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: 2513 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 2513 => Number of feature type (3rd column): 2 * Level1: 0 => * level2: 0 => * level3: 2 => exon CDS * unknown: 0 => =>Check because only level3 features: * Number of feature with Parent attribute:0 * Number of feature with a common attribute:2513 => 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: BPTF--ARL17A HAVANA gene 1001 44099 . + . FI_gene_label "BPTF^ENSG00000171634.18" ; ID "BPTF--ARL17A^BPTF^ENSG00000171634.18" ; ccdsid "CCDS11673.1" ; exon_id "ENSE00002689718.2" ; exon_number 1 ; gene_id "BPTF--ARL17A^BPTF^ENSG00000171634.18" ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6" ; havana_transcript "OTTHUMT00000255334.3" ; hgnc_id "HGNC:3581" ; level 2 ; orig_coord_info "chr17,67825725,67826337,+" ; protein_id "ENSP00000307208.6" ; tag basic MANE_Select CCDS ; transcript_id "BPTF--ARL17A^ENST00000306378.11" ; transcript_name "BPTF-201" ; transcript_support_level 1 ; transcript_type protein_coding BPTF--ARL17A HAVANA mRNA 1001 44099 . + . FI_gene_label "BPTF^ENSG00000171634.18" ; ID "BPTF--ARL17A^ENST00000306378.11" ; Parent "BPTF--ARL17A^BPTF^ENSG00000171634.18" ; ccdsid "CCDS11673.1" ; exon_id "ENSE00002689718.2" ; exon_number 1 ; gene_id "BPTF--ARL17A^BPTF^ENSG00000171634.18" ; gene_name BPTF ; gene_type protein_coding ; havana_gene "OTTHUMG00000132254.6" ; havana_transcript "OTTHUMT00000255334.3" ; hgnc_id "HGNC:3581" ; level 2 ; orig_coord_info "chr17,67825725,67826337,+" ; protein_id "ENSP00000307208.6" ; tag basic MANE_Select CCDS ; transcript_id "BPTF--ARL17A^ENST00000306378.11" ; transcript_name "BPTF-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: BPTF--ARL17A HAVANA gene 47120 60165 . + . FI_gene_label "ARL17A^ENSG00000185829.18" ; ID "BPTF--ARL17A^ARL17A^ENSG00000185829.18" ; ccdsid "CCDS74087.1" ; exon_id "ENSE00002370780.1" ; exon_number 2 ; gene_id "BPTF--ARL17A^ARL17A^ENSG00000185829.18" ; gene_name ARL17A ; gene_type protein_coding ; havana_gene "OTTHUMG00000132817.4" ; havana_transcript "OTTHUMT00000491588.1" ; hgnc_id "HGNC:24096" ; level 2 ; orig_coord_info "chr17,46576175,46576322,-" ; protein_id "ENSP00000331563.5" ; tag basic CCDS ; transcript_id "BPTF--ARL17A^ENST00000329240.10" ; transcript_name "ARL17A-201" ; transcript_support_level 4 ; transcript_type protein_coding BPTF--ARL17A HAVANA mRNA 47120 60165 . + . FI_gene_label "ARL17A^ENSG00000185829.18" ; ID "BPTF--ARL17A^ENST00000329240.10" ; Parent "BPTF--ARL17A^ARL17A^ENSG00000185829.18" ; ccdsid "CCDS74087.1" ; exon_id "ENSE00002370780.1" ; exon_number 2 ; gene_id "BPTF--ARL17A^ARL17A^ENSG00000185829.18" ; gene_name ARL17A ; gene_type protein_coding ; havana_gene "OTTHUMG00000132817.4" ; havana_transcript "OTTHUMT00000491588.1" ; hgnc_id "HGNC:24096" ; level 2 ; orig_coord_info "chr17,46576175,46576322,-" ; protein_id "ENSP00000331563.5" ; tag basic CCDS ; transcript_id "BPTF--ARL17A^ENST00000329240.10" ; transcript_name "ARL17A-201" ; transcript_support_level 4 ; transcript_type protein_coding L1 and L2 created: MDN1--KCNH1 HAVANA gene 100259 120480 . + . FI_gene_label "KCNH1^ENSG00000143473.13" ; ID "MDN1--KCNH1^KCNH1^ENSG00000143473.13" ; ccdsid "CCDS1496.1" ; exon_id "ENSE00003801336.1" ; exon_number 1 ; gene_id "MDN1--KCNH1^KCNH1^ENSG00000143473.13" ; gene_name KCNH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000036309.9" ; havana_transcript "OTTHUMT00000088332.4" ; hgnc_id "HGNC:6250" ; level 2 ; orig_coord_info "chr1,211133867,211133945,-" ; protein_id "ENSP00000271751.