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: 2755
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2755
=> 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:2755
=> 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:
CD74--ROS1 HAVANA gene 1219 9629 . + . FI_gene_label "CD74^ENSG00000019582.16" ; ID "CD74--ROS1^CD74^ENSG00000019582.16" ; ccdsid "CCDS47309.1" ; exon_id "ENSE00003588448.1" ; exon_number 1 ; gene_id "CD74--ROS1^CD74^ENSG00000019582.16" ; gene_name CD74 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163559.4" ; havana_transcript "OTTHUMT00000374178.2" ; hgnc_id "HGNC:1697" ; level 2 ; orig_coord_info "chr5,150412625,150412749,-" ; protein_id "ENSP00000009530.7" ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "CD74--ROS1^ENST00000009530.12" ; transcript_name "CD74-201" ; transcript_support_level 2 ; transcript_type protein_coding
CD74--ROS1 HAVANA mRNA 1219 9629 . + . FI_gene_label "CD74^ENSG00000019582.16" ; ID "CD74--ROS1^ENST00000009530.12" ; Parent "CD74--ROS1^CD74^ENSG00000019582.16" ; ccdsid "CCDS47309.1" ; exon_id "ENSE00003588448.1" ; exon_number 1 ; gene_id "CD74--ROS1^CD74^ENSG00000019582.16" ; gene_name CD74 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163559.4" ; havana_transcript "OTTHUMT00000374178.2" ; hgnc_id "HGNC:1697" ; level 2 ; orig_coord_info "chr5,150412625,150412749,-" ; protein_id "ENSP00000009530.7" ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "CD74--ROS1^ENST00000009530.12" ; transcript_name "CD74-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
CD74--ROS1 HAVANA gene 12630 60009 . + . FI_gene_label "ROS1^ENSG00000047936.11" ; ID "CD74--ROS1^ROS1^ENSG00000047936.11" ; exon_id "ENSE00003906517.1" ; exon_number 1 ; gene_id "CD74--ROS1^ROS1^ENSG00000047936.11" ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1" ; havana_transcript "OTTHUMT00000043465.1" ; hgnc_id "HGNC:10261" ; level 2 ; orig_coord_info "chr6,117425534,117425656,-" ; protein_id "ENSP00000357493.3" ; tag basic MANE_Select appris_principal_4 ; transcript_id "CD74--ROS1^ENST00000368507.8" ; transcript_name "ROS1-201" ; transcript_support_level 5 ; transcript_type protein_coding
CD74--ROS1 HAVANA mRNA 12630 60009 . + . FI_gene_label "ROS1^ENSG00000047936.11" ; ID "CD74--ROS1^ENST00000368507.8" ; Parent "CD74--ROS1^ROS1^ENSG00000047936.11" ; exon_id "ENSE00003906517.1" ; exon_number 1 ; gene_id "CD74--ROS1^ROS1^ENSG00000047936.11" ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1" ; havana_transcript "OTTHUMT00000043465.1" ; hgnc_id "HGNC:10261" ; level 2 ; orig_coord_info "chr6,117425534,117425656,-" ; protein_id "ENSP00000357493.3" ; tag basic MANE_Select appris_principal_4 ; transcript_id "CD74--ROS1^ENST00000368507.8" ; transcript_name "ROS1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ETV6--NTRK3 HAVANA gene 13392 15151 . + . FI_gene_label "ETV6^ENSG00000139083.11" ; ID "ETV6--NTRK3^ETV6^ENSG00000139083.11" ; exon_id "ENSE00002245284.1" ; exon_number 1 ; gene_id "ETV6--NTRK3^ETV6^ENSG00000139083.11" ; gene_name ETV6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168538.3" ; havana_transcript "OTTHUMT00000400134.1" ; hgnc_id "HGNC:3495" ; level 2 ; orig_coord_info "chr12,11885937,11886026,+" ; protein_id "ENSP00000266427.3" ; tag mRNA_start_NF cds_start_NF ; transcript_id "ETV6--NTRK3^ENST00000266427.3" ; transcript_name "ETV6-201" ; transcript_support_level 3 ; transcript_type protein_coding
