File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/47a0b109bf9e3e3e6ae396a8b9f7c7/.command.log
Size
44.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-f8efb2-R1_A23YTGFLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/3fb69b28e4494fc2952160132e07de/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/47a0b109bf9e3e3e6ae396a8b9f7c7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/47a0b109bf9e3e3e6ae396a8b9f7c7/.command.run
==> STAGING COMPLETE (3 inputs)

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

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 1853
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1853
=> 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:1853
  => 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: 
ATP9A--KIF3B	HAVANA	gene	1063	36153	.	+	.	FI_gene_label "ATP9A^ENSG00000054793.14"  ; ID "ATP9A--KIF3B^ATP9A^ENSG00000054793.14"  ; exon_id "ENSE00001455504.1"  ; exon_number 1 ; gene_id "ATP9A--KIF3B^ATP9A^ENSG00000054793.14"  ; gene_name ATP9A ; gene_type protein_coding ; havana_gene "OTTHUMG00000032751.4"  ; havana_transcript "OTTHUMT00000079736.3"  ; hgnc_id "HGNC:13540"  ; level 2 ; orig_coord_info "chr20,51768302,51768324,-"  ; protein_id "ENSP00000309086.5"  ; tag basic ; transcript_id "ATP9A--KIF3B^ENST00000311637.9"  ; transcript_name "ATP9A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATP9A--KIF3B	HAVANA	mRNA	1063	36153	.	+	.	FI_gene_label "ATP9A^ENSG00000054793.14"  ; ID "ATP9A--KIF3B^ENST00000311637.9"  ; Parent "ATP9A--KIF3B^ATP9A^ENSG00000054793.14"  ; exon_id "ENSE00001455504.1"  ; exon_number 1 ; gene_id "ATP9A--KIF3B^ATP9A^ENSG00000054793.14"  ; gene_name ATP9A ; gene_type protein_coding ; havana_gene "OTTHUMG00000032751.4"  ; havana_transcript "OTTHUMT00000079736.3"  ; hgnc_id "HGNC:13540"  ; level 2 ; orig_coord_info "chr20,51768302,51768324,-"  ; protein_id "ENSP00000309086.5"  ; tag basic ; transcript_id "ATP9A--KIF3B^ENST00000311637.9"  ; transcript_name "ATP9A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ATP9A--KIF3B	HAVANA	gene	39154	51156	.	+	.	FI_gene_label "KIF3B^ENSG00000101350.8"  ; ID "ATP9A--KIF3B^KIF3B^ENSG00000101350.8"  ; ccdsid "CCDS13200.1"  ; exon_id "ENSE00001468136.1"  ; exon_number 2 ; gene_id "ATP9A--KIF3B^KIF3B^ENSG00000101350.8"  ; gene_name KIF3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000032214.2"  ; havana_transcript "OTTHUMT00000078619.2"  ; hgnc_id "HGNC:6320"  ; level 2 ; orig_coord_info "chr20,32309778,32311181,+"  ; protein_id "ENSP00000364864.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ATP9A--KIF3B^ENST00000375712.4"  ; transcript_name "KIF3B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATP9A--KIF3B	HAVANA	mRNA	39154	51156	.	+	.	FI_gene_label "KIF3B^ENSG00000101350.8"  ; ID "ATP9A--KIF3B^ENST00000375712.4"  ; Parent "ATP9A--KIF3B^KIF3B^ENSG00000101350.8"  ; ccdsid "CCDS13200.1"  ; exon_id "ENSE00001468136.1"  ; exon_number 2 ; gene_id "ATP9A--KIF3B^KIF3B^ENSG00000101350.8"  ; gene_name KIF3B ; gene_type protein_coding ; havana_gene "OTTHUMG00000032214.2"  ; havana_transcript "OTTHUMT00000078619.2"  ; hgnc_id "HGNC:6320"  ; level 2 ; orig_coord_info "chr20,32309778,32311181,+"  ; protein_id "ENSP00000364864.