.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_epZ-T1-TRNA-1_B23MHV2LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/7111d666225a2e7153750182ace098/.command.log
Size: 41.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_epZ-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/7111d666225a2e7153750182ace098/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/425be8caec576e8fc5fff9141398b1/fi_workdir/659_epZ-T1-TRNA-1_B23MHV2LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/7111d666225a2e7153750182ace098/.command.run
==> STAGING COMPLETE (3 inputs)

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 2524
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2524
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:2524
  => 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: 
ATF1--EWSR1	HAVANA	gene	1392	11425	.	+	.	FI_gene_label "ATF1^ENSG00000123268.9"  ; ID "ATF1--EWSR1^ATF1^ENSG00000123268.9"  ; ccdsid "CCDS8803.1"  ; exon_id "ENSE00003503033.1"  ; exon_number 2 ; gene_id "ATF1--EWSR1^ATF1^ENSG00000123268.9"  ; gene_name ATF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169482.3"  ; havana_transcript "OTTHUMT00000404285.2"  ; hgnc_id "HGNC:783"  ; level 2 ; orig_coord_info "chr12,50780146,50780238,+"  ; protein_id "ENSP00000262053.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ATF1--EWSR1^ENST00000262053.8"  ; transcript_name "ATF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATF1--EWSR1	HAVANA	mRNA	1392	11425	.	+	.	FI_gene_label "ATF1^ENSG00000123268.9"  ; ID "ATF1--EWSR1^ENST00000262053.8"  ; Parent "ATF1--EWSR1^ATF1^ENSG00000123268.9"  ; ccdsid "CCDS8803.1"  ; exon_id "ENSE00003503033.1"  ; exon_number 2 ; gene_id "ATF1--EWSR1^ATF1^ENSG00000123268.9"  ; gene_name ATF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169482.3"  ; havana_transcript "OTTHUMT00000404285.2"  ; hgnc_id "HGNC:783"  ; level 2 ; orig_coord_info "chr12,50780146,50780238,+"  ; protein_id "ENSP00000262053.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ATF1--EWSR1^ENST00000262053.8"  ; transcript_name "ATF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ATF1--EWSR1	HAVANA	gene	14708	35522	.	+	.	FI_gene_label "EWSR1^ENSG00000182944.18"  ; ID "ATF1--EWSR1^EWSR1^ENSG00000182944.18"  ; exon_id "ENSE00001930494.1"  ; exon_number 1 ; gene_id "ATF1--EWSR1^EWSR1^ENSG00000182944.18"  ; gene_name EWSR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151107.9"  ; havana_transcript "OTTHUMT00000321351.1"  ; hgnc_id "HGNC:3508"  ; level 2 ; orig_coord_info "chr22,29268337,29268349,+"  ; protein_id "ENSP00000330516.7"  ; tag not_organism_supported basic ; transcript_id "ATF1--EWSR1^ENST00000331029.11"  ; transcript_name "EWSR1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ATF1--EWSR1	HAVANA	mRNA	14708	35522	.	+	.	FI_gene_label "EWSR1^ENSG00000182944.18"  ; ID "ATF1--EWSR1^ENST00000331029.11"  ; Parent "ATF1--EWSR1^EWSR1^ENSG00000182944.18"  ; exon_id "ENSE00001930494.1"  ; exon_number 1 ; gene_id "ATF1--EWSR1^EWSR1^ENSG00000182944.18"  ; gene_name EWSR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151107.9"  ; havana_transcript "OTTHUMT00000321351.1"  ; hgnc_id "HGNC:3508"  ; level 2 ; orig_coord_info "chr22,29268337,29268349,+"  ; protein_id "ENSP00000330516.7"  ; tag not_organism_supported basic ; transcript_id "ATF1--EWSR1^ENST00000331029.11"  ; transcript_name "EWSR1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
