.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/025d403ac09677e7cf2519164b45ca/.command.out
Size: 47.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2)
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: 6677
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 6677
=> 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:6677
  => 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 2 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: 
AP1M2--ZFR2	HAVANA	gene	1004	11481	.	+	.	FI_gene_label "AP1M2^ENSG00000129354.12"  ; ID "AP1M2--ZFR2^AP1M2^ENSG00000129354.12"  ; ccdsid "CCDS45964.1"  ; exon_id "ENSE00002744955.2"  ; exon_number 1 ; gene_id "AP1M2--ZFR2^AP1M2^ENSG00000129354.12"  ; gene_name AP1M2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180584.2"  ; havana_transcript "OTTHUMT00000452034.1"  ; hgnc_id "HGNC:558"  ; level 2 ; orig_coord_info "chr19,10587190,10587231,-"  ; protein_id "ENSP00000250244.5"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "AP1M2--ZFR2^ENST00000250244.11"  ; transcript_name "AP1M2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AP1M2--ZFR2	HAVANA	mRNA	1004	11481	.	+	.	FI_gene_label "AP1M2^ENSG00000129354.12"  ; ID "AP1M2--ZFR2^ENST00000250244.11"  ; Parent "AP1M2--ZFR2^AP1M2^ENSG00000129354.12"  ; ccdsid "CCDS45964.1"  ; exon_id "ENSE00002744955.2"  ; exon_number 1 ; gene_id "AP1M2--ZFR2^AP1M2^ENSG00000129354.12"  ; gene_name AP1M2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180584.2"  ; havana_transcript "OTTHUMT00000452034.1"  ; hgnc_id "HGNC:558"  ; level 2 ; orig_coord_info "chr19,10587190,10587231,-"  ; protein_id "ENSP00000250244.5"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "AP1M2--ZFR2^ENST00000250244.11"  ; transcript_name "AP1M2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AP1M2--ZFR2	HAVANA	gene	14482	40416	.	+	.	FI_gene_label "ZFR2^ENSG00000105278.12"  ; ID "AP1M2--ZFR2^ZFR2^ENSG00000105278.12"  ; ccdsid "CCDS45921.1"  ; exon_id "ENSE00003845290.1"  ; exon_number 1 ; gene_id "AP1M2--ZFR2^ZFR2^ENSG00000105278.12"  ; gene_name ZFR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180918.7"  ; havana_transcript "OTTHUMT00000453648.3"  ; hgnc_id "HGNC:29189"  ; level 2 ; orig_coord_info "chr19,3868965,3869017,-"  ; protein_id "ENSP00000262961.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AP1M2--ZFR2^ENST00000262961.9"  ; transcript_name "ZFR2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AP1M2--ZFR2	HAVANA	mRNA	14482	40416	.	+	.	FI_gene_label "ZFR2^ENSG00000105278.12"  ; ID "AP1M2--ZFR2^ENST00000262961.9"  ; Parent "AP1M2--ZFR2^ZFR2^ENSG00000105278.12"  ; ccdsid "CCDS45921.1"  ; exon_id "ENSE00003845290.1"  ; exon_number 1 ; gene_id "AP1M2--ZFR2^ZFR2^ENSG00000105278.12"  ; gene_name ZFR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180918.7"  ; havana_transcript "OTTHUMT00000453648.3"  ; hgnc_id "HGNC:29189"  ; level 2 ; orig_coord_info "chr19,3868965,3869017,-"  ; protein_id "ENSP00000262961.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AP1M2--ZFR2^ENST00000262961.9"  ; transcript_name "ZFR2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
DNMT1--ZFR2	HAVANA	gene	42613	68547	.	+	.	FI_gene_label "ZFR2^ENSG00000105278.12"  ; ID "DNMT1--ZFR2^ZFR2^ENSG00000105278.12"  ; ccdsid "CCDS45921.1"  ; exon_id "ENSE00003845290.1"  ; exon_number 1 ; gene_id "DNMT1--ZFR2^ZFR2^ENSG00000105278.12"  ; gene_name ZFR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180918.7"  ; havana_transcript "OTTHUMT00000453648.3"  ; hgnc_id "HGNC:29189"  ; level 2 ; orig_coord_info "chr19,3868965,3869017,-"  ; protein_id "ENSP00000262961.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNMT1--ZFR2^ENST00000262961.9"  ; transcript_name "ZFR2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