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ATP9A--KIF3B^ENST00000375712.4"  ; transcript_name "KIF3B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP1LC3A--TTLL9	HAVANA	gene	7874	29379	.	+	.	FI_gene_label "TTLL9^ENSG00000131044.17"  ; ID "MAP1LC3A--TTLL9^TTLL9^ENSG00000131044.17"  ; exon_id "ENSE00003612330.1"  ; exon_number 2 ; gene_id "MAP1LC3A--TTLL9^TTLL9^ENSG00000131044.17"  ; gene_name TTLL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000186843.3"  ; havana_transcript "OTTHUMT00000473885.2"  ; hgnc_id "HGNC:16118"  ; level 2 ; orig_coord_info "chr20,31871127,31871195,+"  ; protein_id "ENSP00000308980.5"  ; transcript_id "MAP1LC3A--TTLL9^ENST00000310998.8"  ; transcript_name "TTLL9-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
MAP1LC3A--TTLL9	HAVANA	mRNA	7874	29379	.	+	.	FI_gene_label "TTLL9^ENSG00000131044.17"  ; ID "MAP1LC3A--TTLL9^ENST00000310998.8"  ; Parent "MAP1LC3A--TTLL9^TTLL9^ENSG00000131044.17"  ; exon_id "ENSE00003612330.1"  ; exon_number 2 ; gene_id "MAP1LC3A--TTLL9^TTLL9^ENSG00000131044.17"  ; gene_name TTLL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000186843.3"  ; havana_transcript "OTTHUMT00000473885.2"  ; hgnc_id "HGNC:16118"  ; level 2 ; orig_coord_info "chr20,31871127,31871195,+"  ; protein_id "ENSP00000308980.5"  ; transcript_id "MAP1LC3A--TTLL9^ENST00000310998.8"  ; transcript_name "TTLL9-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
MAP1LC3A--TTLL9	HAVANA	gene	3189	4816	.	+	.	FI_gene_label "MAP1LC3A^ENSG00000101460.13"  ; ID "MAP1LC3A--TTLL9^MAP1LC3A^ENSG00000101460.13"  ; ccdsid "CCDS13238.1"  ; exon_id "ENSE00001529814.1"  ; exon_number 1 ; gene_id "MAP1LC3A--TTLL9^MAP1LC3A^ENSG00000101460.13"  ; gene_name MAP1LC3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000032306.4"  ; havana_transcript "OTTHUMT00000078801.3"  ; hgnc_id "HGNC:6838"  ; level 2 ; orig_coord_info "chr20,34558869,34558908,+"  ; protein_id "ENSP00000353886.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP1LC3A--TTLL9^ENST00000360668.8"  ; transcript_name "MAP1LC3A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP1LC3A--TTLL9	HAVANA	mRNA	3189	4816	.	+	.	FI_gene_label "MAP1LC3A^ENSG00000101460.13"  ; ID "MAP1LC3A--TTLL9^ENST00000360668.8"  ; Parent "MAP1LC3A--TTLL9^MAP1LC3A^ENSG00000101460.13"  ; ccdsid "CCDS13238.1"  ; exon_id "ENSE00001529814.1"  ; exon_number 1 ; gene_id "MAP1LC3A--TTLL9^MAP1LC3A^ENSG00000101460.13"  ; gene_name MAP1LC3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000032306.4"  ; havana_transcript "OTTHUMT00000078801.3"  ; hgnc_id "HGNC:6838"  ; level 2 ; orig_coord_info "chr20,34558869,34558908,+"  ; protein_id "ENSP00000353886.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAP1LC3A--TTLL9^ENST00000360668.8"  ; transcript_name "MAP1LC3A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA10--PCDHA13	HAVANA	gene	16359	24799	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHA13	HAVANA	mRNA	16359	24799	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA10--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA10--PCDHA13	HAVANA	gene	1001	13358	.	+	.	