.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00582_B23MVV7LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/2e8f95a890ba00edeb539b5d4e7fc0/.command.log
Size: 39.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00582_B23MVV7LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/56f3ba5098a26e57a4657ff13fdc3b/fi_workdir/tih_rna_sample_00582_B23MVV7LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/2e8f95a890ba00edeb539b5d4e7fc0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/2e8f95a890ba00edeb539b5d4e7fc0/.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         |
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                          ------ 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: 2570
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2570
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => CDS exon
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:2570
  => 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: 
ABCA2--AOPEP	ENSEMBL	gene	1635	19851	.	+	.	FI_gene_label "ABCA2^ENSG00000107331.17"  ; ID "ABCA2--AOPEP^ABCA2^ENSG00000107331.17"  ; exon_id "ENSE00001303902.2"  ; exon_number 1 ; gene_id "ABCA2--AOPEP^ABCA2^ENSG00000107331.17"  ; gene_name ABCA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020958.6"  ; hgnc_id "HGNC:32"  ; level 3 ; orig_coord_info "chr9,137028075,137028140,-"  ; protein_id "ENSP00000265662.5"  ; tag basic appris_alternative_2 ; transcript_id "ABCA2--AOPEP^ENST00000265662.9"  ; transcript_name "ABCA2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ABCA2--AOPEP	ENSEMBL	mRNA	1635	19851	.	+	.	FI_gene_label "ABCA2^ENSG00000107331.17"  ; ID "ABCA2--AOPEP^ENST00000265662.9"  ; Parent "ABCA2--AOPEP^ABCA2^ENSG00000107331.17"  ; exon_id "ENSE00001303902.2"  ; exon_number 1 ; gene_id "ABCA2--AOPEP^ABCA2^ENSG00000107331.17"  ; gene_name ABCA2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020958.6"  ; hgnc_id "HGNC:32"  ; level 3 ; orig_coord_info "chr9,137028075,137028140,-"  ; protein_id "ENSP00000265662.5"  ; tag basic appris_alternative_2 ; transcript_id "ABCA2--AOPEP^ENST00000265662.9"  ; transcript_name "ABCA2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ABCA2--AOPEP	HAVANA	gene	22949	35570	.	+	.	FI_gene_label "AOPEP^ENSG00000148120.17"  ; ID "ABCA2--AOPEP^AOPEP^ENSG00000148120.17"  ; ccdsid "CCDS55327.1"  ; exon_id "ENSE00001335355.1"  ; exon_number 2 ; gene_id "ABCA2--AOPEP^AOPEP^ENSG00000148120.17"  ; gene_name AOPEP ; gene_type protein_coding ; havana_gene "OTTHUMG00000020276.4"  ; havana_transcript "OTTHUMT00000053199.1"  ; hgnc_id "HGNC:1361"  ; level 2 ; orig_coord_info "chr9,94759784,94760580,+"  ; protein_id "ENSP00000277198.2"  ; tag basic CCDS ; transcript_id "ABCA2--AOPEP^ENST00000277198.6"  ; transcript_name "AOPEP-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ABCA2--AOPEP	HAVANA	mRNA	22949	35570	.	+	.	FI_gene_label "AOPEP^ENSG00000148120.17"  ; ID "ABCA2--AOPEP^ENST00000277198.6"  ; Parent "ABCA2--AOPEP^AOPEP^ENSG00000148120.17"  ; ccdsid "CCDS55327.1"  ; exon_id "ENSE00001335355.1"  ; exon_number 2 ; gene_id "ABCA2--AOPEP^AOPEP^ENSG00000148120.17"  ; gene_name AOPEP ; gene_type protein_coding ; havana_gene "OTTHUMG00000020276.4"  ; havana_transcript "OTTHUMT00000053199.1"  ; hgnc_id "HGNC:1361"  ; level 2 ; orig_coord_info "chr9,94759784,94760580,+"  ; protein_id "ENSP00000277198.2"  ; tag basic CCDS ; transcript_id "ABCA2--AOPEP^ENST00000277198.6"  ; transcript_name "AOPEP-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