DNMT1--ZFR2	HAVANA	mRNA	42613	68547	.	+	.	FI_gene_label "ZFR2^ENSG00000105278.12"  ; ID "DNMT1--ZFR2^ENST00000262961.9"  ; Parent "DNMT1--ZFR2^ZFR2^ENSG00000105278.12"  ; ccdsid "CCDS45921.1"  ; exon_id "ENSE00003845290.1"  ; exon_number 1 ; gene_id "DNMT1--ZFR2^ZFR2^ENSG00000105278.12"  ; gene_name ZFR2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180918.7"  ; havana_transcript "OTTHUMT00000453648.3"  ; hgnc_id "HGNC:29189"  ; level 2 ; orig_coord_info "chr19,3868965,3869017,-"  ; protein_id "ENSP00000262961.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNMT1--ZFR2^ENST00000262961.9"  ; transcript_name "ZFR2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
DNMT1--ZFR2	HAVANA	gene	2325	39608	.	+	.	FI_gene_label "DNMT1^ENSG00000130816.17"  ; ID "DNMT1--ZFR2^DNMT1^ENSG00000130816.17"  ; ccdsid "CCDS12228.1"  ; exon_id "ENSE00002754963.1"  ; exon_number 1 ; gene_id "DNMT1--ZFR2^DNMT1^ENSG00000130816.17"  ; gene_name DNMT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180397.4"  ; havana_transcript "OTTHUMT00000451166.1"  ; hgnc_id "HGNC:2976"  ; level 2 ; orig_coord_info "chr19,10194820,10194899,-"  ; protein_id "ENSP00000345739.3"  ; tag upstream_ATG basic appris_principal_4 CCDS ; transcript_id "DNMT1--ZFR2^ENST00000340748.8"  ; transcript_name "DNMT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DNMT1--ZFR2	HAVANA	mRNA	2325	39608	.	+	.	FI_gene_label "DNMT1^ENSG00000130816.17"  ; ID "DNMT1--ZFR2^ENST00000340748.8"  ; Parent "DNMT1--ZFR2^DNMT1^ENSG00000130816.17"  ; ccdsid "CCDS12228.1"  ; exon_id "ENSE00002754963.1"  ; exon_number 1 ; gene_id "DNMT1--ZFR2^DNMT1^ENSG00000130816.17"  ; gene_name DNMT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180397.4"  ; havana_transcript "OTTHUMT00000451166.1"  ; hgnc_id "HGNC:2976"  ; level 2 ; orig_coord_info "chr19,10194820,10194899,-"  ; protein_id "ENSP00000345739.3"  ; tag upstream_ATG basic appris_principal_4 CCDS ; transcript_id "DNMT1--ZFR2^ENST00000340748.8"  ; transcript_name "DNMT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GTF2F1--SCUBE1	HAVANA	gene	12959	27191	.	+	.	FI_gene_label "SCUBE1^ENSG00000159307.19"  ; ID "GTF2F1--SCUBE1^SCUBE1^ENSG00000159307.19"  ; exon_id "ENSE00001874075.1"  ; exon_number 1 ; gene_id "GTF2F1--SCUBE1^SCUBE1^ENSG00000159307.19"  ; gene_name SCUBE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150679.6"  ; havana_transcript "OTTHUMT00000319584.1"  ; hgnc_id "HGNC:13441"  ; level 2 ; orig_coord_info "chr22,43343174,43343261,-"  ; protein_id "ENSP00000290460.7"  ; tag basic ; transcript_id "GTF2F1--SCUBE1^ENST00000290460.7"  ; transcript_name "SCUBE1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GTF2F1--SCUBE1	HAVANA	mRNA	12959	27191	.	+	.	FI_gene_label "SCUBE1^ENSG00000159307.19"  ; ID "GTF2F1--SCUBE1^ENST00000290460.7"  ; Parent "GTF2F1--SCUBE1^SCUBE1^ENSG00000159307.19"  ; exon_id "ENSE00001874075.1"  ; exon_number 1 ; gene_id "GTF2F1--SCUBE1^SCUBE1^ENSG00000159307.19"  ; gene_name SCUBE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150679.6"  ; havana_transcript "OTTHUMT00000319584.1"  ; hgnc_id "HGNC:13441"  ; level 2 ; orig_coord_info "chr22,43343174,43343261,-"  ; protein_id "ENSP00000290460.7"  ; tag basic ; transcript_id "GTF2F1--SCUBE1^ENST00000290460.7"  ; transcript_name "SCUBE1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GTF2F1--SCUBE1	HAVANA	gene	1818	9909	.	+	.	FI_gene_label "GTF2F1^ENSG00000125651.14"  ; ID "GTF2F1--SCUBE1^GTF2F1^ENSG00000125651.14"  ; ccdsid "CCDS12165.1"  ; exon_id "ENSE00003187061.2"  ; exon_number 1 ; gene_id "GTF2F1--SCUBE1^GTF2F1^ENSG00000125651.14"  ; gene_name GTF2F1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168087.4"  ; havana_transcript "OTTHUMT00000398033.2"  ; hgnc_id "HGNC:4652"  ; level 2 ; orig_coord_info "chr19,6392984,6392995,-"  ; protein_id "ENSP00000377969.