.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/0404fdfe47e04792b69dc790bda698/.command.log
Size: 46.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/0404fdfe47e04792b69dc790bda698/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/ead37e96e44133d7089b7e60be801c/fi_workdir/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/0404fdfe47e04792b69dc790bda698/.command.run
==> STAGING COMPLETE (3 inputs)

Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file

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|   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: 3298
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3298
=> 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:3298
  => 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: 
DTX2--PTPN12	HAVANA	gene	23984	48846	.	+	.	FI_gene_label "PTPN12^ENSG00000127947.16"  ; ID "DTX2--PTPN12^PTPN12^ENSG00000127947.16"  ; ccdsid "CCDS5592.1"  ; exon_id "ENSE00001819992.2"  ; exon_number 1 ; gene_id "DTX2--PTPN12^PTPN12^ENSG00000127947.16"  ; gene_name PTPN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023501.10"  ; havana_transcript "OTTHUMT00000253183.4"  ; hgnc_id "HGNC:9645"  ; level 2 ; orig_coord_info "chr7,77537547,77537645,+"  ; protein_id "ENSP00000248594.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DTX2--PTPN12^ENST00000248594.11"  ; transcript_name "PTPN12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DTX2--PTPN12	HAVANA	mRNA	23984	48846	.	+	.	FI_gene_label "PTPN12^ENSG00000127947.16"  ; ID "DTX2--PTPN12^ENST00000248594.11"  ; Parent "DTX2--PTPN12^PTPN12^ENSG00000127947.16"  ; ccdsid "CCDS5592.1"  ; exon_id "ENSE00001819992.2"  ; exon_number 1 ; gene_id "DTX2--PTPN12^PTPN12^ENSG00000127947.16"  ; gene_name PTPN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023501.10"  ; havana_transcript "OTTHUMT00000253183.4"  ; hgnc_id "HGNC:9645"  ; level 2 ; orig_coord_info "chr7,77537547,77537645,+"  ; protein_id "ENSP00000248594.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DTX2--PTPN12^ENST00000248594.11"  ; transcript_name "PTPN12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DTX2--PTPN12	HAVANA	gene	1026	20979	.	+	.	FI_gene_label "DTX2^ENSG00000091073.19"  ; ID "DTX2--PTPN12^DTX2^ENSG00000091073.19"  ; ccdsid "CCDS5587.1"  ; exon_id "ENSE00003639247.1"  ; exon_number 4 ; gene_id "DTX2--PTPN12^DTX2^ENSG00000091073.19"  ; gene_name DTX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162594.3"  ; havana_transcript "OTTHUMT00000253104.2"  ; hgnc_id "HGNC:15973"  ; level 2 ; orig_coord_info "chr7,76480510,76480777,+"  ; protein_id "ENSP00000322885.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "DTX2--PTPN12^ENST00000324432.9"  ; transcript_name "DTX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DTX2--PTPN12	HAVANA	mRNA	1026	20979	.	+	.	FI_gene_label "DTX2^ENSG00000091073.19"  ; ID "DTX2--PTPN12^ENST00000324432.9"  ; Parent "DTX2--PTPN12^DTX2^ENSG00000091073.19"  ; ccdsid "CCDS5587.1"  ; exon_id "ENSE00003639247.1"  ; exon_number 4 ; gene_id "DTX2--PTPN12^DTX2^ENSG00000091073.19"  ; gene_name DTX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162594.3"  ; havana_transcript "OTTHUMT00000253104.2"  ; hgnc_id "HGNC:15973"  ; level 2 ; orig_coord_info "chr7,76480510,76480777,+"  ; protein_id "ENSP00000322885.