ETV6--NTRK3 HAVANA mRNA 13392 15151 . + . FI_gene_label "ETV6^ENSG00000139083.11" ; ID "ETV6--NTRK3^ENST00000266427.3" ; Parent "ETV6--NTRK3^ETV6^ENSG00000139083.11" ; exon_id "ENSE00002245284.1" ; exon_number 1 ; gene_id "ETV6--NTRK3^ETV6^ENSG00000139083.11" ; gene_name ETV6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168538.3" ; havana_transcript "OTTHUMT00000400134.1" ; hgnc_id "HGNC:3495" ; level 2 ; orig_coord_info "chr12,11885937,11886026,+" ; protein_id "ENSP00000266427.3" ; tag mRNA_start_NF cds_start_NF ; transcript_id "ETV6--NTRK3^ENST00000266427.3" ; transcript_name "ETV6-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
ETV6--NTRK3 HAVANA gene 22528 45237 . + . FI_gene_label "NTRK3^ENSG00000140538.16" ; ID "ETV6--NTRK3^NTRK3^ENSG00000140538.16" ; ccdsid "CCDS32323.1" ; exon_id "ENSE00002296343.1" ; exon_number 1 ; gene_id "ETV6--NTRK3^NTRK3^ENSG00000140538.16" ; gene_name NTRK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148677.12" ; havana_transcript "OTTHUMT00000403049.3" ; hgnc_id "HGNC:8033" ; level 2 ; orig_coord_info "chr15,88255906,88256153,-" ; protein_id "ENSP00000318328.3" ; tag basic CCDS ; transcript_id "ETV6--NTRK3^ENST00000317501.7" ; transcript_name "NTRK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
ETV6--NTRK3 HAVANA mRNA 22528 45237 . + . FI_gene_label "NTRK3^ENSG00000140538.16" ; ID "ETV6--NTRK3^ENST00000317501.7" ; Parent "ETV6--NTRK3^NTRK3^ENSG00000140538.16" ; ccdsid "CCDS32323.1" ; exon_id "ENSE00002296343.1" ; exon_number 1 ; gene_id "ETV6--NTRK3^NTRK3^ENSG00000140538.16" ; gene_name NTRK3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148677.12" ; havana_transcript "OTTHUMT00000403049.3" ; hgnc_id "HGNC:8033" ; level 2 ; orig_coord_info "chr15,88255906,88256153,-" ; protein_id "ENSP00000318328.3" ; tag basic CCDS ; transcript_id "ETV6--NTRK3^ENST00000317501.7" ; transcript_name "NTRK3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FGFR3--BAIAP2L1 HAVANA gene 14817 31823 . + . FI_gene_label "BAIAP2L1^ENSG00000006453.14" ; ID "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14" ; ccdsid "CCDS34687.1" ; exon_id "ENSE00003618813.2" ; exon_number 1 ; gene_id "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14" ; gene_name BAIAP2L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165117.2" ; havana_transcript "OTTHUMT00000334681.2" ; hgnc_id "HGNC:21649" ; level 2 ; orig_coord_info "chr7,98400802,98400852,-" ; protein_id "ENSP00000005260.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FGFR3--BAIAP2L1^ENST00000005260.9" ; transcript_name "BAIAP2L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--BAIAP2L1 HAVANA mRNA 14817 31823 . + . FI_gene_label "BAIAP2L1^ENSG00000006453.14" ; ID "FGFR3--BAIAP2L1^ENST00000005260.9" ; Parent "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14" ; ccdsid "CCDS34687.1" ; exon_id "ENSE00003618813.2" ; exon_number 1 ; gene_id "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14" ; gene_name BAIAP2L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165117.2" ; havana_transcript "OTTHUMT00000334681.2" ; hgnc_id "HGNC:21649" ; level 2 ; orig_coord_info "chr7,98400802,98400852,-" ; protein_id "ENSP00000005260.