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2F1--SCUBE1^ENST00000394456.10"  ; transcript_name "GTF2F1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GTF2F1--SCUBE1	HAVANA	mRNA	1818	9909	.	+	.	FI_gene_label "GTF2F1^ENSG00000125651.14"  ; ID "GTF2F1--SCUBE1^ENST00000394456.10"  ; Parent "GTF2F1--SCUBE1^GTF2F1^ENSG00000125651.14"  ; ccdsid "CCDS12165.1"  ; exon_id "ENSE00003187061.2"  ; exon_number 1 ; gene_id "GTF2F1--SCUBE1^GTF2F1^ENSG00000125651.14"  ; gene_name GTF2F1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168087.4"  ; havana_transcript "OTTHUMT00000398033.2"  ; hgnc_id "HGNC:4652"  ; level 2 ; orig_coord_info "chr19,6392984,6392995,-"  ; protein_id "ENSP00000377969.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GTF2F1--SCUBE1^ENST00000394456.10"  ; transcript_name "GTF2F1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAN2B1--CACNA1A	HAVANA	gene	1009	16238	.	+	.	FI_gene_label "MAN2B1^ENSG00000104774.13"  ; ID "MAN2B1--CACNA1A^MAN2B1^ENSG00000104774.13"  ; ccdsid "CCDS54224.1"  ; exon_id "ENSE00001747592.1"  ; exon_number 1 ; gene_id "MAN2B1--CACNA1A^MAN2B1^ENSG00000104774.13"  ; gene_name MAN2B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156397.5"  ; havana_transcript "OTTHUMT00000344064.1"  ; hgnc_id "HGNC:6826"  ; level 1 ; orig_coord_info "chr19,12666543,12666701,-"  ; protein_id "ENSP00000221363.4"  ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "MAN2B1--CACNA1A^ENST00000221363.8"  ; transcript_name "MAN2B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAN2B1--CACNA1A	HAVANA	mRNA	1009	16238	.	+	.	FI_gene_label "MAN2B1^ENSG00000104774.13"  ; ID "MAN2B1--CACNA1A^ENST00000221363.8"  ; Parent "MAN2B1--CACNA1A^MAN2B1^ENSG00000104774.13"  ; ccdsid "CCDS54224.1"  ; exon_id "ENSE00001747592.1"  ; exon_number 1 ; gene_id "MAN2B1--CACNA1A^MAN2B1^ENSG00000104774.13"  ; gene_name MAN2B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156397.5"  ; havana_transcript "OTTHUMT00000344064.1"  ; hgnc_id "HGNC:6826"  ; level 1 ; orig_coord_info "chr19,12666543,12666701,-"  ; protein_id "ENSP00000221363.4"  ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "MAN2B1--CACNA1A^ENST00000221363.8"  ; transcript_name "MAN2B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAN2B1--CACNA1A	HAVANA	gene	25789	103166	.	+	.	FI_gene_label "CACNA1A^ENSG00000141837.22"  ; ID "MAN2B1--CACNA1A^CACNA1A^ENSG00000141837.22"  ; ccdsid "CCDS45998.1"  ; exon_id "ENSE00003896325.1"  ; exon_number 1 ; gene_id "MAN2B1--CACNA1A^CACNA1A^ENSG00000141837.22"  ; gene_name CACNA1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000044590.18"  ; havana_transcript "OTTHUMT00000104062.4"  ; hgnc_id "HGNC:1388"  ; level 2 ; orig_coord_info "chr19,13505932,13506224,-"  ; protein_id "ENSP00000353362.5"  ; tag non_canonical_U12 basic MANE_Select appris_principal_4 CCDS ; transcript_id "MAN2B1--CACNA1A^ENST00000360228.11"  ; transcript_name "CACNA1A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAN2B1--CACNA1A	HAVANA	mRNA	25789	103166	.	+	.	FI_gene_label "CACNA1A^ENSG00000141837.22"  ; ID "MAN2B1--CACNA1A^ENST00000360228.11"  ; Parent "MAN2B1--CACNA1A^CACNA1A^ENSG00000141837.22"  ; ccdsid "CCDS45998.1"  ; exon_id "ENSE00003896325.1"  ; exon_number 1 ; gene_id "MAN2B1--CACNA1A^CACNA1A^ENSG00000141837.22"  ; gene_name CACNA1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000044590.18"  ; havana_transcript "OTTHUMT00000104062.4"  ; hgnc_id "HGNC:1388"  ; level 2 ; orig_coord_info "chr19,13505932,13506224,-"  ; protein_id "ENSP00000353362.5"  ; tag non_canonical_U12 basic MANE_Select appris_principal_4 CCDS ; transcript_id "MAN2B1--CACNA1A^ENST00000360228.11"  ; transcript_name "CACNA1A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAN2B1--CCDC130	HAVANA	gene	1009	16238	.	