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "DTX2--PTPN12^ENST00000324432.9"  ; transcript_name "DTX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^ENST00000240618.11"  ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^ENST00000309384.2"  ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PTPN12--MAGI2	HAVANA	gene	1001	25863	.	+	.	FI_gene_label "PTPN12^ENSG00000127947.16"  ; ID "PTPN12--MAGI2^PTPN12^ENSG00000127947.16"  ; ccdsid "CCDS5592.1"  ; exon_id "ENSE00001819992.2"  ; exon_number 1 ; gene_id "PTPN12--MAGI2^PTPN12^ENSG00000127947.16"  ; gene_name PTPN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023501.10"  ; havana_transcript "OTTHUMT00000253183.4"  ; hgnc_id "HGNC:9645"  ; level 2 ; orig_coord_info "chr7,77537547,77537645,+"  ; protein_id "ENSP00000248594.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PTPN12--MAGI2^ENST00000248594.11"  ; transcript_name "PTPN12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PTPN12--MAGI2	HAVANA	mRNA	1001	25863	.	+	.	FI_gene_label "PTPN12^ENSG00000127947.16"  ; ID "PTPN12--MAGI2^ENST00000248594.11"  ; Parent "PTPN12--MAGI2^PTPN12^ENSG00000127947.16"  ; ccdsid "CCDS5592.1"  ; exon_id "ENSE00001819992.2"  ; exon_number 1 ; gene_id "PTPN12--MAGI2^PTPN12^ENSG00000127947.16"  ; gene_name PTPN12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023501.10"  ; havana_transcript "OTTHUMT00000253183.4"  ; hgnc_id "HGNC:9645"  ; level 2 ; orig_coord_info "chr7,77537547,77537645,+"  ; protein_id "ENSP00000248594.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PTPN12--MAGI2^ENST00000248594.11"  ; transcript_name "PTPN12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PTPN12--MAGI2	HAVANA	gene	28864	111262	.	+	.	FI_gene_label "MAGI2^ENSG00000187391.22"  ; ID "PTPN12--MAGI2^MAGI2^ENSG00000187391.22"  ; ccdsid "CCDS5594.1"  ; exon_id "ENSE00001597225.2"  ; exon_number 1 ; gene_id "PTPN12--MAGI2^MAGI2^ENSG00000187391.22"  ; gene_name MAGI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130697.19"  ; havana_transcript "OTTHUMT00000253197.5"  ; hgnc_id "HGNC:18957"  ; level 2 ; orig_coord_info "chr7,79453020,79453320,-"  ; protein_id "ENSP00000346151.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PTPN12--MAGI2^ENST00000354212.9"  ; transcript_name "MAGI2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PTPN12--MAGI2	HAVANA	mRNA	28864	111262	.	+	.	FI_gene_label "MAGI2^ENSG00000187391.22"  ; ID "PTPN12--MAGI2^ENST00000354212.9"  ; Parent "PTPN12--MAGI2^MAGI2^ENSG00000187391.22"  ; ccdsid "CCDS5594.1"  ; exon_id "ENSE00001597225.2"  ; exon_number 1 ; gene_id "PTPN12--MAGI2^MAGI2^ENSG00000187391.22"  ; gene_name MAGI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130697.19"  ; havana_transcript "OTTHUMT00000253197.5"  ; hgnc_id "HGNC:18957"  ; level 2 ; orig_coord_info "chr7,79453020,79453320,-"  ; protein_id "ENSP00000346151.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "PTPN12--MAGI2^ENST00000354212.9"  ; transcript_name "MAGI2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SRRM1--CLIC4	HAVANA	gene	5570	25576	.	+	.	FI_gene_label "SRRM1^ENSG00000133226.17"  ; ID "SRRM1--CLIC4^SRRM1^ENSG00000133226.17"  ; ccdsid "CCDS255.1"  ; exon_id "ENSE00002225700.3"  ; exon_number 1 ; gene_id "SRRM1--CLIC4^SRRM1^ENSG00000133226.17"  ; gene_name SRRM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003320.5"  ; havana_transcript "OTTHUMT00000009292.3"  ; hgnc_id "HGNC:16638"  ; level 2 ; orig_coord_info "chr1,24643327,24643347,+"  ; protein_id "ENSP00000326261.8"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SRRM1--CLIC4^ENST00000323848.14"  ; transcript_name "SRRM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SRRM1--CLIC4	HAVANA	mRNA	5570	25576	.	