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "MDN1--KCNH1^ENST00000271751.10" ; transcript_name "KCNH1-201" ; transcript_support_level 2 ; transcript_type protein_coding MDN1--KCNH1 HAVANA mRNA 100259 120480 . + . FI_gene_label "KCNH1^ENSG00000143473.13" ; ID "MDN1--KCNH1^ENST00000271751.10" ; Parent "MDN1--KCNH1^KCNH1^ENSG00000143473.13" ; ccdsid "CCDS1496.1" ; exon_id "ENSE00003801336.1" ; exon_number 1 ; gene_id "MDN1--KCNH1^KCNH1^ENSG00000143473.13" ; gene_name KCNH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000036309.9" ; havana_transcript "OTTHUMT00000088332.4" ; hgnc_id "HGNC:6250" ; level 2 ; orig_coord_info "chr1,211133867,211133945,-" ; protein_id "ENSP00000271751.4" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "MDN1--KCNH1^ENST00000271751.10" ; transcript_name "KCNH1-201" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: MDN1--KCNH1 HAVANA gene 1001 97241 . + . FI_gene_label "MDN1^ENSG00000112159.12" ; ID "MDN1--KCNH1^MDN1^ENSG00000112159.12" ; ccdsid "CCDS5024.1" ; exon_id "ENSE00003846986.1" ; exon_number 1 ; gene_id "MDN1--KCNH1^MDN1^ENSG00000112159.12" ; gene_name MDN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015213.4" ; havana_transcript "OTTHUMT00000041514.3" ; hgnc_id "HGNC:18302" ; level 2 ; orig_coord_info "chr6,89819506,89819607,-" ; protein_id "ENSP00000358400.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MDN1--KCNH1^ENST00000369393.8" ; transcript_name "MDN1-201" ; transcript_support_level 1 ; transcript_type protein_coding MDN1--KCNH1 HAVANA mRNA 1001 97241 . + . FI_gene_label "MDN1^ENSG00000112159.12" ; ID "MDN1--KCNH1^ENST00000369393.8" ; Parent "MDN1--KCNH1^MDN1^ENSG00000112159.12" ; ccdsid "CCDS5024.1" ; exon_id "ENSE00003846986.1" ; exon_number 1 ; gene_id "MDN1--KCNH1^MDN1^ENSG00000112159.12" ; gene_name MDN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015213.4" ; havana_transcript "OTTHUMT00000041514.3" ; hgnc_id "HGNC:18302" ; level 2 ; orig_coord_info "chr6,89819506,89819607,-" ; protein_id "ENSP00000358400.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MDN1--KCNH1^ENST00000369393.8" ; transcript_name "MDN1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PI4KA--LINC02564 HAVANA gene 1607 51209 . + . FI_gene_label "PI4KA^ENSG00000241973.11" ; ID "PI4KA--LINC02564^PI4KA^ENSG00000241973.11" ; ccdsid "CCDS33603.2" ; exon_id "ENSE00003649653.2" ; exon_number 1 ; gene_id "PI4KA--LINC02564^PI4KA^ENSG00000241973.11" ; gene_name PI4KA ; gene_type protein_coding ; havana_gene "OTTHUMG00000167440.4" ; havana_transcript "OTTHUMT00000075723.6" ; hgnc_id "HGNC:8983" ; level 2 ; orig_coord_info "chr22,20858570,20858725,-" ; protein_id "ENSP00000255882.