+	.	FI_gene_label "MAN2B1^ENSG00000104774.13"  ; ID "MAN2B1--CCDC130^MAN2B1^ENSG00000104774.13"  ; ccdsid "CCDS54224.1"  ; exon_id "ENSE00001747592.1"  ; exon_number 1 ; gene_id "MAN2B1--CCDC130^MAN2B1^ENSG00000104774.13"  ; gene_name MAN2B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156397.5"  ; havana_transcript "OTTHUMT00000344064.1"  ; hgnc_id "HGNC:6826"  ; level 1 ; orig_coord_info "chr19,12666543,12666701,-"  ; protein_id "ENSP00000221363.4"  ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "MAN2B1--CCDC130^ENST00000221363.8"  ; transcript_name "MAN2B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAN2B1--CCDC130	HAVANA	mRNA	1009	16238	.	+	.	FI_gene_label "MAN2B1^ENSG00000104774.13"  ; ID "MAN2B1--CCDC130^ENST00000221363.8"  ; Parent "MAN2B1--CCDC130^MAN2B1^ENSG00000104774.13"  ; ccdsid "CCDS54224.1"  ; exon_id "ENSE00001747592.1"  ; exon_number 1 ; gene_id "MAN2B1--CCDC130^MAN2B1^ENSG00000104774.13"  ; gene_name MAN2B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156397.5"  ; havana_transcript "OTTHUMT00000344064.1"  ; hgnc_id "HGNC:6826"  ; level 1 ; orig_coord_info "chr19,12666543,12666701,-"  ; protein_id "ENSP00000221363.4"  ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "MAN2B1--CCDC130^ENST00000221363.8"  ; transcript_name "MAN2B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAN2B1--CCDC130	HAVANA	gene	21118	30606	.	+	.	FI_gene_label "CCDC130^ENSG00000104957.14"  ; ID "MAN2B1--CCDC130^CCDC130^ENSG00000104957.14"  ; ccdsid "CCDS12296.1"  ; exon_id "ENSE00003462914.1"  ; exon_number 2 ; gene_id "MAN2B1--CCDC130^CCDC130^ENSG00000104957.14"  ; gene_name CCDC130 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180837.7"  ; havana_transcript "OTTHUMT00000453218.3"  ; hgnc_id "HGNC:28118"  ; level 2 ; orig_coord_info "chr19,13751809,13751811,+"  ; protein_id "ENSP00000221554.7"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAN2B1--CCDC130^ENST00000221554.13"  ; transcript_name "CCDC130-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAN2B1--CCDC130	HAVANA	mRNA	21118	30606	.	+	.	FI_gene_label "CCDC130^ENSG00000104957.14"  ; ID "MAN2B1--CCDC130^ENST00000221554.13"  ; Parent "MAN2B1--CCDC130^CCDC130^ENSG00000104957.14"  ; ccdsid "CCDS12296.1"  ; exon_id "ENSE00003462914.1"  ; exon_number 2 ; gene_id "MAN2B1--CCDC130^CCDC130^ENSG00000104957.14"  ; gene_name CCDC130 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180837.7"  ; havana_transcript "OTTHUMT00000453218.3"  ; hgnc_id "HGNC:28118"  ; level 2 ; orig_coord_info "chr19,13751809,13751811,+"  ; protein_id "ENSP00000221554.7"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAN2B1--CCDC130^ENST00000221554.13"  ; transcript_name "CCDC130-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MON1B--AC106733.1	HAVANA	gene	1356	10336	.	+	.	FI_gene_label "MON1B^ENSG00000103111.15"  ; ID "MON1B--AC106733.1^MON1B^ENSG00000103111.15"  ; ccdsid "CCDS10925.1"  ; exon_id "ENSE00003626624.1"  ; exon_number 2 ; gene_id "MON1B--AC106733.1^MON1B^ENSG00000103111.15"  ; gene_name MON1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000137618.4"  ; havana_transcript "OTTHUMT00000269036.3"  ; hgnc_id "HGNC:25020"  ; level 2 ; orig_coord_info "chr16,77191486,77191633,+"  ; protein_id "ENSP00000248248.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MON1B--AC106733.1^ENST00000248248.8"  ; transcript_name "MON1B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MON1B--AC106733.1	HAVANA	mRNA	1356	10336	.	+	.	