COLGALT1--AK6P1	HAVANA	gene	1001	16069	.	+	.	FI_gene_label "COLGALT1^ENSG00000130309.11"  ; ID "COLGALT1--AK6P1^COLGALT1^ENSG00000130309.11"  ; ccdsid "CCDS12363.1"  ; exon_id "ENSE00002206399.3"  ; exon_number 1 ; gene_id "COLGALT1--AK6P1^COLGALT1^ENSG00000130309.11"  ; gene_name COLGALT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182893.3"  ; havana_transcript "OTTHUMT00000464216.2"  ; hgnc_id "HGNC:26182"  ; level 2 ; orig_coord_info "chr19,17555714,17555973,+"  ; protein_id "ENSP00000252599.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COLGALT1--AK6P1^ENST00000252599.9"  ; transcript_name "COLGALT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COLGALT1--AK6P1	HAVANA	mRNA	1001	16069	.	+	.	FI_gene_label "COLGALT1^ENSG00000130309.11"  ; ID "COLGALT1--AK6P1^ENST00000252599.9"  ; Parent "COLGALT1--AK6P1^COLGALT1^ENSG00000130309.11"  ; ccdsid "CCDS12363.1"  ; exon_id "ENSE00002206399.3"  ; exon_number 1 ; gene_id "COLGALT1--AK6P1^COLGALT1^ENSG00000130309.11"  ; gene_name COLGALT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182893.3"  ; havana_transcript "OTTHUMT00000464216.2"  ; hgnc_id "HGNC:26182"  ; level 2 ; orig_coord_info "chr19,17555714,17555973,+"  ; protein_id "ENSP00000252599.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COLGALT1--AK6P1^ENST00000252599.9"  ; transcript_name "COLGALT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COLGALT1--ZNF970P	HAVANA	gene	1001	16069	.	+	.	FI_gene_label "COLGALT1^ENSG00000130309.11"  ; ID "COLGALT1--ZNF970P^COLGALT1^ENSG00000130309.11"  ; ccdsid "CCDS12363.1"  ; exon_id "ENSE00002206399.3"  ; exon_number 1 ; gene_id "COLGALT1--ZNF970P^COLGALT1^ENSG00000130309.11"  ; gene_name COLGALT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182893.3"  ; havana_transcript "OTTHUMT00000464216.2"  ; hgnc_id "HGNC:26182"  ; level 2 ; orig_coord_info "chr19,17555714,17555973,+"  ; protein_id "ENSP00000252599.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COLGALT1--ZNF970P^ENST00000252599.9"  ; transcript_name "COLGALT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COLGALT1--ZNF970P	HAVANA	mRNA	1001	16069	.	+	.	FI_gene_label "COLGALT1^ENSG00000130309.11"  ; ID "COLGALT1--ZNF970P^ENST00000252599.9"  ; Parent "COLGALT1--ZNF970P^COLGALT1^ENSG00000130309.11"  ; ccdsid "CCDS12363.1"  ; exon_id "ENSE00002206399.3"  ; exon_number 1 ; gene_id "COLGALT1--ZNF970P^COLGALT1^ENSG00000130309.11"  ; gene_name COLGALT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182893.3"  ; havana_transcript "OTTHUMT00000464216.2"  ; hgnc_id "HGNC:26182"  ; level 2 ; orig_coord_info "chr19,17555714,17555973,+"  ; protein_id "ENSP00000252599.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COLGALT1--ZNF970P^ENST00000252599.9"  ; transcript_name "COLGALT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EFL1--GOLGA6L11P	HAVANA	gene	1001	25062	.	+	.	FI_gene_label "EFL1^ENSG00000140598.15"  ; ID "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15"  ; ccdsid "CCDS42071.1"  ; exon_id "ENSE00003786417.1"  ; exon_number 2 ; gene_id "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15"  ; gene_name EFL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172573.5"  ; havana_transcript "OTTHUMT00000419252.2"  ; hgnc_id "HGNC:25789"  ; level 2 ; orig_coord_info "chr15,82261688,82261778,-"  ; protein_id "ENSP00000268206.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFL1--GOLGA6L11P^ENST00000268206.12"  ; transcript_name "EFL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EFL1--GOLGA6L11P	HAVANA	mRNA	1001	25062	.	+	.	FI_gene_label "EFL1^ENSG00000140598.15"  ; ID "EFL1--GOLGA6L11P^ENST00000268206.12"  ; Parent "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15"  ; ccdsid "CCDS42071.1"  ; exon_id "ENSE00003786417.1"  ; exon_number 2 ; gene_id "EFL1--GOLGA6L11P^EFL1^ENSG00000140598.15"  ; gene_name EFL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172573.5"  ; havana_transcript "OTTHUMT00000419252.2"  ; hgnc_id "HGNC:25789"  ; level 2 ; orig_coord_info "chr15,82261688,82261778,-"  ; protein_id "ENSP00000268206.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EFL1--GOLGA6L11P^ENST00000268206.12"  ; transcript_name "EFL1-201"  ; 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: 