+	.	FI_gene_label "SRRM1^ENSG00000133226.17"  ; ID "SRRM1--CLIC4^ENST00000323848.14"  ; Parent "SRRM1--CLIC4^SRRM1^ENSG00000133226.17"  ; ccdsid "CCDS255.1"  ; exon_id "ENSE00002225700.3"  ; exon_number 1 ; gene_id "SRRM1--CLIC4^SRRM1^ENSG00000133226.17"  ; gene_name SRRM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003320.5"  ; havana_transcript "OTTHUMT00000009292.3"  ; hgnc_id "HGNC:16638"  ; level 2 ; orig_coord_info "chr1,24643327,24643347,+"  ; protein_id "ENSP00000326261.8"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SRRM1--CLIC4^ENST00000323848.14"  ; transcript_name "SRRM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SRRM1--CLIC4	HAVANA	gene	28642	38774	.	+	.	FI_gene_label "CLIC4^ENSG00000169504.15"  ; ID "SRRM1--CLIC4^CLIC4^ENSG00000169504.15"  ; ccdsid "CCDS256.1"  ; exon_id "ENSE00001463371.4"  ; exon_number 1 ; gene_id "SRRM1--CLIC4^CLIC4^ENSG00000169504.15"  ; gene_name CLIC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003327.5"  ; havana_transcript "OTTHUMT00000009332.2"  ; hgnc_id "HGNC:13518"  ; level 2 ; orig_coord_info "chr1,24745554,24745625,+"  ; protein_id "ENSP00000363500.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRRM1--CLIC4^ENST00000374379.9"  ; transcript_name "CLIC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SRRM1--CLIC4	HAVANA	mRNA	28642	38774	.	+	.	FI_gene_label "CLIC4^ENSG00000169504.15"  ; ID "SRRM1--CLIC4^ENST00000374379.9"  ; Parent "SRRM1--CLIC4^CLIC4^ENSG00000169504.15"  ; ccdsid "CCDS256.1"  ; exon_id "ENSE00001463371.4"  ; exon_number 1 ; gene_id "SRRM1--CLIC4^CLIC4^ENSG00000169504.15"  ; gene_name CLIC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003327.5"  ; havana_transcript "OTTHUMT00000009332.2"  ; hgnc_id "HGNC:13518"  ; level 2 ; orig_coord_info "chr1,24745554,24745625,+"  ; protein_id "ENSP00000363500.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRRM1--CLIC4^ENST00000374379.9"  ; transcript_name "CLIC4-201"  ; 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: 
TOPORS--AL162725.2	HAVANA	gene	1001	7131	.	+	.	FI_gene_label "TOPORS^ENSG00000197579.8"  ; ID "TOPORS--AL162725.2^TOPORS^ENSG00000197579.8"  ; ccdsid "CCDS6527.1"  ; exon_id "ENSE00003844059.1"  ; exon_number 1 ; gene_id "TOPORS--AL162725.2^TOPORS^ENSG00000197579.8"  ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2"  ; havana_transcript "OTTHUMT00000052007.2"  ; hgnc_id "HGNC:21653"  ; level 2 ; orig_coord_info "chr9,32552434,32552436,-"  ; protein_id "ENSP00000353735.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--AL162725.2^ENST00000360538.7"  ; transcript_name "TOPORS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TOPORS--AL162725.2	HAVANA	mRNA	1001	7131	.	+	.	FI_gene_label "TOPORS^ENSG00000197579.8"  ; ID "TOPORS--AL162725.2^ENST00000360538.7"  ; Parent "TOPORS--AL162725.2^TOPORS^ENSG00000197579.8"  ; ccdsid "CCDS6527.1"  ; exon_id "ENSE00003844059.1"  ; exon_number 1 ; gene_id "TOPORS--AL162725.2^TOPORS^ENSG00000197579.8"  ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2"  ; havana_transcript "OTTHUMT00000052007.2"  ; hgnc_id "HGNC:21653"  ; level 2 ; orig_coord_info "chr9,32552434,32552436,-"  ; protein_id "ENSP00000353735.