FI_gene_label "PCDHA10^ENSG00000250120.8"  ; ID "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8"  ; ccdsid "CCDS75325.1"  ; exon_id "ENSE00002616704.2"  ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8"  ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5"  ; havana_transcript "OTTHUMT00000477562.1"  ; hgnc_id "HGNC:8664"  ; level 2 ; orig_coord_info "chr5,140856049,140858580,+"  ; protein_id "ENSP00000478748.1"  ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2"  ; transcript_name "PCDHA10-203"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHA13	HAVANA	mRNA	1001	13358	.	+	.	FI_gene_label "PCDHA10^ENSG00000250120.8"  ; ID "PCDHA10--PCDHA13^ENST00000562220.2"  ; Parent "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8"  ; ccdsid "CCDS75325.1"  ; exon_id "ENSE00002616704.2"  ; exon_number 1 ; gene_id "PCDHA10--PCDHA13^PCDHA10^ENSG00000250120.8"  ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5"  ; havana_transcript "OTTHUMT00000477562.1"  ; hgnc_id "HGNC:8664"  ; level 2 ; orig_coord_info "chr5,140856049,140858580,+"  ; protein_id "ENSP00000478748.1"  ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHA13^ENST00000562220.2"  ; transcript_name "PCDHA10-203"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA10--PCDHAC1	HAVANA	gene	16359	26374	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHAC1	HAVANA	mRNA	16359	26374	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA10--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA10--PCDHAC1	HAVANA	gene	1001	13358	.	+	.	FI_gene_label "PCDHA10^ENSG00000250120.8"  ; ID "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8"  ; ccdsid "CCDS75325.1"  ; exon_id "ENSE00002616704.2"  ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8"  ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5"  ; havana_transcript "OTTHUMT00000477562.1"  ; hgnc_id "HGNC:8664"  ; level 2 ; orig_coord_info "chr5,140856049,140858580,+"  ; protein_id "ENSP00000478748.1"  ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2"  ; transcript_name "PCDHA10-203"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHAC1	HAVANA	mRNA	1001	13358	.	+	.	FI_gene_label "PCDHA10^ENSG00000250120.8"  ; ID "PCDHA10--PCDHAC1^ENST00000562220.2"  ; Parent "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8"  ; ccdsid "CCDS75325.1"  ; exon_id "ENSE00002616704.2"  ; exon_number 1 ; gene_id "PCDHA10--PCDHAC1^PCDHA10^ENSG00000250120.8"  ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5"  ; havana_transcript "OTTHUMT00000477562.1"  ; hgnc_id "HGNC:8664"  ; level 2 ; orig_coord_info "chr5,140856049,140858580,+"  ; protein_id "ENSP00000478748.1"  ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC1^ENST00000562220.2"  ; transcript_name "PCDHA10-203"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA10--PCDHAC2	HAVANA	gene	16365	27100	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA10--PCDHAC2	HAVANA	mRNA	16365	27100	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA10--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA10--PCDHAC2	HAVANA	gene	1001	13358	.	+	.	FI_gene_label "PCDHA10^ENSG00000250120.8"  ; ID "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8"  ; ccdsid "CCDS75325.1"  ; exon_id "ENSE00002616704.2"  ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8"  ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5"  ; havana_transcript "OTTHUMT00000477562.1"  ; hgnc_id "HGNC:8664"  ; level 2 ; orig_coord_info "chr5,140856049,140858580,+"  ; protein_id "ENSP00000478748.1"  ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2"  ; transcript_name "PCDHA10-203"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA10--PCDHAC2	HAVANA	mRNA	1001	13358	.	