FI_gene_label "MON1B^ENSG00000103111.15"  ; ID "MON1B--AC106733.1^ENST00000248248.8"  ; Parent "MON1B--AC106733.1^MON1B^ENSG00000103111.15"  ; ccdsid "CCDS10925.1"  ; exon_id "ENSE00003626624.1"  ; exon_number 2 ; gene_id "MON1B--AC106733.1^MON1B^ENSG00000103111.15"  ; gene_name MON1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000137618.4"  ; havana_transcript "OTTHUMT00000269036.3"  ; hgnc_id "HGNC:25020"  ; level 2 ; orig_coord_info "chr16,77191486,77191633,+"  ; protein_id "ENSP00000248248.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MON1B--AC106733.1^ENST00000248248.8"  ; transcript_name "MON1B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MYB--ADGRB3	HAVANA	gene	41227	58131	.	+	.	FI_gene_label "ADGRB3^ENSG00000135298.14"  ; ID "MYB--ADGRB3^ADGRB3^ENSG00000135298.14"  ; exon_id "ENSE00002256139.1"  ; exon_number 1 ; gene_id "MYB--ADGRB3^ADGRB3^ENSG00000135298.14"  ; gene_name ADGRB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014982.4"  ; havana_transcript "OTTHUMT00000468343.1"  ; hgnc_id "HGNC:945"  ; level 1 ; orig_coord_info "chr6,69232532,69232629,+"  ; protein_id "ENSP00000238918.8"  ; tag basic exp_conf ; transcript_id "MYB--ADGRB3^ENST00000238918.12"  ; transcript_name "ADGRB3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
MYB--ADGRB3	HAVANA	mRNA	41227	58131	.	+	.	FI_gene_label "ADGRB3^ENSG00000135298.14"  ; ID "MYB--ADGRB3^ENST00000238918.12"  ; Parent "MYB--ADGRB3^ADGRB3^ENSG00000135298.14"  ; exon_id "ENSE00002256139.1"  ; exon_number 1 ; gene_id "MYB--ADGRB3^ADGRB3^ENSG00000135298.14"  ; gene_name ADGRB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000014982.4"  ; havana_transcript "OTTHUMT00000468343.1"  ; hgnc_id "HGNC:945"  ; level 1 ; orig_coord_info "chr6,69232532,69232629,+"  ; protein_id "ENSP00000238918.8"  ; tag basic exp_conf ; transcript_id "MYB--ADGRB3^ENST00000238918.12"  ; transcript_name "ADGRB3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
MYB--ADGRB3	ENSEMBL	gene	1008	19077	.	+	.	FI_gene_label "MYB^ENSG00000118513.19"  ; ID "MYB--ADGRB3^MYB^ENSG00000118513.19"  ; exon_id "ENSE00002174682.1"  ; exon_number 1 ; gene_id "MYB--ADGRB3^MYB^ENSG00000118513.19"  ; gene_name MYB ; gene_type protein_coding ; havana_gene "OTTHUMG00000015629.11"  ; hgnc_id "HGNC:7545"  ; level 3 ; orig_coord_info "chr6,135181514,135181536,+"  ; protein_id "ENSP00000326328.8"  ; tag basic ; transcript_id "MYB--ADGRB3^ENST00000316528.12"  ; transcript_name "MYB-201"  ; transcript_support_level 5 ; transcript_type protein_coding
MYB--ADGRB3	ENSEMBL	mRNA	1008	19077	.	+	.	FI_gene_label "MYB^ENSG00000118513.19"  ; ID "MYB--ADGRB3^ENST00000316528.12"  ; Parent "MYB--ADGRB3^MYB^ENSG00000118513.19"  ; exon_id "ENSE00002174682.1"  ; exon_number 1 ; gene_id "MYB--ADGRB3^MYB^ENSG00000118513.19"  ; gene_name MYB ; gene_type protein_coding ; havana_gene "OTTHUMG00000015629.11"  ; hgnc_id "HGNC:7545"  ; level 3 ; orig_coord_info "chr6,135181514,135181536,+"  ; protein_id "ENSP00000326328.8"  ; tag basic ; transcript_id "MYB--ADGRB3^ENST00000316528.12"  ; transcript_name "MYB-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MYO18B--IGL-@-ext	HAVANA	gene	1045	55899	.	+	.	FI_gene_label "MYO18B^ENSG00000133454.16"  ; ID "MYO18B--IGL-@-ext^MYO18B^ENSG00000133454.16"  ; ccdsid "CCDS54507.1"  ; exon_id "ENSE00001364972.3"  ; exon_number 2 ; gene_id "MYO18B--IGL-@-ext^MYO18B^ENSG00000133454.16"  ; gene_name MYO18B ; gene_type protein_coding ; havana_gene "OTTHUMG00000151129.2"  ; havana_transcript "OTTHUMT00000320371.2"  ; hgnc_id "HGNC:18150"  ; level 2 ; orig_coord_info "chr22,25761093,25761131,+"  ; protein_id "ENSP00000334563.8"  ; tag non_canonical_conserved dotter_confirmed basic MANE_Select appris_principal_4 CCDS ; transcript_id "MYO18B--IGL-@-ext^ENST00000335473.12"  ; transcript_name "MYO18B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MYO18B--IGL-@-ext	HAVANA	mRNA	1045	55899	.	+	.	