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--AL162725.2^ENST00000360538.7"  ; transcript_name "TOPORS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TOPORS--BNC2	HAVANA	gene	1001	7131	.	+	.	FI_gene_label "TOPORS^ENSG00000197579.8"  ; ID "TOPORS--BNC2^TOPORS^ENSG00000197579.8"  ; ccdsid "CCDS6527.1"  ; exon_id "ENSE00003844059.1"  ; exon_number 1 ; gene_id "TOPORS--BNC2^TOPORS^ENSG00000197579.8"  ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2"  ; havana_transcript "OTTHUMT00000052007.2"  ; hgnc_id "HGNC:21653"  ; level 2 ; orig_coord_info "chr9,32552434,32552436,-"  ; protein_id "ENSP00000353735.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--BNC2^ENST00000360538.7"  ; transcript_name "TOPORS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TOPORS--BNC2	HAVANA	mRNA	1001	7131	.	+	.	FI_gene_label "TOPORS^ENSG00000197579.8"  ; ID "TOPORS--BNC2^ENST00000360538.7"  ; Parent "TOPORS--BNC2^TOPORS^ENSG00000197579.8"  ; ccdsid "CCDS6527.1"  ; exon_id "ENSE00003844059.1"  ; exon_number 1 ; gene_id "TOPORS--BNC2^TOPORS^ENSG00000197579.8"  ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2"  ; havana_transcript "OTTHUMT00000052007.2"  ; hgnc_id "HGNC:21653"  ; level 2 ; orig_coord_info "chr9,32552434,32552436,-"  ; protein_id "ENSP00000353735.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--BNC2^ENST00000360538.7"  ; transcript_name "TOPORS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TOPORS--BNC2	HAVANA	gene	11330	21161	.	+	.	FI_gene_label "BNC2^ENSG00000173068.18"  ; ID "TOPORS--BNC2^BNC2^ENSG00000173068.18"  ; exon_id "ENSE00003666105.1"  ; exon_number 2 ; gene_id "TOPORS--BNC2^BNC2^ENSG00000173068.18"  ; gene_name BNC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019593.13"  ; havana_transcript "OTTHUMT00000476395.2"  ; hgnc_id "HGNC:30988"  ; level 2 ; orig_coord_info "chr9,16727797,16727892,-"  ; protein_id "ENSP00000370041.3"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "TOPORS--BNC2^ENST00000380666.6"  ; transcript_name "BNC2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TOPORS--BNC2	HAVANA	mRNA	11330	21161	.	+	.	FI_gene_label "BNC2^ENSG00000173068.18"  ; ID "TOPORS--BNC2^ENST00000380666.6"  ; Parent "TOPORS--BNC2^BNC2^ENSG00000173068.18"  ; exon_id "ENSE00003666105.1"  ; exon_number 2 ; gene_id "TOPORS--BNC2^BNC2^ENSG00000173068.18"  ; gene_name BNC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019593.13"  ; havana_transcript "OTTHUMT00000476395.2"  ; hgnc_id "HGNC:30988"  ; level 2 ; orig_coord_info "chr9,16727797,16727892,-"  ; protein_id "ENSP00000370041.3"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "TOPORS--BNC2^ENST00000380666.6"  ; transcript_name "BNC2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TOPORS--LINGO2	ENSEMBL	gene	10133	20603	.	+	.	FI_gene_label "LINGO2^ENSG00000174482.10"  ; ID "TOPORS--LINGO2^LINGO2^ENSG00000174482.10"  ; ccdsid "CCDS6524.1"  ; exon_id "ENSE00001200037.5"  ; exon_number 6 ; gene_id "TOPORS--LINGO2^LINGO2^ENSG00000174482.10"  ; gene_name LINGO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019721.2"  ; hgnc_id "HGNC:21207"  ; level 3 ; orig_coord_info "chr9,27948854,27950671,-"  ; protein_id "ENSP00000310126.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "TOPORS--LINGO2^ENST00000308675.5"  ; transcript_name "LINGO2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TOPORS--LINGO2	ENSEMBL	mRNA	10133	20603	.	+	.	