.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00581_B23MVV7LT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/8ba78e13ed96d317d58078255257fc/.command.out
Size: 38.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00581_B23MVV7LT4_1)
Attempt
Content

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: 4531
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4531
=> 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:4531
  => 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: 
ITCH--RUSC2	HAVANA	gene	1072	35781	.	+	.	FI_gene_label "ITCH^ENSG00000078747.16"  ; ID "ITCH--RUSC2^ITCH^ENSG00000078747.16"  ; ccdsid "CCDS58768.1"  ; exon_id "ENSE00003669122.1"  ; exon_number 3 ; gene_id "ITCH--RUSC2^ITCH^ENSG00000078747.16"  ; gene_name ITCH ; gene_type protein_coding ; havana_gene "OTTHUMG00000032300.6"  ; havana_transcript "OTTHUMT00000078783.2"  ; hgnc_id "HGNC:13890"  ; level 2 ; orig_coord_info "chr20,34393812,34393881,+"  ; protein_id "ENSP00000262650.5"  ; tag basic CCDS ; transcript_id "ITCH--RUSC2^ENST00000262650.10"  ; transcript_name "ITCH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ITCH--RUSC2	HAVANA	mRNA	1072	35781	.	+	.	FI_gene_label "ITCH^ENSG00000078747.16"  ; ID "ITCH--RUSC2^ENST00000262650.10"  ; Parent "ITCH--RUSC2^ITCH^ENSG00000078747.16"  ; ccdsid "CCDS58768.1"  ; exon_id "ENSE00003669122.1"  ; exon_number 3 ; gene_id "ITCH--RUSC2^ITCH^ENSG00000078747.16"  ; gene_name ITCH ; gene_type protein_coding ; havana_gene "OTTHUMG00000032300.6"  ; havana_transcript "OTTHUMT00000078783.2"  ; hgnc_id "HGNC:13890"  ; level 2 ; orig_coord_info "chr20,34393812,34393881,+"  ; protein_id "ENSP00000262650.5"  ; tag basic CCDS ; transcript_id "ITCH--RUSC2^ENST00000262650.10"  ; transcript_name "ITCH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ITCH--RUSC2	HAVANA	gene	45932	57947	.	+	.	FI_gene_label "RUSC2^ENSG00000198853.12"  ; ID "ITCH--RUSC2^RUSC2^ENSG00000198853.12"  ; ccdsid "CCDS35008.1"  ; exon_id "ENSE00001150629.1"  ; exon_number 2 ; gene_id "ITCH--RUSC2^RUSC2^ENSG00000198853.12"  ; gene_name RUSC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019861.2"  ; havana_transcript "OTTHUMT00000052309.2"  ; hgnc_id "HGNC:23625"  ; level 2 ; orig_coord_info "chr9,35546522,35548535,+"  ; protein_id "ENSP00000355177.3"  ; tag mRNA_end_NF MANE_Select appris_principal_1 CCDS ; transcript_id "ITCH--RUSC2^ENST00000361226.8"  ; transcript_name "RUSC2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ITCH--RUSC2	HAVANA	mRNA	45932	57947	.	+	.	FI_gene_label "RUSC2^ENSG00000198853.12"  ; ID "ITCH--RUSC2^ENST00000361226.8"  ; Parent "ITCH--RUSC2^RUSC2^ENSG00000198853.12"  ; ccdsid "CCDS35008.1"  ; exon_id "ENSE00001150629.1"  ; exon_number 2 ; gene_id "ITCH--RUSC2^RUSC2^ENSG00000198853.12"  ; gene_name RUSC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019861.2"  ; havana_transcript "OTTHUMT00000052309.2"  ; hgnc_id "HGNC:23625"  ; level 2 ; orig_coord_info "chr9,35546522,35548535,+"  ; protein_id "ENSP00000355177.3"  ; tag mRNA_end_NF MANE_Select appris_principal_1 CCDS ; transcript_id "ITCH--RUSC2^ENST00000361226.8"  ; transcript_name "RUSC2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ITPR1--SETMAR	ENSEMBL	gene	1004	92901	.	+	.	