PRSS27--TPSB2	HAVANA	gene	1328	8540	.	+	.	FI_gene_label "PRSS27^ENSG00000172382.10"  ; ID "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; ccdsid "CCDS10476.1"  ; exon_id "ENSE00001215985.4"  ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3"  ; havana_transcript "OTTHUMT00000250908.2"  ; hgnc_id "HGNC:15475"  ; level 2 ; orig_coord_info "chr16,2720115,2720160,-"  ; protein_id "ENSP00000306390.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8"  ; transcript_name "PRSS27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2	HAVANA	mRNA	1328	8540	.	+	.	FI_gene_label "PRSS27^ENSG00000172382.10"  ; ID "PRSS27--TPSB2^ENST00000302641.8"  ; Parent "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; ccdsid "CCDS10476.1"  ; exon_id "ENSE00001215985.4"  ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3"  ; havana_transcript "OTTHUMT00000250908.2"  ; hgnc_id "HGNC:15475"  ; level 2 ; orig_coord_info "chr16,2720115,2720160,-"  ; protein_id "ENSP00000306390.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8"  ; transcript_name "PRSS27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRSS27--TPSB2	HAVANA	gene	11544	13392	.	+	.	FI_gene_label "TPSB2^ENSG00000197253.13"  ; ID "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; exon_id "ENSE00003747406.1"  ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4"  ; havana_transcript "OTTHUMT00000342363.2"  ; hgnc_id "HGNC:14120"  ; level 2 ; orig_coord_info "chr16,1229891,1229951,-"  ; protein_id "ENSP00000482743.1"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5"  ; transcript_name "TPSB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2	HAVANA	mRNA	11544	13392	.	+	.	FI_gene_label "TPSB2^ENSG00000197253.13"  ; ID "PRSS27--TPSB2^ENST00000606293.5"  ; Parent "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; exon_id "ENSE00003747406.1"  ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4"  ; havana_transcript "OTTHUMT00000342363.2"  ; hgnc_id "HGNC:14120"  ; level 2 ; orig_coord_info "chr16,1229891,1229951,-"  ; protein_id "ENSP00000482743.1"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5"  ; transcript_name "TPSB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RABL6--DAPK1	HAVANA	gene	1006	19420	.	+	.	FI_gene_label "RABL6^ENSG00000196642.19"  ; ID "RABL6--DAPK1^RABL6^ENSG00000196642.19"  ; ccdsid "CCDS48058.1"  ; exon_id "ENSE00003849626.1"  ; exon_number 1 ; gene_id "RABL6--DAPK1^RABL6^ENSG00000196642.19"  ; gene_name RABL6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020947.13"  ; havana_transcript "OTTHUMT00000055141.5"  ; hgnc_id "HGNC:24703"  ; level 2 ; orig_coord_info "chr9,136808197,136808326,+"  ; protein_id "ENSP00000311134.7"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RABL6--DAPK1^ENST00000311502.12"  ; transcript_name "RABL6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RABL6--DAPK1	HAVANA	mRNA	1006	19420	.	+	.	FI_gene_label "RABL6^ENSG00000196642.19"  ; ID "RABL6--DAPK1^ENST00000311502.12"  ; Parent "RABL6--DAPK1^RABL6^ENSG00000196642.19"  ; ccdsid "CCDS48058.1"  ; exon_id "ENSE00003849626.1"  ; exon_number 1 ; gene_id "RABL6--DAPK1^RABL6^ENSG00000196642.19"  ; gene_name RABL6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020947.13"  ; havana_transcript "OTTHUMT00000055141.5"  ; hgnc_id "HGNC:24703"  ; level 2 ; orig_coord_info "chr9,136808197,136808326,+"  ; protein_id "ENSP00000311134.7"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RABL6--DAPK1^ENST00000311502.12"  ; transcript_name "RABL6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RABL6--DAPK1	HAVANA	gene	22421	54058	.	