FI_gene_label "LINGO2^ENSG00000174482.10"  ; ID "TOPORS--LINGO2^ENST00000308675.5"  ; Parent "TOPORS--LINGO2^LINGO2^ENSG00000174482.10"  ; ccdsid "CCDS6524.1"  ; exon_id "ENSE00001200037.5"  ; exon_number 6 ; gene_id "TOPORS--LINGO2^LINGO2^ENSG00000174482.10"  ; gene_name LINGO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019721.2"  ; hgnc_id "HGNC:21207"  ; level 3 ; orig_coord_info "chr9,27948854,27950671,-"  ; protein_id "ENSP00000310126.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "TOPORS--LINGO2^ENST00000308675.5"  ; transcript_name "LINGO2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TOPORS--LINGO2	HAVANA	gene	1001	7131	.	+	.	FI_gene_label "TOPORS^ENSG00000197579.8"  ; ID "TOPORS--LINGO2^TOPORS^ENSG00000197579.8"  ; ccdsid "CCDS6527.1"  ; exon_id "ENSE00003844059.1"  ; exon_number 1 ; gene_id "TOPORS--LINGO2^TOPORS^ENSG00000197579.8"  ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2"  ; havana_transcript "OTTHUMT00000052007.2"  ; hgnc_id "HGNC:21653"  ; level 2 ; orig_coord_info "chr9,32552434,32552436,-"  ; protein_id "ENSP00000353735.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--LINGO2^ENST00000360538.7"  ; transcript_name "TOPORS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TOPORS--LINGO2	HAVANA	mRNA	1001	7131	.	+	.	FI_gene_label "TOPORS^ENSG00000197579.8"  ; ID "TOPORS--LINGO2^ENST00000360538.7"  ; Parent "TOPORS--LINGO2^TOPORS^ENSG00000197579.8"  ; ccdsid "CCDS6527.1"  ; exon_id "ENSE00003844059.1"  ; exon_number 1 ; gene_id "TOPORS--LINGO2^TOPORS^ENSG00000197579.8"  ; gene_name TOPORS ; gene_type protein_coding ; havana_gene "OTTHUMG00000019743.2"  ; havana_transcript "OTTHUMT00000052007.2"  ; hgnc_id "HGNC:21653"  ; level 2 ; orig_coord_info "chr9,32552434,32552436,-"  ; protein_id "ENSP00000353735.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TOPORS--LINGO2^ENST00000360538.7"  ; transcript_name "TOPORS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TSBP1--NOTCH4	HAVANA	gene	1006	24941	.	+	.	FI_gene_label "TSBP1^ENSG00000204296.12"  ; ID "TSBP1--NOTCH4^TSBP1^ENSG00000204296.12"  ; exon_id "ENSE00001877826.1"  ; exon_number 1 ; gene_id "TSBP1--NOTCH4^TSBP1^ENSG00000204296.12"  ; gene_name TSBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031107.5"  ; havana_transcript "OTTHUMT00000076177.2"  ; hgnc_id "HGNC:13922"  ; level 2 ; orig_coord_info "chr6,32371694,32371706,-"  ; protein_id "ENSP00000364155.4"  ; tag basic appris_alternative_2 ; transcript_id "TSBP1--NOTCH4^ENST00000375015.8"  ; transcript_name "TSBP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TSBP1--NOTCH4	HAVANA	mRNA	1006	24941	.	+	.	FI_gene_label "TSBP1^ENSG00000204296.12"  ; ID "TSBP1--NOTCH4^ENST00000375015.8"  ; Parent "TSBP1--NOTCH4^TSBP1^ENSG00000204296.12"  ; exon_id "ENSE00001877826.1"  ; exon_number 1 ; gene_id "TSBP1--NOTCH4^TSBP1^ENSG00000204296.12"  ; gene_name TSBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031107.5"  ; havana_transcript "OTTHUMT00000076177.2"  ; hgnc_id "HGNC:13922"  ; level 2 ; orig_coord_info "chr6,32371694,32371706,-"  ; protein_id "ENSP00000364155.4"  ; tag basic appris_alternative_2 ; transcript_id "TSBP1--NOTCH4^ENST00000375015.8"  ; transcript_name "TSBP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TSBP1--NOTCH4	HAVANA	gene	29086	51058	.	+	.	