+	.	FI_gene_label "PCDHA10^ENSG00000250120.8"  ; ID "PCDHA10--PCDHAC2^ENST00000562220.2"  ; Parent "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8"  ; ccdsid "CCDS75325.1"  ; exon_id "ENSE00002616704.2"  ; exon_number 1 ; gene_id "PCDHA10--PCDHAC2^PCDHA10^ENSG00000250120.8"  ; gene_name PCDHA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163372.5"  ; havana_transcript "OTTHUMT00000477562.1"  ; hgnc_id "HGNC:8664"  ; level 2 ; orig_coord_info "chr5,140856049,140858580,+"  ; protein_id "ENSP00000478748.1"  ; tag RNA_Seq_supported_partial basic CCDS ; transcript_id "PCDHA10--PCDHAC2^ENST00000562220.2"  ; transcript_name "PCDHA10-203"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
RPRD1A--MOCOS	HAVANA	gene	23167	43395	.	+	.	FI_gene_label "MOCOS^ENSG00000075643.6"  ; ID "RPRD1A--MOCOS^MOCOS^ENSG00000075643.6"  ; ccdsid "CCDS11919.1"  ; exon_id "ENSE00000916114.8"  ; exon_number 1 ; gene_id "RPRD1A--MOCOS^MOCOS^ENSG00000075643.6"  ; gene_name MOCOS ; gene_type protein_coding ; havana_gene "OTTHUMG00000132590.3"  ; havana_transcript "OTTHUMT00000255801.2"  ; hgnc_id "HGNC:18234"  ; level 2 ; orig_coord_info "chr18,36187540,36187681,+"  ; protein_id "ENSP00000261326.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RPRD1A--MOCOS^ENST00000261326.6"  ; transcript_name "MOCOS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RPRD1A--MOCOS	HAVANA	mRNA	23167	43395	.	+	.	FI_gene_label "MOCOS^ENSG00000075643.6"  ; ID "RPRD1A--MOCOS^ENST00000261326.6"  ; Parent "RPRD1A--MOCOS^MOCOS^ENSG00000075643.6"  ; ccdsid "CCDS11919.1"  ; exon_id "ENSE00000916114.8"  ; exon_number 1 ; gene_id "RPRD1A--MOCOS^MOCOS^ENSG00000075643.6"  ; gene_name MOCOS ; gene_type protein_coding ; havana_gene "OTTHUMG00000132590.3"  ; havana_transcript "OTTHUMT00000255801.2"  ; hgnc_id "HGNC:18234"  ; level 2 ; orig_coord_info "chr18,36187540,36187681,+"  ; protein_id "ENSP00000261326.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RPRD1A--MOCOS^ENST00000261326.6"  ; transcript_name "MOCOS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RPRD1A--MOCOS	HAVANA	gene	1021	17012	.	+	.	FI_gene_label "RPRD1A^ENSG00000141425.18"  ; ID "RPRD1A--MOCOS^RPRD1A^ENSG00000141425.18"  ; ccdsid "CCDS11917.1"  ; exon_id "ENSE00001729580.1"  ; exon_number 1 ; gene_id "RPRD1A--MOCOS^RPRD1A^ENSG00000141425.18"  ; gene_name RPRD1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000132591.8"  ; havana_transcript "OTTHUMT00000444161.1"  ; hgnc_id "HGNC:25560"  ; level 2 ; orig_coord_info "chr18,36067254,36067404,-"  ; protein_id "ENSP00000349955.4"  ; tag alternative_3_UTR basic appris_principal_1 CCDS ; transcript_id "RPRD1A--MOCOS^ENST00000357384.8"  ; transcript_name "RPRD1A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
RPRD1A--MOCOS	HAVANA	mRNA	1021	17012	.	+	.	FI_gene_label "RPRD1A^ENSG00000141425.18"  ; ID "RPRD1A--MOCOS^ENST00000357384.8"  ; Parent "RPRD1A--MOCOS^RPRD1A^ENSG00000141425.18"  ; ccdsid "CCDS11917.1"  ; exon_id "ENSE00001729580.1"  ; exon_number 1 ; gene_id "RPRD1A--MOCOS^RPRD1A^ENSG00000141425.18"  ; gene_name RPRD1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000132591.8"  ; havana_transcript "OTTHUMT00000444161.1"  ; hgnc_id "HGNC:25560"  ; level 2 ; orig_coord_info "chr18,36067254,36067404,-"  ; protein_id "ENSP00000349955.4"  ; tag alternative_3_UTR basic appris_principal_1 CCDS ; transcript_id "RPRD1A--MOCOS^ENST00000357384.8"  ; transcript_name "RPRD1A-201"  ; transcript_support_level 5 ; 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: 