+	.	FI_gene_label "DAPK1^ENSG00000196730.13"  ; ID "RABL6--DAPK1^DAPK1^ENSG00000196730.13"  ; ccdsid "CCDS43842.1"  ; exon_id "ENSE00003689619.1"  ; exon_number 2 ; gene_id "RABL6--DAPK1^DAPK1^ENSG00000196730.13"  ; gene_name DAPK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020150.5"  ; havana_transcript "OTTHUMT00000052942.3"  ; hgnc_id "HGNC:2674"  ; level 2 ; orig_coord_info "chr9,87499078,87499139,+"  ; protein_id "ENSP00000350785.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "RABL6--DAPK1^ENST00000358077.9"  ; transcript_name "DAPK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RABL6--DAPK1	HAVANA	mRNA	22421	54058	.	+	.	FI_gene_label "DAPK1^ENSG00000196730.13"  ; ID "RABL6--DAPK1^ENST00000358077.9"  ; Parent "RABL6--DAPK1^DAPK1^ENSG00000196730.13"  ; ccdsid "CCDS43842.1"  ; exon_id "ENSE00003689619.1"  ; exon_number 2 ; gene_id "RABL6--DAPK1^DAPK1^ENSG00000196730.13"  ; gene_name DAPK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020150.5"  ; havana_transcript "OTTHUMT00000052942.3"  ; hgnc_id "HGNC:2674"  ; level 2 ; orig_coord_info "chr9,87499078,87499139,+"  ; protein_id "ENSP00000350785.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "RABL6--DAPK1^ENST00000358077.9"  ; transcript_name "DAPK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SUSD1--CORO2A	HAVANA	gene	27129	42845	.	+	.	FI_gene_label "CORO2A^ENSG00000106789.13"  ; ID "SUSD1--CORO2A^CORO2A^ENSG00000106789.13"  ; ccdsid "CCDS6735.1"  ; exon_id "ENSE00001465687.1"  ; exon_number 2 ; gene_id "SUSD1--CORO2A^CORO2A^ENSG00000106789.13"  ; gene_name CORO2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000020340.2"  ; havana_transcript "OTTHUMT00000053357.1"  ; hgnc_id "HGNC:2255"  ; level 2 ; orig_coord_info "chr9,98157460,98157660,-"  ; protein_id "ENSP00000343746.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "SUSD1--CORO2A^ENST00000343933.9"  ; transcript_name "CORO2A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SUSD1--CORO2A	HAVANA	mRNA	27129	42845	.	+	.	FI_gene_label "CORO2A^ENSG00000106789.13"  ; ID "SUSD1--CORO2A^ENST00000343933.9"  ; Parent "SUSD1--CORO2A^CORO2A^ENSG00000106789.13"  ; ccdsid "CCDS6735.1"  ; exon_id "ENSE00001465687.1"  ; exon_number 2 ; gene_id "SUSD1--CORO2A^CORO2A^ENSG00000106789.13"  ; gene_name CORO2A ; gene_type protein_coding ; havana_gene "OTTHUMG00000020340.2"  ; havana_transcript "OTTHUMT00000053357.1"  ; hgnc_id "HGNC:2255"  ; level 2 ; orig_coord_info "chr9,98157460,98157660,-"  ; protein_id "ENSP00000343746.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "SUSD1--CORO2A^ENST00000343933.9"  ; transcript_name "CORO2A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SUSD1--CORO2A	HAVANA	gene	1113	23047	.	+	.	FI_gene_label "SUSD1^ENSG00000106868.17"  ; ID "SUSD1--CORO2A^SUSD1^ENSG00000106868.17"  ; exon_id "ENSE00001706926.1"  ; exon_number 1 ; gene_id "SUSD1--CORO2A^SUSD1^ENSG00000106868.17"  ; gene_name SUSD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020499.5"  ; havana_transcript "OTTHUMT00000053667.2"  ; hgnc_id "HGNC:25413"  ; level 1 ; orig_coord_info "chr9,112175133,112175185,-"  ; protein_id "ENSP00000347558.3"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "SUSD1--CORO2A^ENST00000355396.7"  ; transcript_name "SUSD1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