FI_gene_label "NOTCH4^ENSG00000204301.6"  ; ID "TSBP1--NOTCH4^NOTCH4^ENSG00000204301.6"  ; ccdsid "CCDS34420.1"  ; exon_id "ENSE00001658736.1"  ; exon_number 1 ; gene_id "TSBP1--NOTCH4^NOTCH4^ENSG00000204301.6"  ; gene_name NOTCH4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031044.2"  ; havana_transcript "OTTHUMT00000076045.2"  ; hgnc_id "HGNC:7884"  ; level 2 ; orig_coord_info "chr6,32223856,32223928,-"  ; protein_id "ENSP00000364163.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TSBP1--NOTCH4^ENST00000375023.3"  ; transcript_name "NOTCH4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TSBP1--NOTCH4	HAVANA	mRNA	29086	51058	.	+	.	FI_gene_label "NOTCH4^ENSG00000204301.6"  ; ID "TSBP1--NOTCH4^ENST00000375023.3"  ; Parent "TSBP1--NOTCH4^NOTCH4^ENSG00000204301.6"  ; ccdsid "CCDS34420.1"  ; exon_id "ENSE00001658736.1"  ; exon_number 1 ; gene_id "TSBP1--NOTCH4^NOTCH4^ENSG00000204301.6"  ; gene_name NOTCH4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031044.2"  ; havana_transcript "OTTHUMT00000076045.2"  ; hgnc_id "HGNC:7884"  ; level 2 ; orig_coord_info "chr6,32223856,32223928,-"  ; protein_id "ENSP00000364163.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TSBP1--NOTCH4^ENST00000375023.3"  ; transcript_name "NOTCH4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TSBP1--TSBP1-AS1	HAVANA	gene	1006	24941	.	+	.	FI_gene_label "TSBP1^ENSG00000204296.12"  ; ID "TSBP1--TSBP1-AS1^TSBP1^ENSG00000204296.12"  ; exon_id "ENSE00001877826.1"  ; exon_number 1 ; gene_id "TSBP1--TSBP1-AS1^TSBP1^ENSG00000204296.12"  ; gene_name TSBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031107.5"  ; havana_transcript "OTTHUMT00000076177.2"  ; hgnc_id "HGNC:13922"  ; level 2 ; orig_coord_info "chr6,32371694,32371706,-"  ; protein_id "ENSP00000364155.4"  ; tag basic appris_alternative_2 ; transcript_id "TSBP1--TSBP1-AS1^ENST00000375015.8"  ; transcript_name "TSBP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TSBP1--TSBP1-AS1	HAVANA	mRNA	1006	24941	.	+	.	FI_gene_label "TSBP1^ENSG00000204296.12"  ; ID "TSBP1--TSBP1-AS1^ENST00000375015.8"  ; Parent "TSBP1--TSBP1-AS1^TSBP1^ENSG00000204296.12"  ; exon_id "ENSE00001877826.1"  ; exon_number 1 ; gene_id "TSBP1--TSBP1-AS1^TSBP1^ENSG00000204296.12"  ; gene_name TSBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031107.5"  ; havana_transcript "OTTHUMT00000076177.2"  ; hgnc_id "HGNC:13922"  ; level 2 ; orig_coord_info "chr6,32371694,32371706,-"  ; protein_id "ENSP00000364155.4"  ; tag basic appris_alternative_2 ; transcript_id "TSBP1--TSBP1-AS1^ENST00000375015.8"  ; transcript_name "TSBP1-201"  ; transcript_support_level 5 ; 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: 
FRG1DP--5_8S_rRNA	HAVANA	gene	1001	9531	.	+	.	FI_gene_label "FRG1DP^ENSG00000282870.1"  ; ID "FRG1DP--5_8S_rRNA^FRG1DP^ENSG00000282870.1"  ; exon_id "ENSE00003790844.1"  ; exon_number 1 ; gene_id "FRG1DP--5_8S_rRNA^FRG1DP^ENSG00000282870.1"  ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1"  ; havana_transcript "OTTHUMT00000488295.1"  ; hgnc_id "HGNC:51763"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr20,29080390,29080455,+"  ; tag basic ; transcript_id "FRG1DP--5_8S_rRNA^ENST00000635586.1"  ; transcript_name "FRG1DP-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
FRG1DP--5_8S_rRNA	HAVANA	RNA	1001	9531	.	+	.	FI_gene_label "FRG1DP^ENSG00000282870.1"  ; ID "FRG1DP--5_8S_rRNA^ENST00000635586.1"  ; Parent "FRG1DP--5_8S_rRNA^FRG1DP^ENSG00000282870.1"  ; exon_id "ENSE00003790844.1"  ; exon_number 1 ; gene_id "FRG1DP--5_8S_rRNA^FRG1DP^ENSG00000282870.1"  ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1"  ; havana_transcript "OTTHUMT00000488295.1"  ; hgnc_id "HGNC:51763"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr20,29080390,29080455,+"  ; tag basic ; transcript_id "FRG1DP--5_8S_rRNA^ENST00000635586.1"  ; transcript_name "FRG1DP-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