FI_gene_label "MYO18B^ENSG00000133454.16"  ; ID "MYO18B--IGL-@-ext^ENST00000335473.12"  ; Parent "MYO18B--IGL-@-ext^MYO18B^ENSG00000133454.16"  ; ccdsid "CCDS54507.1"  ; exon_id "ENSE00001364972.3"  ; exon_number 2 ; gene_id "MYO18B--IGL-@-ext^MYO18B^ENSG00000133454.16"  ; gene_name MYO18B ; gene_type protein_coding ; havana_gene "OTTHUMG00000151129.2"  ; havana_transcript "OTTHUMT00000320371.2"  ; hgnc_id "HGNC:18150"  ; level 2 ; orig_coord_info "chr22,25761093,25761131,+"  ; protein_id "ENSP00000334563.8"  ; tag non_canonical_conserved dotter_confirmed basic MANE_Select appris_principal_4 CCDS ; transcript_id "MYO18B--IGL-@-ext^ENST00000335473.12"  ; transcript_name "MYO18B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPHP3--ACAD11	HAVANA	gene	34363	56719	.	+	.	FI_gene_label "ACAD11^ENSG00000240303.8"  ; ID "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; ccdsid "CCDS3074.1"  ; exon_id "ENSE00001878063.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; gene_name ACAD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159780.6"  ; havana_transcript "OTTHUMT00000357279.4"  ; hgnc_id "HGNC:30211"  ; level 2 ; orig_coord_info "chr3,132659603,132659751,-"  ; protein_id "ENSP00000264990.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000264990.11"  ; transcript_name "ACAD11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPHP3--ACAD11	HAVANA	mRNA	34363	56719	.	+	.	FI_gene_label "ACAD11^ENSG00000240303.8"  ; ID "NPHP3--ACAD11^ENST00000264990.11"  ; Parent "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; ccdsid "CCDS3074.1"  ; exon_id "ENSE00001878063.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; gene_name ACAD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159780.6"  ; havana_transcript "OTTHUMT00000357279.4"  ; hgnc_id "HGNC:30211"  ; level 2 ; orig_coord_info "chr3,132659603,132659751,-"  ; protein_id "ENSP00000264990.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000264990.11"  ; transcript_name "ACAD11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPHP3--ACAD11	HAVANA	gene	1006	31089	.	+	.	FI_gene_label "NPHP3^ENSG00000113971.20"  ; ID "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; ccdsid "CCDS3078.1"  ; exon_id "ENSE00001810363.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; gene_name NPHP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159713.4"  ; havana_transcript "OTTHUMT00000357020.3"  ; hgnc_id "HGNC:7907"  ; level 2 ; orig_coord_info "chr3,132721963,132722355,-"  ; protein_id "ENSP00000338766.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000337331.10"  ; transcript_name "NPHP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPHP3--ACAD11	HAVANA	mRNA	1006	31089	.	+	.	FI_gene_label "NPHP3^ENSG00000113971.20"  ; ID "NPHP3--ACAD11^ENST00000337331.10"  ; Parent "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; ccdsid "CCDS3078.1"  ; exon_id "ENSE00001810363.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; gene_name NPHP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159713.4"  ; havana_transcript "OTTHUMT00000357020.3"  ; hgnc_id "HGNC:7907"  ; level 2 ; orig_coord_info "chr3,132721963,132722355,-"  ; protein_id "ENSP00000338766.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000337331.10"  ; transcript_name "NPHP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHA13	HAVANA	gene	7268	15708	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHA13	HAVANA	mRNA	7268	15708	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA6--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHA13	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHA13	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHA13^ENST00000378126.4"  ; Parent "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC1	HAVANA	gene	7268	17283	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC1	HAVANA	mRNA	7268	17283	