdsid "CCDS47547.1" ; exon_id "ENSE00003526496.1" ; exon_number 1 ; gene_id "EIF2AK1--DGKB^DGKB^ENSG00000136267.14" ; gene_name DGKB ; gene_type protein_coding ; havana_gene "OTTHUMG00000152477.3" ; hgnc_id "HGNC:2850" ; level 3 ; orig_coord_info "chr7,14841194,14841263,-" ; protein_id "ENSP00000382260.3" ; tag basic appris_alternative_1 CCDS ; transcript_id "EIF2AK1--DGKB^ENST00000399322.7" ; transcript_name "DGKB-201" ; transcript_support_level 5 ; transcript_type protein_coding EIF2AK1--DGKB ENSEMBL mRNA 25662 59507 . + . FI_gene_label "DGKB^ENSG00000136267.14" ; ID "EIF2AK1--DGKB^ENST00000399322.7" ; Parent "EIF2AK1--DGKB^DGKB^ENSG00000136267.14" ; ccdsid "CCDS47547.1" ; exon_id "ENSE00003526496.1" ; exon_number 1 ; gene_id "EIF2AK1--DGKB^DGKB^ENSG00000136267.14" ; gene_name DGKB ; gene_type protein_coding ; havana_gene "OTTHUMG00000152477.3" ; hgnc_id "HGNC:2850" ; level 3 ; orig_coord_info "chr7,14841194,14841263,-" ; protein_id "ENSP00000382260.3" ; tag basic appris_alternative_1 CCDS ; transcript_id "EIF2AK1--DGKB^ENST00000399322.7" ; transcript_name "DGKB-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: EIF2AK1--HDAC9 HAVANA gene 1001 19804 . + . FI_gene_label "EIF2AK1^ENSG00000086232.13" ; ID "EIF2AK1--HDAC9^EIF2AK1^ENSG00000086232.13" ; ccdsid "CCDS5345.1" ; exon_id "ENSE00001634941.3" ; exon_number 1 ; gene_id "EIF2AK1--HDAC9^EIF2AK1^ENSG00000086232.13" ; gene_name EIF2AK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090689.15" ; havana_transcript "OTTHUMT00000207373.4" ; hgnc_id "HGNC:24921" ; level 2 ; orig_coord_info "chr7,6058966,6059083,-" ; protein_id "ENSP00000199389.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2AK1--HDAC9^ENST00000199389.11" ; transcript_name "EIF2AK1-201" ; transcript_support_level 1 ; transcript_type protein_coding EIF2AK1--HDAC9 HAVANA mRNA 1001 19804 . + . FI_gene_label "EIF2AK1^ENSG00000086232.13" ; ID "EIF2AK1--HDAC9^ENST00000199389.11" ; Parent "EIF2AK1--HDAC9^EIF2AK1^ENSG00000086232.13" ; ccdsid "CCDS5345.1" ; exon_id "ENSE00001634941.3" ; exon_number 1 ; gene_id "EIF2AK1--HDAC9^EIF2AK1^ENSG00000086232.13" ; gene_name EIF2AK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090689.15" ; havana_transcript "OTTHUMT00000207373.4" ; hgnc_id "HGNC:24921" ; level 2 ; orig_coord_info "chr7,6058966,6059083,-" ; protein_id "ENSP00000199389.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2AK1--HDAC9^ENST00000199389.11" ; transcript_name "EIF2AK1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: EIF2AK1--HDAC9 HAVANA gene 33893 74346 . + . FI_gene_label "HDAC9^ENSG00000048052.23" ; ID "EIF2AK1--HDAC9^HDAC9^ENSG00000048052.23" ; ccdsid "CCDS83163.1" ; exon_id "ENSE00003524474.1" ; exon_number 1 ; gene_id "EIF2AK1--HDAC9^HDAC9^ENSG00000048052.23" ; gene_name HDAC9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152487.8" ; havana_transcript "OTTHUMT00000326693.1" ; hgnc_id "HGNC:14065" ; level 2 ; orig_coord_info "chr7,18496303,18496324,+" ; protein_id "ENSP00000383912.1" ; tag basic appris_alternative_1 CCDS ; transcript_id "EIF2AK1--HDAC9^ENST00000401921.5" ; transcript_name "HDAC9-201" ; transcript_support_level 1 ; transcript_type protein_coding EIF2AK1--HDAC9 HAVANA mRNA 33893 74346 . + . FI_gene_label "HDAC9^ENSG00000048052.23" ; ID "EIF2AK1--HDAC9^ENST00000401921.5" ; Parent "EIF2AK1--HDAC9^HDAC9^ENSG00000048052.23" ; ccdsid "CCDS83163.1" ; exon_id "ENSE00003524474.1" ; exon_number 1 ; gene_id "EIF2AK1--HDAC9^HDAC9^ENSG00000048052.23" ; gene_name HDAC9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152487.8" ; havana_transcript "OTTHUMT00000326693.1" ; hgnc_id "HGNC:14065" ; level 2 ; orig_coord_info "chr7,18496303,18496324,+" ; protein_id "ENSP00000383912.1" ; tag basic appris_alternative_1 CCDS ; transcript_id "EIF2AK1--HDAC9^ENST00000401921.5" ; transcript_name "HDAC9-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: GTF2IRD1--NCF1 HAVANA gene 1001 30976 . + . FI_gene_label "GTF2IRD1^ENSG00000006704.11" ; ID "GTF2IRD1--NCF1^GTF2IRD1^ENSG00000006704.11" ; ccdsid "CCDS5571.1" ; exon_id "ENSE00003523203.1" ; exon_number 2 ; gene_id "GTF2IRD1--NCF1^GTF2IRD1^ENSG00000006704.11" ; gene_name GTF2IRD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023782.4" ; havana_transcript "OTTHUMT00000252654.2" ; hgnc_id "HGNC:4661" ; level 2 ; orig_coord_info "chr7,74508081,74508203,+" ; protein_id "ENSP00000265755.3" ; tag basic CCDS ; transcript_id "GTF2IRD1--NCF1^ENST00000265755.7" ; transcript_name "GTF2IRD1-201" ; transcript_support_level 1 ; transcript_type protein_coding GTF2IRD1--NCF1 HAVANA mRNA 1001 30976 . + . FI_gene_label "GTF2IRD1^ENSG00000006704.11" ; ID "GTF2IRD1--NCF1^ENST00000265755.7" ; Parent "GTF2IRD1--NCF1^GTF2IRD1^ENSG00000006704.11" ; ccdsid "CCDS5571.1" ; exon_id "ENSE00003523203.1" ; exon_number 2 ; gene_id "GTF2IRD1--NCF1^GTF2IRD1^ENSG00000006704.11" ; gene_name GTF2IRD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023782.4" ; havana_transcript "OTTHUMT00000252654.2" ; hgnc_id "HGNC:4661" ; level 2 ; orig_coord_info "chr7,74508081,74508203,+" ; protein_id "ENSP00000265755.3" ; tag basic CCDS ; transcript_id "GTF2IRD1--NCF1^ENST00000265755.7" ; transcript_name "GTF2IRD1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: GTF2IRD1--NCF1 HAVANA gene 33992 45399 . + . FI_gene_label "NCF1^ENSG00000158517.15" ; ID "GTF2IRD1--NCF1^NCF1^ENSG00000158517.15" ; ccdsid "CCDS34657.1" ; exon_id "ENSE00001128348.5" ; exon_number 1 ; gene_id "GTF2IRD1--NCF1^NCF1^ENSG00000158517.15" ; gene_name NCF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149965.14" ; havana_transcript "OTTHUMT00000314560.4" ; hgnc_id "HGNC:7660" ; level 2 ; orig_coord_info "chr7,74774032,74774103,+" ; protein_id "ENSP00000289473.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2IRD1--NCF1^ENST00000289473.10" ; transcript_name "NCF1-201" ; transcript_support_level 1 ; transcript_type protein_coding GTF2IRD1--NCF1 HAVANA mRNA 33992 45399 . + . FI_gene_label "NCF1^ENSG00000158517.15" ; ID "GTF2IRD1--NCF1^ENST00000289473.10" ; Parent "GTF2IRD1--NCF1^NCF1^ENSG00000158517.15" ; ccdsid "CCDS34657.1" ; exon_id "ENSE00001128348.5" ; exon_number 1 ; gene_id "GTF2IRD1--NCF1^NCF1^ENSG00000158517.15" ; gene_name NCF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149965.14" ; havana_transcript "OTTHUMT00000314560.4" ; hgnc_id "HGNC:7660" ; level 2 ; orig_coord_info "chr7,74774032,74774103,+" ; protein_id "ENSP00000289473.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2IRD1--NCF1^ENST00000289473.10" ; transcript_name "NCF1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MLLT1--RANBP3 HAVANA gene 17653 39431 . + . FI_gene_label "RANBP3^ENSG00000031823.14" ; ID "MLLT1--RANBP3^RANBP3^ENSG00000031823.14" ; ccdsid "CCDS42477.1" ; exon_id "ENSE00002787098.1" ; exon_number 1 ; gene_id "MLLT1--RANBP3^RANBP3^ENSG00000031823.14" ; gene_name RANBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180636.6" ; havana_transcript "OTTHUMT00000452308.1" ; hgnc_id "HGNC:9850" ; level 2 ; orig_coord_info "chr19,5978061,5978082,-" ; protein_id "ENSP00000034275.7" ; tag basic appris_alternative_2 CCDS ; transcript_id "MLLT1--RANBP3^ENST00000034275.12" ; transcript_name "RANBP3-201" ; transcript_support_level 1 ; transcript_type protein_coding MLLT1--RANBP3 HAVANA mRNA 17653 39431 . + . FI_gene_label "RANBP3^ENSG00000031823.14" ; ID "MLLT1--RANBP3^ENST00000034275.12" ; Parent "MLLT1--RANBP3^RANBP3^ENSG00000031823.14" ; ccdsid "CCDS42477.1" ; exon_id "ENSE00002787098.1" ; exon_number 1 ; gene_id "MLLT1--RANBP3^RANBP3^ENSG00000031823.14" ; gene_name RANBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180636.6" ; havana_transcript "OTTHUMT00000452308.1" ; hgnc_id "HGNC:9850" ; level 2 ; orig_coord_info "chr19,5978061,5978082,-" ; protein_id "ENSP00000034275.7" ; tag basic appris_alternative_2 CCDS ; transcript_id "MLLT1--RANBP3^ENST00000034275.12" ; transcript_name "RANBP3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: MLLT1--RANBP3 HAVANA gene 1001 14596 . + . FI_gene_label "MLLT1^ENSG00000130382.9" ; ID "MLLT1--RANBP3^MLLT1^ENSG00000130382.9" ; ccdsid "CCDS12160.1" ; exon_id "ENSE00001295439.3" ; exon_number 1 ; gene_id "MLLT1--RANBP3^MLLT1^ENSG00000130382.9" ; gene_name MLLT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180757.3" ; havana_transcript "OTTHUMT00000452909.3" ; hgnc_id "HGNC:7134" ; level 2 ; orig_coord_info "chr19,6279773,6279784,-" ; protein_id "ENSP00000252674.6" ; tag RNA_Seq_supported_partial basic MANE_Select appris_principal_1 CCDS ; transcript_id "MLLT1--RANBP3^ENST00000252674.9" ; transcript_name "MLLT1-201" ; transcript_support_level 1 ; transcript_type protein_coding MLLT1--RANBP3 HAVANA mRNA 1001 14596 . + . FI_gene_label "MLLT1^ENSG00000130382.9" ; ID "MLLT1--RANBP3^ENST00000252674.9" ; Parent "MLLT1--RANBP3^MLLT1^ENSG00000130382.9" ; ccdsid "CCDS12160.1" ; exon_id "ENSE00001295439.3" ; exon_number 1 ; gene_id "MLLT1--RANBP3^MLLT1^ENSG00000130382.9" ; gene_name MLLT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180757.3" ; havana_transcript "OTTHUMT00000452909.3" ; hgnc_id "HGNC:7134" ; level 2 ; orig_coord_info "chr19,6279773,6279784,-" ; protein_id "ENSP00000252674.6" ; tag RNA_Seq_supported_partial basic MANE_Select appris_principal_1 CCDS ; transcript_id "MLLT1--RANBP3^ENST00000252674.9" ; transcript_name "MLLT1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript 192 cases fixed where L3 features have parent feature(s) missing ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check5: l1 linked to l2 ---------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check6: remove orphan l1 --------------------------- We remove only those not supposed to be orphan None found ------------------------------ done in 0 seconds ------------------------------- ------------------------- Check7: all level3 locations ------------------------- ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check8: check cds ------------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- ----------------------------- Check9: check exons ------------------------------ No exons created No exons locations modified No supernumerary exons removed No level2 locations modified ------------------------------ done in 0 seconds ------------------------------- ----------------------------- Check10: check utrs ------------------------------ 360 UTRs created that were missing No UTRs locations modified No supernumerary UTRs removed ------------------------------ done in 0 seconds ------------------------------- ------------------------ Check11: all level2 locations ------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- ------------------------ Check12: all level1 locations ------------------------- We fixed 8 wrong level1 location cases ------------------------------ done in 0 seconds ------------------------------- ---------------------- Check13: remove identical isoforms ---------------------- None found ------------------------------ done in 0 seconds ------------------------------- ------ End checks (done in 0 second) ------ GFF3 file parsed