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FGFR3--BAIAP2L1^ENST00000005260.9" ; transcript_name "BAIAP2L1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FGFR3--BAIAP2L1 HAVANA gene 1020 10219 . + . FI_gene_label "FGFR3^ENSG00000068078.20" ; ID "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20" ; exon_id "ENSE00001596390.1" ; exon_number 2 ; gene_id "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20" ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7" ; havana_transcript "OTTHUMT00000495785.1" ; hgnc_id "HGNC:3690" ; level 2 ; orig_coord_info "chr4,1793935,1794043,+" ; protein_id "ENSP00000260795.3" ; transcript_id "FGFR3--BAIAP2L1^ENST00000260795.8" ; transcript_name "FGFR3-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--BAIAP2L1 HAVANA mRNA 1020 10219 . + . FI_gene_label "FGFR3^ENSG00000068078.20" ; ID "FGFR3--BAIAP2L1^ENST00000260795.8" ; Parent "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20" ; exon_id "ENSE00001596390.1" ; exon_number 2 ; gene_id "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20" ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7" ; havana_transcript "OTTHUMT00000495785.1" ; hgnc_id "HGNC:3690" ; level 2 ; orig_coord_info "chr4,1793935,1794043,+" ; protein_id "ENSP00000260795.3" ; transcript_id "FGFR3--BAIAP2L1^ENST00000260795.8" ; transcript_name "FGFR3-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
FGFR3--TACC3 HAVANA gene 1020 10219 . + . FI_gene_label "FGFR3^ENSG00000068078.20" ; ID "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; exon_id "ENSE00001596390.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7" ; havana_transcript "OTTHUMT00000495785.1" ; hgnc_id "HGNC:3690" ; level 2 ; orig_coord_info "chr4,1793935,1794043,+" ; protein_id "ENSP00000260795.3" ; transcript_id "FGFR3--TACC3^ENST00000260795.8" ; transcript_name "FGFR3-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--TACC3 HAVANA mRNA 1020 10219 . + . FI_gene_label "FGFR3^ENSG00000068078.20" ; ID "FGFR3--TACC3^ENST00000260795.8" ; Parent "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; exon_id "ENSE00001596390.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7" ; havana_transcript "OTTHUMT00000495785.1" ; hgnc_id "HGNC:3690" ; level 2 ; orig_coord_info "chr4,1793935,1794043,+" ; protein_id "ENSP00000260795.3" ; transcript_id "FGFR3--TACC3^ENST00000260795.8" ; transcript_name "FGFR3-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
FGFR3--TACC3 HAVANA gene 16535 31742 . + . FI_gene_label "TACC3^ENSG00000013810.20" ; ID "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; ccdsid "CCDS3352.1" ; exon_id "ENSE00003597099.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25" ; havana_transcript "OTTHUMT00000203730.4" ; hgnc_id "HGNC:11524" ; level 2 ; orig_coord_info "chr4,1723422,1723583,+" ; protein_id "ENSP00000326550.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9" ; transcript_name "TACC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--TACC3 HAVANA mRNA 16535 31742 . + . FI_gene_label "TACC3^ENSG00000013810.20" ; ID "FGFR3--TACC3^ENST00000313288.9" ; Parent "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; ccdsid "CCDS3352.1" ; exon_id "ENSE00003597099.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25" ; havana_transcript "OTTHUMT00000203730.4" ; hgnc_id "HGNC:11524" ; level 2 ; orig_coord_info "chr4,1723422,1723583,+" ; protein_id "ENSP00000326550.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9" ; transcript_name "TACC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KIF5B--RET HAVANA gene 1001 24630 . + . FI_gene_label "KIF5B^ENSG00000170759.11" ; ID "KIF5B--RET^KIF5B^ENSG00000170759.11" ; ccdsid "CCDS7171.1" ; exon_id "ENSE00001551533.4" ; exon_number 1 ; gene_id "KIF5B--RET^KIF5B^ENSG00000170759.11" ; gene_name KIF5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017913.2" ; havana_transcript "OTTHUMT00000047467.2" ; hgnc_id "HGNC:6324" ; level 2 ; orig_coord_info "chr10,32055848,32055973,-" ; protein_id "ENSP00000307078.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KIF5B--RET^ENST00000302418.5" ; transcript_name "KIF5B-201" ; transcript_support_level 1 ; transcript_type protein_coding