FI_gene_label "ITPR1^ENSG00000150995.20"  ; ID "ITPR1--SETMAR^ITPR1^ENSG00000150995.20"  ; ccdsid "CCDS54551.1"  ; exon_id "ENSE00003473040.1"  ; exon_number 3 ; gene_id "ITPR1--SETMAR^ITPR1^ENSG00000150995.20"  ; gene_name ITPR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154996.16"  ; hgnc_id "HGNC:6180"  ; level 3 ; orig_coord_info "chr3,4516492,4516583,+"  ; protein_id "ENSP00000306253.8"  ; tag basic CCDS ; transcript_id "ITPR1--SETMAR^ENST00000302640.12"  ; transcript_name "ITPR1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ITPR1--SETMAR	ENSEMBL	mRNA	1004	92901	.	+	.	FI_gene_label "ITPR1^ENSG00000150995.20"  ; ID "ITPR1--SETMAR^ENST00000302640.12"  ; Parent "ITPR1--SETMAR^ITPR1^ENSG00000150995.20"  ; ccdsid "CCDS54551.1"  ; exon_id "ENSE00003473040.1"  ; exon_number 3 ; gene_id "ITPR1--SETMAR^ITPR1^ENSG00000150995.20"  ; gene_name ITPR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154996.16"  ; hgnc_id "HGNC:6180"  ; level 3 ; orig_coord_info "chr3,4516492,4516583,+"  ; protein_id "ENSP00000306253.8"  ; tag basic CCDS ; transcript_id "ITPR1--SETMAR^ENST00000302640.12"  ; transcript_name "ITPR1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ITPR1--SETMAR	HAVANA	gene	95902	101549	.	+	.	FI_gene_label "SETMAR^ENSG00000170364.12"  ; ID "ITPR1--SETMAR^SETMAR^ENSG00000170364.12"  ; ccdsid "CCDS2563.2"  ; exon_id "ENSE00001498847.2"  ; exon_number 1 ; gene_id "ITPR1--SETMAR^SETMAR^ENSG00000170364.12"  ; gene_name SETMAR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090265.9"  ; havana_transcript "OTTHUMT00000206587.4"  ; hgnc_id "HGNC:10762"  ; level 2 ; orig_coord_info "chr3,4303371,4303526,+"  ; protein_id "ENSP00000373354.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "ITPR1--SETMAR^ENST00000358065.4"  ; transcript_name "SETMAR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ITPR1--SETMAR	HAVANA	mRNA	95902	101549	.	+	.	FI_gene_label "SETMAR^ENSG00000170364.12"  ; ID "ITPR1--SETMAR^ENST00000358065.4"  ; Parent "ITPR1--SETMAR^SETMAR^ENSG00000170364.12"  ; ccdsid "CCDS2563.2"  ; exon_id "ENSE00001498847.2"  ; exon_number 1 ; gene_id "ITPR1--SETMAR^SETMAR^ENSG00000170364.12"  ; gene_name SETMAR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090265.9"  ; havana_transcript "OTTHUMT00000206587.4"  ; hgnc_id "HGNC:10762"  ; level 2 ; orig_coord_info "chr3,4303371,4303526,+"  ; protein_id "ENSP00000373354.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "ITPR1--SETMAR^ENST00000358065.4"  ; transcript_name "SETMAR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NFE2L1--CDK5RAP3	HAVANA	gene	16772	26320	.	+	.	FI_gene_label "CDK5RAP3^ENSG00000108465.15"  ; ID "NFE2L1--CDK5RAP3^CDK5RAP3^ENSG00000108465.15"  ; ccdsid "CCDS42356.1"  ; exon_id "ENSE00002705962.2"  ; exon_number 1 ; gene_id "NFE2L1--CDK5RAP3^CDK5RAP3^ENSG00000108465.15"  ; gene_name CDK5RAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178682.4"  ; havana_transcript "OTTHUMT00000442913.2"  ; hgnc_id "HGNC:18673"  ; level 2 ; orig_coord_info "chr17,47971147,47971152,+"  ; protein_id "ENSP00000344683.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NFE2L1--CDK5RAP3^ENST00000338399.9"  ; transcript_name "CDK5RAP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NFE2L1--CDK5RAP3	HAVANA	mRNA	16772	26320	.	+	.	FI_gene_label "CDK5RAP3^ENSG00000108465.15"  ; ID "NFE2L1--CDK5RAP3^ENST00000338399.9"  ; Parent "NFE2L1--CDK5RAP3^CDK5RAP3^ENSG00000108465.15"  ; ccdsid "CCDS42356.1"  ; exon_id "ENSE00002705962.2"  ; exon_number 1 ; gene_id "NFE2L1--CDK5RAP3^CDK5RAP3^ENSG00000108465.15"  ; gene_name CDK5RAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178682.4"  ; havana_transcript "OTTHUMT00000442913.2"  ; hgnc_id "HGNC:18673"  ; level 2 ; orig_coord_info "chr17,47971147,47971152,+"  ; protein_id "ENSP00000344683.