TOX2--AL109930.1	HAVANA	gene	1001	15711	.	+	.	FI_gene_label "TOX2^ENSG00000124191.18"  ; ID "TOX2--AL109930.1^TOX2^ENSG00000124191.18"  ; ccdsid "CCDS46603.1"  ; exon_id "ENSE00001771384.2"  ; exon_number 1 ; gene_id "TOX2--AL109930.1^TOX2^ENSG00000124191.18"  ; gene_name TOX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032517.6"  ; havana_transcript "OTTHUMT00000079331.3"  ; hgnc_id "HGNC:16095"  ; level 2 ; orig_coord_info "chr20,43914892,43914990,+"  ; protein_id "ENSP00000344724.3"  ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "TOX2--AL109930.1^ENST00000341197.9"  ; transcript_name "TOX2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TOX2--AL109930.1	HAVANA	mRNA	1001	15711	.	+	.	FI_gene_label "TOX2^ENSG00000124191.18"  ; ID "TOX2--AL109930.1^ENST00000341197.9"  ; Parent "TOX2--AL109930.1^TOX2^ENSG00000124191.18"  ; ccdsid "CCDS46603.1"  ; exon_id "ENSE00001771384.2"  ; exon_number 1 ; gene_id "TOX2--AL109930.1^TOX2^ENSG00000124191.18"  ; gene_name TOX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032517.6"  ; havana_transcript "OTTHUMT00000079331.3"  ; hgnc_id "HGNC:16095"  ; level 2 ; orig_coord_info "chr20,43914892,43914990,+"  ; protein_id "ENSP00000344724.3"  ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "TOX2--AL109930.1^ENST00000341197.9"  ; transcript_name "TOX2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
TOX2--TSHZ2	ENSEMBL	gene	21051	25143	.	+	.	FI_gene_label "TSHZ2^ENSG00000182463.16"  ; ID "TOX2--TSHZ2^TSHZ2^ENSG00000182463.16"  ; exon_id "ENSE00003593980.2"  ; exon_number 1 ; gene_id "TOX2--TSHZ2^TSHZ2^ENSG00000182463.16"  ; gene_name TSHZ2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033058.9"  ; hgnc_id "HGNC:13010"  ; level 3 ; orig_coord_info "chr20,53185646,53185676,+"  ; protein_id "ENSP00000333114.5"  ; tag basic ; transcript_id "TOX2--TSHZ2^ENST00000329613.7"  ; transcript_name "TSHZ2-201"  ; transcript_support_level 4 ; transcript_type protein_coding
TOX2--TSHZ2	ENSEMBL	mRNA	21051	25143	.	+	.	FI_gene_label "TSHZ2^ENSG00000182463.16"  ; ID "TOX2--TSHZ2^ENST00000329613.7"  ; Parent "TOX2--TSHZ2^TSHZ2^ENSG00000182463.16"  ; exon_id "ENSE00003593980.2"  ; exon_number 1 ; gene_id "TOX2--TSHZ2^TSHZ2^ENSG00000182463.16"  ; gene_name TSHZ2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033058.9"  ; hgnc_id "HGNC:13010"  ; level 3 ; orig_coord_info "chr20,53185646,53185676,+"  ; protein_id "ENSP00000333114.5"  ; tag basic ; transcript_id "TOX2--TSHZ2^ENST00000329613.7"  ; transcript_name "TSHZ2-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