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA6--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC1	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC1	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC1^ENST00000378126.4"  ; Parent "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC2	HAVANA	gene	7274	18009	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC2	HAVANA	mRNA	7274	18009	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA6--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA6--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 "PCDHA6--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC2	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC2	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC2^ENST00000378126.4"  ; Parent "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
SREBF2--NCLN	HAVANA	gene	29776	42039	.	+	.	FI_gene_label "NCLN^ENSG00000125912.11"  ; ID "SREBF2--NCLN^NCLN^ENSG00000125912.11"  ; ccdsid "CCDS32869.1"  ; exon_id "ENSE00002864069.2"  ; exon_number 1 ; gene_id "SREBF2--NCLN^NCLN^ENSG00000125912.11"  ; gene_name NCLN ; gene_type protein_coding ; havana_gene "OTTHUMG00000180687.5"  ; havana_transcript "OTTHUMT00000452545.2"  ; hgnc_id "HGNC:26923"  ; level 2 ; orig_coord_info "chr19,3186031,3186214,+"  ; protein_id "ENSP00000246117.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SREBF2--NCLN^ENST00000246117.9"  ; transcript_name "NCLN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SREBF2--NCLN	HAVANA	mRNA	29776	42039	.	+	.	FI_gene_label "NCLN^ENSG00000125912.11"  ; ID "SREBF2--NCLN^ENST00000246117.9"  ; Parent "SREBF2--NCLN^NCLN^ENSG00000125912.11"  ; ccdsid "CCDS32869.1"  ; exon_id "ENSE00002864069.2"  ; exon_number 1 ; gene_id "SREBF2--NCLN^NCLN^ENSG00000125912.11"  ; gene_name NCLN ; gene_type protein_coding ; havana_gene "OTTHUMG00000180687.5"  ; havana_transcript "OTTHUMT00000452545.2"  ; hgnc_id "HGNC:26923"  ; level 2 ; orig_coord_info "chr19,3186031,3186214,+"  ; protein_id "ENSP00000246117.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SREBF2--NCLN^ENST00000246117.9"  ; transcript_name "NCLN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SREBF2--NCLN	HAVANA	gene	1027	26406	.	+	.	FI_gene_label "SREBF2^ENSG00000198911.12"  ; ID "SREBF2--NCLN^SREBF2^ENSG00000198911.12"  ; ccdsid "CCDS14023.1"  ; exon_id "ENSE00001912807.1"  ; exon_number 1 ; gene_id "SREBF2--NCLN^SREBF2^ENSG00000198911.12"  ; gene_name SREBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151261.3"  ; havana_transcript "OTTHUMT00000321956.2"  ; hgnc_id "HGNC:11290"  ; level 2 ; orig_coord_info "chr22,41833271,41833358,+"  ; protein_id "ENSP00000354476.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SREBF2--NCLN^ENST00000361204.9"  ; transcript_name "SREBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SREBF2--NCLN	HAVANA	mRNA	1027	26406	.	+	.	FI_gene_label "SREBF2^ENSG00000198911.12"  ; ID "SREBF2--NCLN^ENST00000361204.9"  ; Parent "SREBF2--NCLN^SREBF2^ENSG00000198911.12"  ; ccdsid "CCDS14023.1"  ; exon_id "ENSE00001912807.1"  ; exon_number 1 ; gene_id "SREBF2--NCLN^SREBF2^ENSG00000198911.12"  ; gene_name SREBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151261.3"  ; havana_transcript "OTTHUMT00000321956.2"  ; hgnc_id "HGNC:11290"  ; level 2 ; orig_coord_info "chr22,41833271,41833358,+"  ; protein_id "ENSP00000354476.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SREBF2--NCLN^ENST00000361204.9"  ; transcript_name "SREBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AL669831.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AL669831.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AL669831.1^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--AL669831.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AL669831.