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NFE2L1--CDK5RAP3^ENST00000338399.9"  ; transcript_name "CDK5RAP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NFE2L1--CDK5RAP3	HAVANA	gene	1042	12006	.	+	.	FI_gene_label "NFE2L1^ENSG00000082641.16"  ; ID "NFE2L1--CDK5RAP3^NFE2L1^ENSG00000082641.16"  ; ccdsid "CCDS82150.1"  ; exon_id "ENSE00001340556.2"  ; exon_number 2 ; gene_id "NFE2L1--CDK5RAP3^NFE2L1^ENSG00000082641.16"  ; gene_name NFE2L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178706.5"  ; havana_transcript "OTTHUMT00000443021.1"  ; hgnc_id "HGNC:7781"  ; level 2 ; orig_coord_info "chr17,48051119,48051628,+"  ; protein_id "ENSP00000350072.5"  ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "NFE2L1--CDK5RAP3^ENST00000357480.9"  ; transcript_name "NFE2L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NFE2L1--CDK5RAP3	HAVANA	mRNA	1042	12006	.	+	.	FI_gene_label "NFE2L1^ENSG00000082641.16"  ; ID "NFE2L1--CDK5RAP3^ENST00000357480.9"  ; Parent "NFE2L1--CDK5RAP3^NFE2L1^ENSG00000082641.16"  ; ccdsid "CCDS82150.1"  ; exon_id "ENSE00001340556.2"  ; exon_number 2 ; gene_id "NFE2L1--CDK5RAP3^NFE2L1^ENSG00000082641.16"  ; gene_name NFE2L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178706.5"  ; havana_transcript "OTTHUMT00000443021.1"  ; hgnc_id "HGNC:7781"  ; level 2 ; orig_coord_info "chr17,48051119,48051628,+"  ; protein_id "ENSP00000350072.5"  ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "NFE2L1--CDK5RAP3^ENST00000357480.9"  ; transcript_name "NFE2L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RRP1B--HSF2BP	HAVANA	gene	22083	31991	.	+	.	FI_gene_label "HSF2BP^ENSG00000160207.9"  ; ID "RRP1B--HSF2BP^HSF2BP^ENSG00000160207.9"  ; ccdsid "CCDS13697.1"  ; exon_id "ENSE00001138002.1"  ; exon_number 2 ; gene_id "RRP1B--HSF2BP^HSF2BP^ENSG00000160207.9"  ; gene_name HSF2BP ; gene_type protein_coding ; havana_gene "OTTHUMG00000086863.3"  ; havana_transcript "OTTHUMT00000195620.2"  ; hgnc_id "HGNC:5226"  ; level 2 ; orig_coord_info "chr21,43658061,43658096,-"  ; protein_id "ENSP00000291560.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RRP1B--HSF2BP^ENST00000291560.7"  ; transcript_name "HSF2BP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RRP1B--HSF2BP	HAVANA	mRNA	22083	31991	.	+	.	FI_gene_label "HSF2BP^ENSG00000160207.9"  ; ID "RRP1B--HSF2BP^ENST00000291560.7"  ; Parent "RRP1B--HSF2BP^HSF2BP^ENSG00000160207.9"  ; ccdsid "CCDS13697.1"  ; exon_id "ENSE00001138002.1"  ; exon_number 2 ; gene_id "RRP1B--HSF2BP^HSF2BP^ENSG00000160207.9"  ; gene_name HSF2BP ; gene_type protein_coding ; havana_gene "OTTHUMG00000086863.3"  ; havana_transcript "OTTHUMT00000195620.2"  ; hgnc_id "HGNC:5226"  ; level 2 ; orig_coord_info "chr21,43658061,43658096,-"  ; protein_id "ENSP00000291560.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RRP1B--HSF2BP^ENST00000291560.7"  ; transcript_name "HSF2BP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RRP1B--HSF2BP	HAVANA	gene	1001	19082	.	+	.	