EWSR1--ATF1	HAVANA	gene	25489	35522	.	+	.	FI_gene_label "ATF1^ENSG00000123268.9"  ; ID "EWSR1--ATF1^ATF1^ENSG00000123268.9"  ; ccdsid "CCDS8803.1"  ; exon_id "ENSE00003503033.1"  ; exon_number 2 ; gene_id "EWSR1--ATF1^ATF1^ENSG00000123268.9"  ; gene_name ATF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169482.3"  ; havana_transcript "OTTHUMT00000404285.2"  ; hgnc_id "HGNC:783"  ; level 2 ; orig_coord_info "chr12,50780146,50780238,+"  ; protein_id "ENSP00000262053.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EWSR1--ATF1^ENST00000262053.8"  ; transcript_name "ATF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EWSR1--ATF1	HAVANA	mRNA	25489	35522	.	+	.	FI_gene_label "ATF1^ENSG00000123268.9"  ; ID "EWSR1--ATF1^ENST00000262053.8"  ; Parent "EWSR1--ATF1^ATF1^ENSG00000123268.9"  ; ccdsid "CCDS8803.1"  ; exon_id "ENSE00003503033.1"  ; exon_number 2 ; gene_id "EWSR1--ATF1^ATF1^ENSG00000123268.9"  ; gene_name ATF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169482.3"  ; havana_transcript "OTTHUMT00000404285.2"  ; hgnc_id "HGNC:783"  ; level 2 ; orig_coord_info "chr12,50780146,50780238,+"  ; protein_id "ENSP00000262053.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EWSR1--ATF1^ENST00000262053.8"  ; transcript_name "ATF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EWSR1--ATF1	HAVANA	gene	1283	22097	.	+	.	FI_gene_label "EWSR1^ENSG00000182944.18"  ; ID "EWSR1--ATF1^EWSR1^ENSG00000182944.18"  ; exon_id "ENSE00001930494.1"  ; exon_number 1 ; gene_id "EWSR1--ATF1^EWSR1^ENSG00000182944.18"  ; gene_name EWSR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151107.9"  ; havana_transcript "OTTHUMT00000321351.1"  ; hgnc_id "HGNC:3508"  ; level 2 ; orig_coord_info "chr22,29268337,29268349,+"  ; protein_id "ENSP00000330516.7"  ; tag not_organism_supported basic ; transcript_id "EWSR1--ATF1^ENST00000331029.11"  ; transcript_name "EWSR1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
EWSR1--ATF1	HAVANA	mRNA	1283	22097	.	+	.	FI_gene_label "EWSR1^ENSG00000182944.18"  ; ID "EWSR1--ATF1^ENST00000331029.11"  ; Parent "EWSR1--ATF1^EWSR1^ENSG00000182944.18"  ; exon_id "ENSE00001930494.1"  ; exon_number 1 ; gene_id "EWSR1--ATF1^EWSR1^ENSG00000182944.18"  ; gene_name EWSR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151107.9"  ; havana_transcript "OTTHUMT00000321351.1"  ; hgnc_id "HGNC:3508"  ; level 2 ; orig_coord_info "chr22,29268337,29268349,+"  ; protein_id "ENSP00000330516.7"  ; tag not_organism_supported basic ; transcript_id "EWSR1--ATF1^ENST00000331029.11"  ; transcript_name "EWSR1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
IGH-@-ext--ARL4D	HAVANA	gene	1295342	1297486	.	+	.	FI_gene_label "ARL4D^ENSG00000175906.5"  ; ID "IGH-@-ext--ARL4D^ARL4D^ENSG00000175906.5"  ; ccdsid "CCDS11463.1"  ; exon_id "ENSE00001280129.7"  ; exon_number 2 ; gene_id "IGH-@-ext--ARL4D^ARL4D^ENSG00000175906.5"  ; gene_name ARL4D ; gene_type protein_coding ; havana_gene "OTTHUMG00000180881.3"  ; havana_transcript "OTTHUMT00000453481.3"  ; hgnc_id "HGNC:656"  ; level 2 ; orig_coord_info "chr17,43399733,43400335,+"  ; protein_id "ENSP00000322628.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IGH-@-ext--ARL4D^ENST00000320033.5"  ; transcript_name "ARL4D-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IGH-@-ext--ARL4D	HAVANA	mRNA	1295342	1297486	.	+	.	FI_gene_label "ARL4D^ENSG00000175906.5"  ; ID "IGH-@-ext--ARL4D^ENST00000320033.5"  ; Parent "IGH-@-ext--ARL4D^ARL4D^ENSG00000175906.5"  ; ccdsid "CCDS11463.1"  ; exon_id "ENSE00001280129.7"  ; exon_number 2 ; gene_id "IGH-@-ext--ARL4D^ARL4D^ENSG00000175906.5"  ; gene_name ARL4D ; gene_type protein_coding ; havana_gene "OTTHUMG00000180881.3"  ; havana_transcript "OTTHUMT00000453481.3"  ; hgnc_id "HGNC:656"  ; level 2 ; orig_coord_info "chr17,43399733,43400335,+"  ; protein_id "ENSP00000322628.