TOX2--TSHZ2	HAVANA	gene	1001	15711	.	+	.	FI_gene_label "TOX2^ENSG00000124191.18"  ; ID "TOX2--TSHZ2^TOX2^ENSG00000124191.18"  ; ccdsid "CCDS46603.1"  ; exon_id "ENSE00001771384.2"  ; exon_number 1 ; gene_id "TOX2--TSHZ2^TOX2^ENSG00000124191.18"  ; gene_name TOX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032517.6"  ; havana_transcript "OTTHUMT00000079331.3"  ; hgnc_id "HGNC:16095"  ; level 2 ; orig_coord_info "chr20,43914892,43914990,+"  ; protein_id "ENSP00000344724.3"  ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "TOX2--TSHZ2^ENST00000341197.9"  ; transcript_name "TOX2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TOX2--TSHZ2	HAVANA	mRNA	1001	15711	.	+	.	FI_gene_label "TOX2^ENSG00000124191.18"  ; ID "TOX2--TSHZ2^ENST00000341197.9"  ; Parent "TOX2--TSHZ2^TOX2^ENSG00000124191.18"  ; ccdsid "CCDS46603.1"  ; exon_id "ENSE00001771384.2"  ; exon_number 1 ; gene_id "TOX2--TSHZ2^TOX2^ENSG00000124191.18"  ; gene_name TOX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032517.6"  ; havana_transcript "OTTHUMT00000079331.3"  ; hgnc_id "HGNC:16095"  ; level 2 ; orig_coord_info "chr20,43914892,43914990,+"  ; protein_id "ENSP00000344724.3"  ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "TOX2--TSHZ2^ENST00000341197.9"  ; transcript_name "TOX2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
TTC39C--CABLES1	HAVANA	gene	28742	47803	.	+	.	FI_gene_label "CABLES1^ENSG00000134508.12"  ; ID "TTC39C--CABLES1^CABLES1^ENSG00000134508.12"  ; ccdsid "CCDS42417.1"  ; exon_id "ENSE00001313025.2"  ; exon_number 1 ; gene_id "TTC39C--CABLES1^CABLES1^ENSG00000134508.12"  ; gene_name CABLES1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179186.5"  ; havana_transcript "OTTHUMT00000445198.2"  ; hgnc_id "HGNC:25097"  ; level 2 ; orig_coord_info "chr18,23135763,23136607,+"  ; protein_id "ENSP00000256925.7"  ; tag basic appris_principal_4 CCDS ; transcript_id "TTC39C--CABLES1^ENST00000256925.11"  ; transcript_name "CABLES1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TTC39C--CABLES1	HAVANA	mRNA	28742	47803	.	+	.	FI_gene_label "CABLES1^ENSG00000134508.12"  ; ID "TTC39C--CABLES1^ENST00000256925.11"  ; Parent "TTC39C--CABLES1^CABLES1^ENSG00000134508.12"  ; ccdsid "CCDS42417.1"  ; exon_id "ENSE00001313025.2"  ; exon_number 1 ; gene_id "TTC39C--CABLES1^CABLES1^ENSG00000134508.12"  ; gene_name CABLES1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179186.5"  ; havana_transcript "OTTHUMT00000445198.2"  ; hgnc_id "HGNC:25097"  ; level 2 ; orig_coord_info "chr18,23135763,23136607,+"  ; protein_id "ENSP00000256925.7"  ; tag basic appris_principal_4 CCDS ; transcript_id "TTC39C--CABLES1^ENST00000256925.11"  ; transcript_name "CABLES1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TTC39C--CABLES1	HAVANA	gene	1001	21959	.	+	.	FI_gene_label "TTC39C^ENSG00000168234.13"  ; ID "TTC39C--CABLES1^TTC39C^ENSG00000168234.13"  ; ccdsid "CCDS32804.1"  ; exon_id "ENSE00003492798.1"  ; exon_number 2 ; gene_id "TTC39C--CABLES1^TTC39C^ENSG00000168234.13"  ; gene_name TTC39C ; gene_type protein_coding ; havana_gene "OTTHUMG00000179403.6"  ; havana_transcript "OTTHUMT00000446105.1"  ; hgnc_id "HGNC:26595"  ; level 2 ; orig_coord_info "chr18,24064156,24064188,+"  ; protein_id "ENSP00000306598.6"  ; tag basic CCDS ; transcript_id "TTC39C--CABLES1^ENST00000304621.10"  ; transcript_name "TTC39C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TTC39C--CABLES1	HAVANA	mRNA	1001	21959	.	+	.	