FI_gene_label "RRP1B^ENSG00000160208.13"  ; ID "RRP1B--HSF2BP^RRP1B^ENSG00000160208.13"  ; ccdsid "CCDS33577.1"  ; exon_id "ENSE00001941645.2"  ; exon_number 1 ; gene_id "RRP1B--HSF2BP^RRP1B^ENSG00000160208.13"  ; gene_name RRP1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000086872.4"  ; havana_transcript "OTTHUMT00000195651.3"  ; hgnc_id "HGNC:23818"  ; level 2 ; orig_coord_info "chr21,43659665,43659794,+"  ; protein_id "ENSP00000339145.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RRP1B--HSF2BP^ENST00000340648.6"  ; transcript_name "RRP1B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RRP1B--HSF2BP	HAVANA	mRNA	1001	19082	.	+	.	FI_gene_label "RRP1B^ENSG00000160208.13"  ; ID "RRP1B--HSF2BP^ENST00000340648.6"  ; Parent "RRP1B--HSF2BP^RRP1B^ENSG00000160208.13"  ; ccdsid "CCDS33577.1"  ; exon_id "ENSE00001941645.2"  ; exon_number 1 ; gene_id "RRP1B--HSF2BP^RRP1B^ENSG00000160208.13"  ; gene_name RRP1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000086872.4"  ; havana_transcript "OTTHUMT00000195651.3"  ; hgnc_id "HGNC:23818"  ; level 2 ; orig_coord_info "chr21,43659665,43659794,+"  ; protein_id "ENSP00000339145.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RRP1B--HSF2BP^ENST00000340648.6"  ; transcript_name "RRP1B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SCYL1--AP000769.1	HAVANA	gene	1007	11237	.	+	.	FI_gene_label "SCYL1^ENSG00000142186.17"  ; ID "SCYL1--AP000769.1^SCYL1^ENSG00000142186.17"  ; ccdsid "CCDS41672.1"  ; exon_id "ENSE00003843086.1"  ; exon_number 1 ; gene_id "SCYL1--AP000769.1^SCYL1^ENSG00000142186.17"  ; gene_name SCYL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166325.6"  ; havana_transcript "OTTHUMT00000389159.3"  ; hgnc_id "HGNC:14372"  ; level 2 ; orig_coord_info "chr11,65525154,65525264,+"  ; protein_id "ENSP00000270176.5"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SCYL1--AP000769.1^ENST00000270176.10"  ; transcript_name "SCYL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SCYL1--AP000769.1	HAVANA	mRNA	1007	11237	.	+	.	FI_gene_label "SCYL1^ENSG00000142186.17"  ; ID "SCYL1--AP000769.1^ENST00000270176.10"  ; Parent "SCYL1--AP000769.1^SCYL1^ENSG00000142186.17"  ; ccdsid "CCDS41672.1"  ; exon_id "ENSE00003843086.1"  ; exon_number 1 ; gene_id "SCYL1--AP000769.1^SCYL1^ENSG00000142186.17"  ; gene_name SCYL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166325.6"  ; havana_transcript "OTTHUMT00000389159.3"  ; hgnc_id "HGNC:14372"  ; level 2 ; orig_coord_info "chr11,65525154,65525264,+"  ; protein_id "ENSP00000270176.5"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SCYL1--AP000769.1^ENST00000270176.10"  ; transcript_name "SCYL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SCYL1--AP000769.4	HAVANA	gene	1007	11237	.	+	.	FI_gene_label "SCYL1^ENSG00000142186.17"  ; ID "SCYL1--AP000769.4^SCYL1^ENSG00000142186.17"  ; ccdsid "CCDS41672.1"  ; exon_id "ENSE00003843086.1"  ; exon_number 1 ; gene_id "SCYL1--AP000769.4^SCYL1^ENSG00000142186.17"  ; gene_name SCYL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166325.6"  ; havana_transcript "OTTHUMT00000389159.3"  ; hgnc_id "HGNC:14372"  ; level 2 ; orig_coord_info "chr11,65525154,65525264,+"  ; protein_id "ENSP00000270176.5"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SCYL1--AP000769.4^ENST00000270176.10"  ; transcript_name "SCYL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SCYL1--AP000769.4	HAVANA	mRNA	1007	11237	.	+	.	