KIF5B--RET HAVANA mRNA 1001 24630 . + . FI_gene_label "KIF5B^ENSG00000170759.11" ; ID "KIF5B--RET^ENST00000302418.5" ; Parent "KIF5B--RET^KIF5B^ENSG00000170759.11" ; ccdsid "CCDS7171.1" ; exon_id "ENSE00001551533.4" ; exon_number 1 ; gene_id "KIF5B--RET^KIF5B^ENSG00000170759.11" ; gene_name KIF5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017913.2" ; havana_transcript "OTTHUMT00000047467.2" ; hgnc_id "HGNC:6324" ; level 2 ; orig_coord_info "chr10,32055848,32055973,-" ; protein_id "ENSP00000307078.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KIF5B--RET^ENST00000302418.5" ; transcript_name "KIF5B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KIF5B--RET HAVANA gene 27636 48256 . + . FI_gene_label "RET^ENSG00000165731.20" ; ID "KIF5B--RET^RET^ENSG00000165731.20" ; ccdsid "CCDS53525.1" ; exon_id "ENSE00003744437.1" ; exon_number 1 ; gene_id "KIF5B--RET^RET^ENSG00000165731.20" ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7" ; havana_transcript "OTTHUMT00000358138.3" ; hgnc_id "HGNC:9967" ; level 2 ; orig_coord_info "chr10,43077259,43077331,+" ; protein_id "ENSP00000344798.4" ; tag basic CCDS ; transcript_id "KIF5B--RET^ENST00000340058.6" ; transcript_name "RET-201" ; transcript_support_level 1 ; transcript_type protein_coding
KIF5B--RET HAVANA mRNA 27636 48256 . + . FI_gene_label "RET^ENSG00000165731.20" ; ID "KIF5B--RET^ENST00000340058.6" ; Parent "KIF5B--RET^RET^ENSG00000165731.20" ; ccdsid "CCDS53525.1" ; exon_id "ENSE00003744437.1" ; exon_number 1 ; gene_id "KIF5B--RET^RET^ENSG00000165731.20" ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7" ; havana_transcript "OTTHUMT00000358138.3" ; hgnc_id "HGNC:9967" ; level 2 ; orig_coord_info "chr10,43077259,43077331,+" ; protein_id "ENSP00000344798.4" ; tag basic CCDS ; transcript_id "KIF5B--RET^ENST00000340058.6" ; transcript_name "RET-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LMNA--NTRK1 HAVANA gene 31461 45545 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "LMNA--NTRK1^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "LMNA--NTRK1^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "LMNA--NTRK1^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding
LMNA--NTRK1 HAVANA mRNA 31461 45545 . + . FI_gene_label "NTRK1^ENSG00000198400.13" ; ID "LMNA--NTRK1^ENST00000358660.3" ; Parent "LMNA--NTRK1^NTRK1^ENSG00000198400.13" ; exon_id "ENSE00001378279.3" ; exon_number 1 ; gene_id "LMNA--NTRK1^NTRK1^ENSG00000198400.13" ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3" ; havana_transcript "OTTHUMT00000392280.1" ; hgnc_id "HGNC:8031" ; level 2 ; orig_coord_info "chr1,156860935,156861146,+" ; protein_id "ENSP00000351486.3" ; tag basic appris_alternative_2 ; transcript_id "LMNA--NTRK1^ENST00000358660.3" ; transcript_name "NTRK1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
LMNA--NTRK1 HAVANA gene 11719 23624 . + . FI_gene_label "LMNA^ENSG00000160789.23" ; ID "LMNA--NTRK1^LMNA^ENSG00000160789.23" ; ccdsid "CCDS1129.1" ; exon_id "ENSE00001554780.1" ; exon_number 2 ; gene_id "LMNA--NTRK1^LMNA^ENSG00000160789.23" ; gene_name LMNA ; gene_type protein_coding ; havana_gene "OTTHUMG00000013961.6" ; hgnc_id "HGNC:6636" ; level 2 ; orig_coord_info "chr1,156114919,156115274,+" ; protein_id "ENSP00000355292.6" ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "LMNA--NTRK1^ENST00000361308.9" ; transcript_name "LMNA-201" ; transcript_support_level 5 ; transcript_type protein_coding