FRG1DP--5_8S_rRNA	ENSEMBL	gene	12532	12682	.	+	.	FI_gene_label "5_8S_rRNA^ENSG00000283274.1"  ; ID "FRG1DP--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1"  ; exon_id "ENSE00003799578.1"  ; exon_number 1 ; gene_id "FRG1DP--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1"  ; gene_name 5_8S_rRNA ; gene_type rRNA ; level 3 ; orig_coord_info "chr14,16057472,16057622,+"  ; tag basic ; transcript_id "FRG1DP--5_8S_rRNA^ENST00000636054.1"  ; transcript_name "5_8S_rRNA.7-201"  ; transcript_support_level NA ; transcript_type rRNA
FRG1DP--5_8S_rRNA	ENSEMBL	RNA	12532	12682	.	+	.	FI_gene_label "5_8S_rRNA^ENSG00000283274.1"  ; ID "FRG1DP--5_8S_rRNA^ENST00000636054.1"  ; Parent "FRG1DP--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1"  ; exon_id "ENSE00003799578.1"  ; exon_number 1 ; gene_id "FRG1DP--5_8S_rRNA^5_8S_rRNA^ENSG00000283274.1"  ; gene_name 5_8S_rRNA ; gene_type rRNA ; level 3 ; orig_coord_info "chr14,16057472,16057622,+"  ; tag basic ; transcript_id "FRG1DP--5_8S_rRNA^ENST00000636054.1"  ; transcript_name "5_8S_rRNA.7-201"  ; transcript_support_level NA ; transcript_type rRNA
L1 and L2 created: 
FRG1DP--MLLT10P1	HAVANA	gene	12532	12793	.	+	.	FI_gene_label "MLLT10P1^ENSG00000238151.1"  ; ID "FRG1DP--MLLT10P1^MLLT10P1^ENSG00000238151.1"  ; exon_id "ENSE00001734098.1"  ; exon_number 1 ; gene_id "FRG1DP--MLLT10P1^MLLT10P1^ENSG00000238151.1"  ; gene_name MLLT10P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000032156.1"  ; havana_transcript "OTTHUMT00000078493.1"  ; hgnc_id "HGNC:15794"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr20,30403123,30403384,-"  ; tag basic ; transcript_id "FRG1DP--MLLT10P1^ENST00000418346.1"  ; transcript_name "MLLT10P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
FRG1DP--MLLT10P1	HAVANA	RNA	12532	12793	.	+	.	FI_gene_label "MLLT10P1^ENSG00000238151.1"  ; ID "FRG1DP--MLLT10P1^ENST00000418346.1"  ; Parent "FRG1DP--MLLT10P1^MLLT10P1^ENSG00000238151.1"  ; exon_id "ENSE00001734098.1"  ; exon_number 1 ; gene_id "FRG1DP--MLLT10P1^MLLT10P1^ENSG00000238151.1"  ; gene_name MLLT10P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000032156.1"  ; havana_transcript "OTTHUMT00000078493.1"  ; hgnc_id "HGNC:15794"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr20,30403123,30403384,-"  ; tag basic ; transcript_id "FRG1DP--MLLT10P1^ENST00000418346.1"  ; transcript_name "MLLT10P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
FRG1DP--MLLT10P1	HAVANA	gene	1001	9531	.	+	.	FI_gene_label "FRG1DP^ENSG00000282870.1"  ; ID "FRG1DP--MLLT10P1^FRG1DP^ENSG00000282870.1"  ; exon_id "ENSE00003790844.1"  ; exon_number 1 ; gene_id "FRG1DP--MLLT10P1^FRG1DP^ENSG00000282870.1"  ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1"  ; havana_transcript "OTTHUMT00000488295.1"  ; hgnc_id "HGNC:51763"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr20,29080390,29080455,+"  ; tag basic ; transcript_id "FRG1DP--MLLT10P1^ENST00000635586.1"  ; transcript_name "FRG1DP-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