FI_gene_label "SCYL1^ENSG00000142186.17"  ; ID "SCYL1--AP000769.4^ENST00000270176.10"  ; Parent "SCYL1--AP000769.4^SCYL1^ENSG00000142186.17"  ; ccdsid "CCDS41672.1"  ; exon_id "ENSE00003843086.1"  ; exon_number 1 ; gene_id "SCYL1--AP000769.4^SCYL1^ENSG00000142186.17"  ; gene_name SCYL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166325.6"  ; havana_transcript "OTTHUMT00000389159.3"  ; hgnc_id "HGNC:14372"  ; level 2 ; orig_coord_info "chr11,65525154,65525264,+"  ; protein_id "ENSP00000270176.5"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SCYL1--AP000769.4^ENST00000270176.10"  ; transcript_name "SCYL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STAG1--AL023754.1	HAVANA	gene	1026	42018	.	+	.	FI_gene_label "STAG1^ENSG00000118007.13"  ; ID "STAG1--AL023754.1^STAG1^ENSG00000118007.13"  ; exon_id "ENSE00003662307.1"  ; exon_number 2 ; gene_id "STAG1--AL023754.1^STAG1^ENSG00000118007.13"  ; gene_name STAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159798.5"  ; havana_transcript "OTTHUMT00000357403.1"  ; hgnc_id "HGNC:11354"  ; level 1 ; orig_coord_info "chr3,136630870,136630898,-"  ; protein_id "ENSP00000236698.5"  ; tag basic exp_conf ; transcript_id "STAG1--AL023754.1^ENST00000236698.9"  ; transcript_name "STAG1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STAG1--AL023754.1	HAVANA	mRNA	1026	42018	.	+	.	FI_gene_label "STAG1^ENSG00000118007.13"  ; ID "STAG1--AL023754.1^ENST00000236698.9"  ; Parent "STAG1--AL023754.1^STAG1^ENSG00000118007.13"  ; exon_id "ENSE00003662307.1"  ; exon_number 2 ; gene_id "STAG1--AL023754.1^STAG1^ENSG00000118007.13"  ; gene_name STAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159798.5"  ; havana_transcript "OTTHUMT00000357403.1"  ; hgnc_id "HGNC:11354"  ; level 1 ; orig_coord_info "chr3,136630870,136630898,-"  ; protein_id "ENSP00000236698.5"  ; tag basic exp_conf ; transcript_id "STAG1--AL023754.1^ENST00000236698.9"  ; transcript_name "STAG1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STAG1--AL023754.2	HAVANA	gene	1026	42018	.	+	.	FI_gene_label "STAG1^ENSG00000118007.13"  ; ID "STAG1--AL023754.2^STAG1^ENSG00000118007.13"  ; exon_id "ENSE00003662307.1"  ; exon_number 2 ; gene_id "STAG1--AL023754.2^STAG1^ENSG00000118007.13"  ; gene_name STAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159798.5"  ; havana_transcript "OTTHUMT00000357403.1"  ; hgnc_id "HGNC:11354"  ; level 1 ; orig_coord_info "chr3,136630870,136630898,-"  ; protein_id "ENSP00000236698.5"  ; tag basic exp_conf ; transcript_id "STAG1--AL023754.2^ENST00000236698.9"  ; transcript_name "STAG1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STAG1--AL023754.2	HAVANA	mRNA	1026	42018	.	+	.	FI_gene_label "STAG1^ENSG00000118007.13"  ; ID "STAG1--AL023754.2^ENST00000236698.9"  ; Parent "STAG1--AL023754.2^STAG1^ENSG00000118007.13"  ; exon_id "ENSE00003662307.1"  ; exon_number 2 ; gene_id "STAG1--AL023754.2^STAG1^ENSG00000118007.13"  ; gene_name STAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159798.5"  ; havana_transcript "OTTHUMT00000357403.1"  ; hgnc_id "HGNC:11354"  ; level 1 ; orig_coord_info "chr3,136630870,136630898,-"  ; protein_id "ENSP00000236698.5"  ; tag basic exp_conf ; transcript_id "STAG1--AL023754.2^ENST00000236698.9"  ; transcript_name "STAG1-201"  ; 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: 