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AL669831.1^ENST00000326270.13"  ; Parent "TLK2--AL669831.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AL669831.1^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--AL669831.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MON1B--AC106733.1	HAVANA	gene	13337	14374	.	+	.	FI_gene_label "AC106733.1^ENSG00000279856.1"  ; ID "MON1B--AC106733.1^AC106733.1^ENSG00000279856.1"  ; exon_id "ENSE00003756467.1"  ; exon_number 1 ; gene_id "MON1B--AC106733.1^AC106733.1^ENSG00000279856.1"  ; gene_name "AC106733.1"  ; gene_type TEC ; havana_gene "OTTHUMG00000176663.1"  ; havana_transcript "OTTHUMT00000433025.1"  ; level 2 ; orig_coord_info "chr16,77104260,77105297,+"  ; tag basic ; transcript_id "MON1B--AC106733.1^ENST00000624476.1"  ; transcript_name "AC106733.1-201"  ; transcript_support_level NA ; transcript_type TEC
MON1B--AC106733.1	HAVANA	RNA	13337	14374	.	+	.	FI_gene_label "AC106733.1^ENSG00000279856.1"  ; ID "MON1B--AC106733.1^ENST00000624476.1"  ; Parent "MON1B--AC106733.1^AC106733.1^ENSG00000279856.1"  ; exon_id "ENSE00003756467.1"  ; exon_number 1 ; gene_id "MON1B--AC106733.1^AC106733.1^ENSG00000279856.1"  ; gene_name "AC106733.1"  ; gene_type TEC ; havana_gene "OTTHUMG00000176663.1"  ; havana_transcript "OTTHUMT00000433025.1"  ; level 2 ; orig_coord_info "chr16,77104260,77105297,+"  ; tag basic ; transcript_id "MON1B--AC106733.1^ENST00000624476.1"  ; transcript_name "AC106733.1-201"  ; transcript_support_level NA ; transcript_type TEC
L1 and L2 created: 
MYO18B--IGL-@-ext	SuperLocus-ext	gene	58900	951000	.	+	.	FI_gene_label "IGL-@-ext^IGL-.g@-ext"  ; ID "MYO18B--IGL-@-ext^IGL-@-ext^IGL-.g@-ext"  ; gene_id "MYO18B--IGL-@-ext^IGL-@-ext^IGL-.g@-ext"  ; gene_name "IGL-@-ext"  ; orig_coord_info "chr22,22030934,22923034,-"  ; transcript_id "MYO18B--IGL-@-ext^IGL-.t@-ext" 
MYO18B--IGL-@-ext	SuperLocus-ext	RNA	58900	951000	.	+	.	FI_gene_label "IGL-@-ext^IGL-.g@-ext"  ; ID "MYO18B--IGL-@-ext^IGL-.t@-ext"  ; Parent "MYO18B--IGL-@-ext^IGL-@-ext^IGL-.g@-ext"  ; gene_id "MYO18B--IGL-@-ext^IGL-@-ext^IGL-.g@-ext"  ; gene_name "IGL-@-ext"  ; orig_coord_info "chr22,22030934,22923034,-"  ; transcript_id "MYO18B--IGL-@-ext^IGL-.t@-ext" 
L1 and L2 created: 
TLK2--AL669831.1	HAVANA	gene	41389	47379	.	+	.	FI_gene_label "AL669831.1^ENSG00000228327.3"  ; ID "TLK2--AL669831.1^AL669831.1^ENSG00000228327.3"  ; exon_id "ENSE00001630466.1"  ; exon_number 1 ; gene_id "TLK2--AL669831.1^AL669831.1^ENSG00000228327.3"  ; gene_name "AL669831.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002406.2"  ; havana_transcript "OTTHUMT00000488438.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr1,774171,774280,-"  ; tag basic ; transcript_id "TLK2--AL669831.1^ENST00000428504.2"  ; transcript_name "AL669831.1-202"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TLK2--AL669831.1	HAVANA	RNA	41389	47379	.	+	.	FI_gene_label "AL669831.1^ENSG00000228327.3"  ; ID "TLK2--AL669831.1^ENST00000428504.2"  ; Parent "TLK2--AL669831.1^AL669831.1^ENSG00000228327.3"  ; exon_id "ENSE00001630466.1"  ; exon_number 1 ; gene_id "TLK2--AL669831.1^AL669831.1^ENSG00000228327.3"  ; gene_name "AL669831.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002406.2"  ; havana_transcript "OTTHUMT00000488438.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr1,774171,774280,-"  ; tag basic ; transcript_id "TLK2--AL669831.1^ENST00000428504.2"  ; transcript_name "AL669831.1-202"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
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
342 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 ------------------------------
806 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 19 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