FI_gene_label "TTC39C^ENSG00000168234.13"  ; ID "TTC39C--CABLES1^ENST00000304621.10"  ; Parent "TTC39C--CABLES1^TTC39C^ENSG00000168234.13"  ; ccdsid "CCDS32804.1"  ; exon_id "ENSE00003492798.1"  ; exon_number 2 ; gene_id "TTC39C--CABLES1^TTC39C^ENSG00000168234.13"  ; gene_name TTC39C ; gene_type protein_coding ; havana_gene "OTTHUMG00000179403.6"  ; havana_transcript "OTTHUMT00000446105.1"  ; hgnc_id "HGNC:26595"  ; level 2 ; orig_coord_info "chr18,24064156,24064188,+"  ; protein_id "ENSP00000306598.6"  ; tag basic CCDS ; transcript_id "TTC39C--CABLES1^ENST00000304621.10"  ; transcript_name "TTC39C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TTLL9--CABLES1	HAVANA	gene	27527	46588	.	+	.	FI_gene_label "CABLES1^ENSG00000134508.12"  ; ID "TTLL9--CABLES1^CABLES1^ENSG00000134508.12"  ; ccdsid "CCDS42417.1"  ; exon_id "ENSE00001313025.2"  ; exon_number 1 ; gene_id "TTLL9--CABLES1^CABLES1^ENSG00000134508.12"  ; gene_name CABLES1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179186.5"  ; havana_transcript "OTTHUMT00000445198.2"  ; hgnc_id "HGNC:25097"  ; level 2 ; orig_coord_info "chr18,23135763,23136607,+"  ; protein_id "ENSP00000256925.7"  ; tag basic appris_principal_4 CCDS ; transcript_id "TTLL9--CABLES1^ENST00000256925.11"  ; transcript_name "CABLES1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TTLL9--CABLES1	HAVANA	mRNA	27527	46588	.	+	.	FI_gene_label "CABLES1^ENSG00000134508.12"  ; ID "TTLL9--CABLES1^ENST00000256925.11"  ; Parent "TTLL9--CABLES1^CABLES1^ENSG00000134508.12"  ; ccdsid "CCDS42417.1"  ; exon_id "ENSE00001313025.2"  ; exon_number 1 ; gene_id "TTLL9--CABLES1^CABLES1^ENSG00000134508.12"  ; gene_name CABLES1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179186.5"  ; havana_transcript "OTTHUMT00000445198.2"  ; hgnc_id "HGNC:25097"  ; level 2 ; orig_coord_info "chr18,23135763,23136607,+"  ; protein_id "ENSP00000256925.7"  ; tag basic appris_principal_4 CCDS ; transcript_id "TTLL9--CABLES1^ENST00000256925.11"  ; transcript_name "CABLES1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TTLL9--CABLES1	HAVANA	gene	1058	22563	.	+	.	FI_gene_label "TTLL9^ENSG00000131044.17"  ; ID "TTLL9--CABLES1^TTLL9^ENSG00000131044.17"  ; exon_id "ENSE00003612330.1"  ; exon_number 2 ; gene_id "TTLL9--CABLES1^TTLL9^ENSG00000131044.17"  ; gene_name TTLL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000186843.3"  ; havana_transcript "OTTHUMT00000473885.2"  ; hgnc_id "HGNC:16118"  ; level 2 ; orig_coord_info "chr20,31871127,31871195,+"  ; protein_id "ENSP00000308980.5"  ; transcript_id "TTLL9--CABLES1^ENST00000310998.8"  ; transcript_name "TTLL9-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
TTLL9--CABLES1	HAVANA	mRNA	1058	22563	.	+	.	FI_gene_label "TTLL9^ENSG00000131044.17"  ; ID "TTLL9--CABLES1^ENST00000310998.8"  ; Parent "TTLL9--CABLES1^TTLL9^ENSG00000131044.17"  ; exon_id "ENSE00003612330.1"  ; exon_number 2 ; gene_id "TTLL9--CABLES1^TTLL9^ENSG00000131044.17"  ; gene_name TTLL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000186843.3"  ; havana_transcript "OTTHUMT00000473885.2"  ; hgnc_id "HGNC:16118"  ; level 2 ; orig_coord_info "chr20,31871127,31871195,+"  ; protein_id "ENSP00000308980.5"  ; transcript_id "TTLL9--CABLES1^ENST00000310998.8"  ; transcript_name "TTLL9-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
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: 