ZNF124--CSRP1	HAVANA	gene	15447	28295	.	+	.	FI_gene_label "CSRP1^ENSG00000159176.14"  ; ID "ZNF124--CSRP1^CSRP1^ENSG00000159176.14"  ; ccdsid "CCDS1413.1"  ; exon_id "ENSE00003653306.1"  ; exon_number 2 ; gene_id "ZNF124--CSRP1^CSRP1^ENSG00000159176.14"  ; gene_name CSRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035773.6"  ; havana_transcript "OTTHUMT00000504292.2"  ; hgnc_id "HGNC:2469"  ; level 2 ; orig_coord_info "chr1,201496192,201496303,-"  ; protein_id "ENSP00000345079.2"  ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF124--CSRP1^ENST00000340006.7"  ; transcript_name "CSRP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF124--CSRP1	HAVANA	mRNA	15447	28295	.	+	.	FI_gene_label "CSRP1^ENSG00000159176.14"  ; ID "ZNF124--CSRP1^ENST00000340006.7"  ; Parent "ZNF124--CSRP1^CSRP1^ENSG00000159176.14"  ; ccdsid "CCDS1413.1"  ; exon_id "ENSE00003653306.1"  ; exon_number 2 ; gene_id "ZNF124--CSRP1^CSRP1^ENSG00000159176.14"  ; gene_name CSRP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035773.6"  ; havana_transcript "OTTHUMT00000504292.2"  ; hgnc_id "HGNC:2469"  ; level 2 ; orig_coord_info "chr1,201496192,201496303,-"  ; protein_id "ENSP00000345079.2"  ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF124--CSRP1^ENST00000340006.7"  ; transcript_name "CSRP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF124--CSRP1	HAVANA	gene	1001	5534	.	+	.	FI_gene_label "ZNF124^ENSG00000196418.12"  ; ID "ZNF124--CSRP1^ZNF124^ENSG00000196418.12"  ; ccdsid "CCDS31089.1"  ; exon_id "ENSE00002725410.1"  ; exon_number 1 ; gene_id "ZNF124--CSRP1^ZNF124^ENSG00000196418.12"  ; gene_name ZNF124 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041112.3"  ; havana_transcript "OTTHUMT00000098573.2"  ; hgnc_id "HGNC:12907"  ; level 2 ; orig_coord_info "chr1,247171848,247171877,-"  ; protein_id "ENSP00000340749.6"  ; tag basic CCDS ; transcript_id "ZNF124--CSRP1^ENST00000340684.10"  ; transcript_name "ZNF124-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF124--CSRP1	HAVANA	mRNA	1001	5534	.	+	.	FI_gene_label "ZNF124^ENSG00000196418.12"  ; ID "ZNF124--CSRP1^ENST00000340684.10"  ; Parent "ZNF124--CSRP1^ZNF124^ENSG00000196418.12"  ; ccdsid "CCDS31089.1"  ; exon_id "ENSE00002725410.1"  ; exon_number 1 ; gene_id "ZNF124--CSRP1^ZNF124^ENSG00000196418.12"  ; gene_name ZNF124 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041112.3"  ; havana_transcript "OTTHUMT00000098573.2"  ; hgnc_id "HGNC:12907"  ; level 2 ; orig_coord_info "chr1,247171848,247171877,-"  ; protein_id "ENSP00000340749.6"  ; tag basic CCDS ; transcript_id "ZNF124--CSRP1^ENST00000340684.10"  ; transcript_name "ZNF124-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC136431.1--PKD1P5	HAVANA	gene	9015	30646	.	+	.	FI_gene_label "PKD1P5^ENSG00000254681.6"  ; ID "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6"  ; exon_id "ENSE00002185250.1"  ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6"  ; gene_name PKD1P5 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166287.2"  ; havana_transcript "OTTHUMT00000388923.1"  ; hgnc_id "HGNC:30069"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr16,18401584,18401940,-"  ; tag basic ; transcript_id "AC136431.1--PKD1P5^ENST00000532415.5"  ; transcript_name "PKD1P5-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