FRG1DP--MLLT10P1	HAVANA	RNA	1001	9531	.	+	.	FI_gene_label "FRG1DP^ENSG00000282870.1"  ; ID "FRG1DP--MLLT10P1^ENST00000635586.1"  ; Parent "FRG1DP--MLLT10P1^FRG1DP^ENSG00000282870.1"  ; exon_id "ENSE00003790844.1"  ; exon_number 1 ; gene_id "FRG1DP--MLLT10P1^FRG1DP^ENSG00000282870.1"  ; gene_name FRG1DP ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191532.1"  ; havana_transcript "OTTHUMT00000488295.1"  ; hgnc_id "HGNC:51763"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr20,29080390,29080455,+"  ; tag basic ; transcript_id "FRG1DP--MLLT10P1^ENST00000635586.1"  ; transcript_name "FRG1DP-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
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
L1 and L2 created: 
TOPORS--AL162725.2	HAVANA	gene	17485	24869	.	+	.	FI_gene_label "AL162725.2^ENSG00000237153.4"  ; ID "TOPORS--AL162725.2^AL162725.2^ENSG00000237153.4"  ; exon_id "ENSE00003809911.2"  ; exon_number 1 ; gene_id "TOPORS--AL162725.2^AL162725.2^ENSG00000237153.4"  ; gene_name "AL162725.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000019594.5"  ; havana_transcript "OTTHUMT00000051787.4"  ; level 2 ; orig_coord_info "chr9,17018520,17018789,+"  ; tag CAGE_supported_TSS TAGENE ; transcript_id "TOPORS--AL162725.2^ENST00000430545.4"  ; transcript_name "AL162725.2-202"  ; transcript_support_level 5 ; transcript_type lncRNA
TOPORS--AL162725.2	HAVANA	RNA	17485	24869	.	+	.	FI_gene_label "AL162725.2^ENSG00000237153.4"  ; ID "TOPORS--AL162725.2^ENST00000430545.4"  ; Parent "TOPORS--AL162725.2^AL162725.2^ENSG00000237153.4"  ; exon_id "ENSE00003809911.2"  ; exon_number 1 ; gene_id "TOPORS--AL162725.2^AL162725.2^ENSG00000237153.4"  ; gene_name "AL162725.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000019594.5"  ; havana_transcript "OTTHUMT00000051787.4"  ; level 2 ; orig_coord_info "chr9,17018520,17018789,+"  ; tag CAGE_supported_TSS TAGENE ; transcript_id "TOPORS--AL162725.2^ENST00000430545.4"  ; transcript_name "AL162725.2-202"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TSBP1--TSBP1-AS1	HAVANA	gene	30157	34671	.	+	.	FI_gene_label "TSBP1-AS1^ENSG00000225914.3"  ; ID "TSBP1--TSBP1-AS1^TSBP1-AS1^ENSG00000225914.3"  ; exon_id "ENSE00001680220.1"  ; exon_number 1 ; gene_id "TSBP1--TSBP1-AS1^TSBP1-AS1^ENSG00000225914.3"  ; gene_name "TSBP1-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000031217.4"  ; havana_transcript "OTTHUMT00000316882.2"  ; hgnc_id "HGNC:39756"  ; level 1 ; orig_coord_info "chr6,32255711,32255941,+"  ; tag exp_conf ; transcript_id "TSBP1--TSBP1-AS1^ENST00000425033.1"  ; transcript_name "TSBP1-AS1-203"  ; transcript_support_level 2 ; transcript_type lncRNA
TSBP1--TSBP1-AS1	HAVANA	RNA	30157	34671	.	+	.	FI_gene_label "TSBP1-AS1^ENSG00000225914.3"  ; ID "TSBP1--TSBP1-AS1^ENST00000425033.1"  ; Parent "TSBP1--TSBP1-AS1^TSBP1-AS1^ENSG00000225914.3"  ; exon_id "ENSE00001680220.1"  ; exon_number 1 ; gene_id "TSBP1--TSBP1-AS1^TSBP1-AS1^ENSG00000225914.3"  ; gene_name "TSBP1-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000031217.4"  ; havana_transcript "OTTHUMT00000316882.2"  ; hgnc_id "HGNC:39756"  ; level 1 ; orig_coord_info "chr6,32255711,32255941,+"  ; tag exp_conf ; transcript_id "TSBP1--TSBP1-AS1^ENST00000425033.1"  ; transcript_name "TSBP1-AS1-203"  ; transcript_support_level 2 ; transcript_type lncRNA
260 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 ------------------------------
438 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 15 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