LMNA--NTRK1 HAVANA mRNA 11719 23624 . + . FI_gene_label "LMNA^ENSG00000160789.23" ; ID "LMNA--NTRK1^ENST00000361308.9" ; Parent "LMNA--NTRK1^LMNA^ENSG00000160789.23" ; ccdsid "CCDS1129.1" ; exon_id "ENSE00001554780.1" ; exon_number 2 ; gene_id "LMNA--NTRK1^LMNA^ENSG00000160789.23" ; gene_name LMNA ; gene_type protein_coding ; havana_gene "OTTHUMG00000013961.6" ; hgnc_id "HGNC:6636" ; level 2 ; orig_coord_info "chr1,156114919,156115274,+" ; protein_id "ENSP00000355292.6" ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "LMNA--NTRK1^ENST00000361308.9" ; transcript_name "LMNA-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PAX8--PPARG ENSEMBL gene 1001 17422 . + . FI_gene_label "PAX8^ENSG00000125618.18" ; ID "PAX8--PPARG^PAX8^ENSG00000125618.18" ; ccdsid "CCDS46398.1" ; exon_id "ENSE00002299701.2" ; exon_number 2 ; gene_id "PAX8--PPARG^PAX8^ENSG00000125618.18" ; gene_name PAX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128529.12" ; hgnc_id "HGNC:8622" ; level 3 ; orig_coord_info "chr2,113278370,113278394,-" ; protein_id "ENSP00000263334.6" ; tag basic appris_principal_1 CCDS ; transcript_id "PAX8--PPARG^ENST00000263334.9" ; transcript_name "PAX8-201" ; transcript_support_level 1 ; transcript_type protein_coding
PAX8--PPARG ENSEMBL mRNA 1001 17422 . + . FI_gene_label "PAX8^ENSG00000125618.18" ; ID "PAX8--PPARG^ENST00000263334.9" ; Parent "PAX8--PPARG^PAX8^ENSG00000125618.18" ; ccdsid "CCDS46398.1" ; exon_id "ENSE00002299701.2" ; exon_number 2 ; gene_id "PAX8--PPARG^PAX8^ENSG00000125618.18" ; gene_name PAX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128529.12" ; hgnc_id "HGNC:8622" ; level 3 ; orig_coord_info "chr2,113278370,113278394,-" ; protein_id "ENSP00000263334.6" ; tag basic appris_principal_1 CCDS ; transcript_id "PAX8--PPARG^ENST00000263334.9" ; transcript_name "PAX8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PAX8--PPARG HAVANA gene 28940 39958 . + . FI_gene_label "PPARG^ENSG00000132170.23" ; ID "PAX8--PPARG^PPARG^ENSG00000132170.23" ; ccdsid "CCDS2609.1" ; exon_id "ENSE00003683648.1" ; exon_number 1 ; gene_id "PAX8--PPARG^PPARG^ENSG00000132170.23" ; gene_name PPARG ; gene_type protein_coding ; havana_gene "OTTHUMG00000129764.15" ; havana_transcript "OTTHUMT00000251979.2" ; hgnc_id "HGNC:9236" ; level 2 ; orig_coord_info "chr3,12351593,12351674,+" ; protein_id "ENSP00000287820.6" ; tag basic CCDS ; transcript_id "PAX8--PPARG^ENST00000287820.10" ; transcript_name "PPARG-201" ; transcript_support_level 1 ; transcript_type protein_coding
PAX8--PPARG HAVANA mRNA 28940 39958 . + . FI_gene_label "PPARG^ENSG00000132170.23" ; ID "PAX8--PPARG^ENST00000287820.10" ; Parent "PAX8--PPARG^PPARG^ENSG00000132170.23" ; ccdsid "CCDS2609.1" ; exon_id "ENSE00003683648.1" ; exon_number 1 ; gene_id "PAX8--PPARG^PPARG^ENSG00000132170.23" ; gene_name PPARG ; gene_type protein_coding ; havana_gene "OTTHUMG00000129764.15" ; havana_transcript "OTTHUMT00000251979.2" ; hgnc_id "HGNC:9236" ; level 2 ; orig_coord_info "chr3,12351593,12351674,+" ; protein_id "ENSP00000287820.6" ; tag basic CCDS ; transcript_id "PAX8--PPARG^ENST00000287820.10" ; transcript_name "PPARG-201" ; transcript_support_level 1 ; transcript_type protein_coding
177 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
445 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 10 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 0 second) ------
GFF3 file parsed