AC136431.1--PKD1P5	HAVANA	RNA	9015	30646	.	+	.	FI_gene_label "PKD1P5^ENSG00000254681.6"  ; ID "AC136431.1--PKD1P5^ENST00000532415.5"  ; Parent "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6"  ; exon_id "ENSE00002185250.1"  ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^PKD1P5^ENSG00000254681.6"  ; gene_name PKD1P5 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000166287.2"  ; havana_transcript "OTTHUMT00000388923.1"  ; hgnc_id "HGNC:30069"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr16,18401584,18401940,-"  ; tag basic ; transcript_id "AC136431.1--PKD1P5^ENST00000532415.5"  ; transcript_name "PKD1P5-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AC136431.1--PKD1P5	HAVANA	gene	1001	6014	.	+	.	FI_gene_label "AC136431.1^ENSG00000260126.2"  ; ID "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2"  ; exon_id "ENSE00003856180.1"  ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2"  ; gene_name "AC136431.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000177276.2"  ; havana_transcript "OTTHUMT00000436080.2"  ; level 2 ; orig_coord_info "chr16,16499533,16499619,+"  ; tag basic TAGENE ; transcript_id "AC136431.1--PKD1P5^ENST00000567465.2"  ; transcript_name "AC136431.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
AC136431.1--PKD1P5	HAVANA	RNA	1001	6014	.	+	.	FI_gene_label "AC136431.1^ENSG00000260126.2"  ; ID "AC136431.1--PKD1P5^ENST00000567465.2"  ; Parent "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2"  ; exon_id "ENSE00003856180.1"  ; exon_number 1 ; gene_id "AC136431.1--PKD1P5^AC136431.1^ENSG00000260126.2"  ; gene_name "AC136431.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000177276.2"  ; havana_transcript "OTTHUMT00000436080.2"  ; level 2 ; orig_coord_info "chr16,16499533,16499619,+"  ; tag basic TAGENE ; transcript_id "AC136431.1--PKD1P5^ENST00000567465.2"  ; transcript_name "AC136431.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
SCYL1--AP000769.1	HAVANA	gene	14293	17226	.	+	.	FI_gene_label "AP000769.1^ENSG00000173727.12"  ; ID "SCYL1--AP000769.1^AP000769.1^ENSG00000173727.12"  ; exon_id "ENSE00003742662.1"  ; exon_number 1 ; gene_id "SCYL1--AP000769.1^AP000769.1^ENSG00000173727.12"  ; gene_name "AP000769.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000186654.3"  ; havana_transcript "OTTHUMT00000473556.1"  ; level 2 ; orig_coord_info "chr11,65455313,65455331,+"  ; tag basic ; transcript_id "SCYL1--AP000769.1^ENST00000309775.8"  ; transcript_name "AP000769.1-204"  ; transcript_support_level 5 ; transcript_type processed_transcript
SCYL1--AP000769.1	HAVANA	RNA	14293	17226	.	+	.	FI_gene_label "AP000769.1^ENSG00000173727.12"  ; ID "SCYL1--AP000769.1^ENST00000309775.8"  ; Parent "SCYL1--AP000769.1^AP000769.1^ENSG00000173727.12"  ; exon_id "ENSE00003742662.1"  ; exon_number 1 ; gene_id "SCYL1--AP000769.1^AP000769.1^ENSG00000173727.12"  ; gene_name "AP000769.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000186654.3"  ; havana_transcript "OTTHUMT00000473556.1"  ; level 2 ; orig_coord_info "chr11,65455313,65455331,+"  ; tag basic ; transcript_id "SCYL1--AP000769.1^ENST00000309775.8"  ; transcript_name "AP000769.1-204"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
SCYL1--AP000769.4	ENSEMBL	gene	14238	14295	.	+	.	FI_gene_label "AP000769.4^ENSG00000275948.1"  ; ID "SCYL1--AP000769.4^AP000769.4^ENSG00000275948.1"  ; exon_id "ENSE00003714886.1"  ; exon_number 1 ; gene_id "SCYL1--AP000769.4^AP000769.4^ENSG00000275948.1"  ; gene_name "AP000769.4"  ; gene_type sRNA ; level 3 ; orig_coord_info "chr11,65445541,65445598,+"  ; tag basic ; transcript_id "SCYL1--AP000769.4^ENST00000616984.1"  ; transcript_name "AP000769.4-201"  ; transcript_support_level NA ; transcript_type sRNA