SUSD1--CORO2A	HAVANA	mRNA	1113	23047	.	+	.	FI_gene_label "SUSD1^ENSG00000106868.17"  ; ID "SUSD1--CORO2A^ENST00000355396.7"  ; Parent "SUSD1--CORO2A^SUSD1^ENSG00000106868.17"  ; exon_id "ENSE00001706926.1"  ; exon_number 1 ; gene_id "SUSD1--CORO2A^SUSD1^ENSG00000106868.17"  ; gene_name SUSD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020499.5"  ; havana_transcript "OTTHUMT00000053667.2"  ; hgnc_id "HGNC:25413"  ; level 1 ; orig_coord_info "chr9,112175133,112175185,-"  ; protein_id "ENSP00000347558.3"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "SUSD1--CORO2A^ENST00000355396.7"  ; transcript_name "SUSD1-201"  ; transcript_support_level 2 ; 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: 
AP001347.1--ANKRD20A11P	HAVANA	gene	8798	22852	.	+	.	FI_gene_label "ANKRD20A11P^ENSG00000215559.8"  ; ID "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; exon_id "ENSE00002284794.1"  ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; gene_name ANKRD20A11P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074237.2"  ; havana_transcript "OTTHUMT00000157750.1"  ; hgnc_id "HGNC:42024"  ; level 2 ; orig_coord_info "chr21,13979702,13980437,-"  ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000344693.5"  ; transcript_name "ANKRD20A11P-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
AP001347.1--ANKRD20A11P	HAVANA	RNA	8798	22852	.	+	.	FI_gene_label "ANKRD20A11P^ENSG00000215559.8"  ; ID "AP001347.1--ANKRD20A11P^ENST00000344693.5"  ; Parent "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; exon_id "ENSE00002284794.1"  ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; gene_name ANKRD20A11P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074237.2"  ; havana_transcript "OTTHUMT00000157750.1"  ; hgnc_id "HGNC:42024"  ; level 2 ; orig_coord_info "chr21,13979702,13980437,-"  ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000344693.5"  ; transcript_name "ANKRD20A11P-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
AP001347.1--ANKRD20A11P	HAVANA	gene	1003	5797	.	+	.	FI_gene_label "AP001347.1^ENSG00000224905.7"  ; ID "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7"  ; exon_id "ENSE00001608016.1"  ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7"  ; gene_name "AP001347.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000074260.3"  ; havana_transcript "OTTHUMT00000157812.1"  ; level 2 ; orig_coord_info "chr21,14027421,14027597,+"  ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000428809.5"  ; transcript_name "AP001347.1-202"  ; transcript_support_level 1 ; transcript_type lncRNA
AP001347.1--ANKRD20A11P	HAVANA	RNA	1003	5797	.	+	.	FI_gene_label "AP001347.1^ENSG00000224905.7"  ; ID "AP001347.1--ANKRD20A11P^ENST00000428809.5"  ; Parent "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7"  ; exon_id "ENSE00001608016.1"  ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7"  ; gene_name "AP001347.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000074260.3"  ; havana_transcript "OTTHUMT00000157812.1"  ; level 2 ; orig_coord_info "chr21,14027421,14027597,+"  ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000428809.5"  ; transcript_name "AP001347.1-202"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
COLGALT1--AK6P1	HAVANA	gene	19075	19552	.	+	.	FI_gene_label "AK6P1^ENSG00000256614.1"  ; ID "COLGALT1--AK6P1^AK6P1^ENSG00000256614.1"  ; exon_id "ENSE00002309684.1"  ; exon_number 1 ; gene_id "COLGALT1--AK6P1^AK6P1^ENSG00000256614.1"  ; gene_name AK6P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000169291.1"  ; havana_transcript "OTTHUMT00000403318.1"  ; hgnc_id "HGNC:51678"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr12,34249481,34249958,+"  ; tag pseudo_consens basic ; transcript_id "COLGALT1--AK6P1^ENST00000540219.1"  ; transcript_name "AK6P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