IGL-@-ext--AC097110.1	HAVANA	gene	896102	897545	.	+	.	FI_gene_label "AC097110.1^ENSG00000251527.1"  ; ID "IGL-@-ext--AC097110.1^AC097110.1^ENSG00000251527.1"  ; exon_id "ENSE00002054672.1"  ; exon_number 1 ; gene_id "IGL-@-ext--AC097110.1^AC097110.1^ENSG00000251527.1"  ; gene_name "AC097110.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000160708.1"  ; havana_transcript "OTTHUMT00000361850.1"  ; level 2 ; orig_coord_info "chr4,65858761,65858879,+"  ; tag basic ; transcript_id "IGL-@-ext--AC097110.1^ENST00000507344.1"  ; transcript_name "AC097110.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
IGL-@-ext--AC097110.1	HAVANA	RNA	896102	897545	.	+	.	FI_gene_label "AC097110.1^ENSG00000251527.1"  ; ID "IGL-@-ext--AC097110.1^ENST00000507344.1"  ; Parent "IGL-@-ext--AC097110.1^AC097110.1^ENSG00000251527.1"  ; exon_id "ENSE00002054672.1"  ; exon_number 1 ; gene_id "IGL-@-ext--AC097110.1^AC097110.1^ENSG00000251527.1"  ; gene_name "AC097110.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000160708.1"  ; havana_transcript "OTTHUMT00000361850.1"  ; level 2 ; orig_coord_info "chr4,65858761,65858879,+"  ; tag basic ; transcript_id "IGL-@-ext--AC097110.1^ENST00000507344.1"  ; transcript_name "AC097110.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
IGL-@-ext--AC097110.1	SuperLocus-ext	gene	1001	893101	.	+	.	FI_gene_label "IGL-@-ext^IGL-.g@-ext"  ; ID "IGL-@-ext--AC097110.1^IGL-@-ext^IGL-.g@-ext"  ; gene_id "IGL-@-ext--AC097110.1^IGL-@-ext^IGL-.g@-ext"  ; gene_name "IGL-@-ext"  ; orig_coord_info "chr22,22030934,22923034,-"  ; transcript_id "IGL-@-ext--AC097110.1^IGL-.t@-ext" 
IGL-@-ext--AC097110.1	SuperLocus-ext	RNA	1001	893101	.	+	.	FI_gene_label "IGL-@-ext^IGL-.g@-ext"  ; ID "IGL-@-ext--AC097110.1^IGL-.t@-ext"  ; Parent "IGL-@-ext--AC097110.1^IGL-@-ext^IGL-.g@-ext"  ; gene_id "IGL-@-ext--AC097110.1^IGL-@-ext^IGL-.g@-ext"  ; gene_name "IGL-@-ext"  ; orig_coord_info "chr22,22030934,22923034,-"  ; transcript_id "IGL-@-ext--AC097110.1^IGL-.t@-ext" 
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: 
TOX2--AL109930.1	HAVANA	gene	18712	21435	.	+	.	FI_gene_label "AL109930.1^ENSG00000271774.1"  ; ID "TOX2--AL109930.1^AL109930.1^ENSG00000271774.1"  ; exon_id "ENSE00003677366.2"  ; exon_number 1 ; gene_id "TOX2--AL109930.1^AL109930.1^ENSG00000271774.1"  ; gene_name "AL109930.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000185603.1"  ; havana_transcript "OTTHUMT00000470820.1"  ; level 2 ; orig_coord_info "chr20,53487142,53487274,-"  ; tag basic ; transcript_id "TOX2--AL109930.1^ENST00000606932.1"  ; transcript_name "AL109930.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TOX2--AL109930.1	HAVANA	RNA	18712	21435	.	+	.	FI_gene_label "AL109930.1^ENSG00000271774.1"  ; ID "TOX2--AL109930.1^ENST00000606932.1"  ; Parent "TOX2--AL109930.1^AL109930.1^ENSG00000271774.1"  ; exon_id "ENSE00003677366.2"  ; exon_number 1 ; gene_id "TOX2--AL109930.1^AL109930.1^ENSG00000271774.1"  ; gene_name "AL109930.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000185603.1"  ; havana_transcript "OTTHUMT00000470820.1"  ; level 2 ; orig_coord_info "chr20,53487142,53487274,-"  ; tag basic ; transcript_id "TOX2--AL109930.1^ENST00000606932.1"  ; transcript_name "AL109930.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
155 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 ------------------------------
428 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 0 second) ------                   


GFF3 file parsed