SCYL1--AP000769.4	ENSEMBL	RNA	14238	14295	.	+	.	FI_gene_label "AP000769.4^ENSG00000275948.1"  ; ID "SCYL1--AP000769.4^ENST00000616984.1"  ; Parent "SCYL1--AP000769.4^AP000769.4^ENSG00000275948.1"  ; exon_id "ENSE00003714886.1"  ; exon_number 1 ; gene_id "SCYL1--AP000769.4^AP000769.4^ENSG00000275948.1"  ; gene_name "AP000769.4"  ; gene_type sRNA ; level 3 ; orig_coord_info "chr11,65445541,65445598,+"  ; tag basic ; transcript_id "SCYL1--AP000769.4^ENST00000616984.1"  ; transcript_name "AP000769.4-201"  ; transcript_support_level NA ; transcript_type sRNA
L1 and L2 created: 
STAG1--AL023754.1	HAVANA	gene	45019	53154	.	+	.	FI_gene_label "AL023754.1^ENSG00000224260.6"  ; ID "STAG1--AL023754.1^AL023754.1^ENSG00000224260.6"  ; exon_id "ENSE00001720313.2"  ; exon_number 1 ; gene_id "STAG1--AL023754.1^AL023754.1^ENSG00000224260.6"  ; gene_name "AL023754.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000036359.2"  ; havana_transcript "OTTHUMT00000088523.2"  ; level 2 ; orig_coord_info "chr1,209567536,209567673,-"  ; tag basic ; transcript_id "STAG1--AL023754.1^ENST00000424696.6"  ; transcript_name "AL023754.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
STAG1--AL023754.1	HAVANA	RNA	45019	53154	.	+	.	FI_gene_label "AL023754.1^ENSG00000224260.6"  ; ID "STAG1--AL023754.1^ENST00000424696.6"  ; Parent "STAG1--AL023754.1^AL023754.1^ENSG00000224260.6"  ; exon_id "ENSE00001720313.2"  ; exon_number 1 ; gene_id "STAG1--AL023754.1^AL023754.1^ENSG00000224260.6"  ; gene_name "AL023754.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000036359.2"  ; havana_transcript "OTTHUMT00000088523.2"  ; level 2 ; orig_coord_info "chr1,209567536,209567673,-"  ; tag basic ; transcript_id "STAG1--AL023754.1^ENST00000424696.6"  ; transcript_name "AL023754.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
STAG1--AL023754.2	HAVANA	gene	45019	46333	.	+	.	FI_gene_label "AL023754.2^ENSG00000287902.1"  ; ID "STAG1--AL023754.2^AL023754.2^ENSG00000287902.1"  ; exon_id "ENSE00003862156.1"  ; exon_number 1 ; gene_id "STAG1--AL023754.2^AL023754.2^ENSG00000287902.1"  ; gene_name "AL023754.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000195075.1"  ; havana_transcript "OTTHUMT00000524282.1"  ; level 2 ; orig_coord_info "chr1,209531236,209531346,+"  ; tag basic TAGENE ; transcript_id "STAG1--AL023754.2^ENST00000657064.1"  ; transcript_name "AL023754.2-201"  ; transcript_type lncRNA
STAG1--AL023754.2	HAVANA	RNA	45019	46333	.	+	.	FI_gene_label "AL023754.2^ENSG00000287902.1"  ; ID "STAG1--AL023754.2^ENST00000657064.1"  ; Parent "STAG1--AL023754.2^AL023754.2^ENSG00000287902.1"  ; exon_id "ENSE00003862156.1"  ; exon_number 1 ; gene_id "STAG1--AL023754.2^AL023754.2^ENSG00000287902.1"  ; gene_name "AL023754.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000195075.1"  ; havana_transcript "OTTHUMT00000524282.1"  ; level 2 ; orig_coord_info "chr1,209531236,209531346,+"  ; tag basic TAGENE ; transcript_id "STAG1--AL023754.2^ENST00000657064.1"  ; transcript_name "AL023754.2-201"  ; 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
253 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 1 seconds -------------------------------

----------------------------- Check10: check utrs ------------------------------
594 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 14 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
                  ------ End checks (done in 1 second) ------                   


GFF3 file parsed