COLGALT1--AK6P1	HAVANA	RNA	19075	19552	.	+	.	FI_gene_label "AK6P1^ENSG00000256614.1"  ; ID "COLGALT1--AK6P1^ENST00000540219.1"  ; Parent "COLGALT1--AK6P1^AK6P1^ENSG00000256614.1"  ; exon_id "ENSE00002309684.1"  ; exon_number 1 ; gene_id "COLGALT1--AK6P1^AK6P1^ENSG00000256614.1"  ; gene_name AK6P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000169291.1"  ; havana_transcript "OTTHUMT00000403318.1"  ; hgnc_id "HGNC:51678"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr12,34249481,34249958,+"  ; tag pseudo_consens basic ; transcript_id "COLGALT1--AK6P1^ENST00000540219.1"  ; transcript_name "AK6P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
COLGALT1--ZNF970P	HAVANA	gene	19075	19872	.	+	.	FI_gene_label "ZNF970P^ENSG00000258368.2"  ; ID "COLGALT1--ZNF970P^ZNF970P^ENSG00000258368.2"  ; exon_id "ENSE00002371322.2"  ; exon_number 1 ; gene_id "COLGALT1--ZNF970P^ZNF970P^ENSG00000258368.2"  ; gene_name ZNF970P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000169295.2"  ; havana_transcript "OTTHUMT00000403346.2"  ; hgnc_id "HGNC:44511"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr12,37575587,37575713,+"  ; tag basic ; transcript_id "COLGALT1--ZNF970P^ENST00000547456.2"  ; transcript_name "ZNF970P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
COLGALT1--ZNF970P	HAVANA	RNA	19075	19872	.	+	.	FI_gene_label "ZNF970P^ENSG00000258368.2"  ; ID "COLGALT1--ZNF970P^ENST00000547456.2"  ; Parent "COLGALT1--ZNF970P^ZNF970P^ENSG00000258368.2"  ; exon_id "ENSE00002371322.2"  ; exon_number 1 ; gene_id "COLGALT1--ZNF970P^ZNF970P^ENSG00000258368.2"  ; gene_name ZNF970P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000169295.2"  ; havana_transcript "OTTHUMT00000403346.2"  ; hgnc_id "HGNC:44511"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr12,37575587,37575713,+"  ; tag basic ; transcript_id "COLGALT1--ZNF970P^ENST00000547456.2"  ; transcript_name "ZNF970P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
EFL1--GOLGA6L11P	HAVANA	gene	28063	33687	.	+	.	FI_gene_label "GOLGA6L11P^ENSG00000223698.3"  ; ID "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3"  ; exon_id "ENSE00001742768.1"  ; exon_number 1 ; gene_id "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3"  ; gene_name GOLGA6L11P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000045042.2"  ; havana_transcript "OTTHUMT00000104689.2"  ; hgnc_id "HGNC:23958"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chrY,24168187,24168270,+"  ; tag pseudo_consens basic ; transcript_id "EFL1--GOLGA6L11P^ENST00000417252.2"  ; transcript_name "GOLGA6L11P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
EFL1--GOLGA6L11P	HAVANA	RNA	28063	33687	.	+	.	FI_gene_label "GOLGA6L11P^ENSG00000223698.3"  ; ID "EFL1--GOLGA6L11P^ENST00000417252.2"  ; Parent "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3"  ; exon_id "ENSE00001742768.1"  ; exon_number 1 ; gene_id "EFL1--GOLGA6L11P^GOLGA6L11P^ENSG00000223698.3"  ; gene_name GOLGA6L11P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000045042.2"  ; havana_transcript "OTTHUMT00000104689.2"  ; hgnc_id "HGNC:23958"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chrY,24168187,24168270,+"  ; tag pseudo_consens basic ; transcript_id "EFL1--GOLGA6L11P^ENST00000417252.2"  ; transcript_name "GOLGA6L11P-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
172 cases fixed where L3 features have parent feature(s) missing
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--------------------------- 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 ------------------------------
284 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 16 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