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PI4KA--LINC02564^ENST00000255882.11" ; transcript_name "PI4KA-201" ; transcript_support_level 1 ; transcript_type protein_coding PI4KA--LINC02564 HAVANA mRNA 1607 51209 . + . FI_gene_label "PI4KA^ENSG00000241973.11" ; ID "PI4KA--LINC02564^ENST00000255882.11" ; Parent "PI4KA--LINC02564^PI4KA^ENSG00000241973.11" ; ccdsid "CCDS33603.2" ; exon_id "ENSE00003649653.2" ; exon_number 1 ; gene_id "PI4KA--LINC02564^PI4KA^ENSG00000241973.11" ; gene_name PI4KA ; gene_type protein_coding ; havana_gene "OTTHUMG00000167440.4" ; havana_transcript "OTTHUMT00000075723.6" ; hgnc_id "HGNC:8983" ; level 2 ; orig_coord_info "chr22,20858570,20858725,-" ; protein_id "ENSP00000255882.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PI4KA--LINC02564^ENST00000255882.11" ; transcript_name "PI4KA-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PTPRK--RSPO3 HAVANA gene 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding PTPRK--RSPO3 HAVANA mRNA 53093 62586 . + . FI_gene_label "RSPO3^ENSG00000146374.14" ; ID "PTPRK--RSPO3^ENST00000356698.9" ; Parent "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; ccdsid "CCDS5135.1" ; exon_id "ENSE00001858691.2" ; exon_number 1 ; gene_id "PTPRK--RSPO3^RSPO3^ENSG00000146374.14" ; gene_name RSPO3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015521.2" ; havana_transcript "OTTHUMT00000042111.2" ; hgnc_id "HGNC:20866" ; level 2 ; orig_coord_info "chr6,127119193,127119289,+" ; protein_id "ENSP00000349131.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PTPRK--RSPO3^ENST00000356698.9" ; transcript_name "RSPO3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PTPRK--RSPO3 HAVANA gene 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding PTPRK--RSPO3 HAVANA mRNA 1034 48764 . + . FI_gene_label "PTPRK^ENSG00000152894.15" ; ID "PTPRK--RSPO3^ENST00000368207.7" ; Parent "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; exon_id "ENSE00002151979.1" ; exon_number 1 ; gene_id "PTPRK--RSPO3^PTPRK^ENSG00000152894.15" ; gene_name PTPRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000015536.10" ; havana_transcript "OTTHUMT00000390045.1" ; hgnc_id "HGNC:9674" ; level 2 ; orig_coord_info "chr6,128520259,128520358,-" ; protein_id "ENSP00000357190.3" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "PTPRK--RSPO3^ENST00000368207.7" ; transcript_name "PTPRK-203" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: RANBP1--LINC01900 HAVANA gene 2611 10069 . + . FI_gene_label "RANBP1^ENSG00000099901.17" ; ID "RANBP1--LINC01900^RANBP1^ENSG00000099901.17" ; ccdsid "CCDS13775.1" ; exon_id "ENSE00001953373.1" ; exon_number 1 ; gene_id "RANBP1--LINC01900^RANBP1^ENSG00000099901.17" ; gene_name RANBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150490.35" ; havana_transcript "OTTHUMT00000343733.1" ; hgnc_id "HGNC:9847" ; level 2 ; orig_coord_info "chr22,20117650,20117664,+" ; protein_id "ENSP00000327583.3" ; tag basic appris_principal_4 CCDS ; transcript_id "RANBP1--LINC01900^ENST00000331821.7" ; transcript_name "RANBP1-201" ; transcript_support_level 1 ; transcript_type protein_coding RANBP1--LINC01900 HAVANA mRNA 2611 10069 . + . FI_gene_label "RANBP1^ENSG00000099901.17" ; ID "RANBP1--LINC01900^ENST00000331821.7" ; Parent "RANBP1--LINC01900^RANBP1^ENSG00000099901.17" ; ccdsid "CCDS13775.1" ; exon_id "ENSE00001953373.1" ; exon_number 1 ; gene_id "RANBP1--LINC01900^RANBP1^ENSG00000099901.17" ; gene_name RANBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150490.35" ; havana_transcript "OTTHUMT00000343733.1" ; hgnc_id "HGNC:9847" ; level 2 ; orig_coord_info "chr22,20117650,20117664,+" ; protein_id "ENSP00000327583.3" ; tag basic appris_principal_4 CCDS ; transcript_id "RANBP1--LINC01900^ENST00000331821.7" ; transcript_name "RANBP1-201" ; 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: TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PI4KA--LINC02564 HAVANA gene 54232 57641 . + . FI_gene_label "LINC02564^ENSG00000262352.2" ; ID "PI4KA--LINC02564^LINC02564^ENSG00000262352.2" ; exon_id "ENSE00002655585.2" ; exon_number 1 ; gene_id "PI4KA--LINC02564^LINC02564^ENSG00000262352.2" ; gene_name LINC02564 ; gene_type lncRNA ; havana_gene "OTTHUMG00000177910.2" ; havana_transcript "OTTHUMT00000439669.2" ; hgnc_id "HGNC:53604" ; level 2 ; orig_coord_info "chr18,11125,11595,+" ; tag basic TAGENE ; transcript_id "PI4KA--LINC02564^ENST00000572573.2" ; transcript_name "LINC02564-201" ; transcript_support_level 3 ; transcript_type lncRNA PI4KA--LINC02564 HAVANA RNA 54232 57641 . + . FI_gene_label "LINC02564^ENSG00000262352.2" ; ID "PI4KA--LINC02564^ENST00000572573.2" ; Parent "PI4KA--LINC02564^LINC02564^ENSG00000262352.2" ; exon_id "ENSE00002655585.2" ; exon_number 1 ; gene_id "PI4KA--LINC02564^LINC02564^ENSG00000262352.2" ; gene_name LINC02564 ; gene_type lncRNA ; havana_gene "OTTHUMG00000177910.2" ; havana_transcript "OTTHUMT00000439669.2" ; hgnc_id "HGNC:53604" ; level 2 ; orig_coord_info "chr18,11125,11595,+" ; tag basic TAGENE ; transcript_id "PI4KA--LINC02564^ENST00000572573.2" ; transcript_name "LINC02564-201" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: RANBP1--LINC01900 HAVANA gene 15421 16769 . + . FI_gene_label "LINC01900^ENSG00000265758.1" ; ID "RANBP1--LINC01900^LINC01900^ENSG00000265758.1" ; exon_id "ENSE00002732333.1" ; exon_number 1 ; gene_id "RANBP1--LINC01900^LINC01900^ENSG00000265758.1" ; gene_name LINC01900 ; gene_type lncRNA ; havana_gene "OTTHUMG00000179438.1" ; havana_transcript "OTTHUMT00000446371.1" ; hgnc_id "HGNC:52719" ; level 2 ; orig_coord_info "chr18,22026024,22026110,+" ; transcript_id "RANBP1--LINC01900^ENST00000584028.1" ; transcript_name "LINC01900-201" ; transcript_support_level 2 ; transcript_type lncRNA RANBP1--LINC01900 HAVANA RNA 15421 16769 . + . FI_gene_label "LINC01900^ENSG00000265758.1" ; ID "RANBP1--LINC01900^ENST00000584028.1" ; Parent "RANBP1--LINC01900^LINC01900^ENSG00000265758.1" ; exon_id "ENSE00002732333.1" ; exon_number 1 ; gene_id "RANBP1--LINC01900^LINC01900^ENSG00000265758.1" ; gene_name LINC01900 ; gene_type lncRNA ; havana_gene "OTTHUMG00000179438.1" ; havana_transcript "OTTHUMT00000446371.1" ; hgnc_id "HGNC:52719" ; level 2 ; orig_coord_info "chr18,22026024,22026110,+" ; transcript_id "RANBP1--LINC01900^ENST00000584028.1" ; transcript_name "LINC01900-201" ; transcript_support_level 2 ; transcript_type lncRNA 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 142 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 ------------------------------ 211 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 10 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