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IGH-@-ext--ARL4D^ENST00000320033.5"  ; transcript_name "ARL4D-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MINDY3--UBR4	HAVANA	gene	1001	18727	.	+	.	FI_gene_label "MINDY3^ENSG00000148481.14"  ; ID "MINDY3--UBR4^MINDY3^ENSG00000148481.14"  ; ccdsid "CCDS7110.1"  ; exon_id "ENSE00001285483.5"  ; exon_number 1 ; gene_id "MINDY3--UBR4^MINDY3^ENSG00000148481.14"  ; gene_name MINDY3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017734.4"  ; havana_transcript "OTTHUMT00000046990.3"  ; hgnc_id "HGNC:23578"  ; level 2 ; orig_coord_info "chr10,15860206,15860299,-"  ; protein_id "ENSP00000277632.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MINDY3--UBR4^ENST00000277632.8"  ; transcript_name "MINDY3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MINDY3--UBR4	HAVANA	mRNA	1001	18727	.	+	.	FI_gene_label "MINDY3^ENSG00000148481.14"  ; ID "MINDY3--UBR4^ENST00000277632.8"  ; Parent "MINDY3--UBR4^MINDY3^ENSG00000148481.14"  ; ccdsid "CCDS7110.1"  ; exon_id "ENSE00001285483.5"  ; exon_number 1 ; gene_id "MINDY3--UBR4^MINDY3^ENSG00000148481.14"  ; gene_name MINDY3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017734.4"  ; havana_transcript "OTTHUMT00000046990.3"  ; hgnc_id "HGNC:23578"  ; level 2 ; orig_coord_info "chr10,15860206,15860299,-"  ; protein_id "ENSP00000277632.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MINDY3--UBR4^ENST00000277632.8"  ; transcript_name "MINDY3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MINDY3--UBR4	HAVANA	gene	80752	87378	.	+	.	FI_gene_label "UBR4^ENSG00000127481.15"  ; ID "MINDY3--UBR4^UBR4^ENSG00000127481.15"  ; exon_id "ENSE00003662944.1"  ; exon_number 2 ; gene_id "MINDY3--UBR4^UBR4^ENSG00000127481.15"  ; gene_name UBR4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002498.6"  ; havana_transcript "OTTHUMT00000007089.2"  ; hgnc_id "HGNC:30313"  ; level 2 ; orig_coord_info "chr1,19117221,19117288,-"  ; protein_id "ENSP00000364366.3"  ; tag basic ; transcript_id "MINDY3--UBR4^ENST00000375218.3"  ; transcript_name "UBR4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
MINDY3--UBR4	HAVANA	mRNA	80752	87378	.	+	.	FI_gene_label "UBR4^ENSG00000127481.15"  ; ID "MINDY3--UBR4^ENST00000375218.3"  ; Parent "MINDY3--UBR4^UBR4^ENSG00000127481.15"  ; exon_id "ENSE00003662944.1"  ; exon_number 2 ; gene_id "MINDY3--UBR4^UBR4^ENSG00000127481.15"  ; gene_name UBR4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002498.6"  ; havana_transcript "OTTHUMT00000007089.2"  ; hgnc_id "HGNC:30313"  ; level 2 ; orig_coord_info "chr1,19117221,19117288,-"  ; protein_id "ENSP00000364366.3"  ; tag basic ; transcript_id "MINDY3--UBR4^ENST00000375218.3"  ; transcript_name "UBR4-201"  ; transcript_support_level 2 ; 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: 
PCDHA4--PCDHA13	HAVANA	gene	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13	HAVANA	mRNA	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^ENST00000378125.4"  ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	HAVANA	gene	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1	HAVANA	mRNA	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	HAVANA	gene	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2	HAVANA	mRNA	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--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 "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
RNF216--EIF2AK1	HAVANA	gene	34260	53063	.	+	.	FI_gene_label "EIF2AK1^ENSG00000086232.13"  ; ID "RNF216--EIF2AK1^EIF2AK1^ENSG00000086232.13"  ; ccdsid "CCDS5345.1"  ; exon_id "ENSE00001634941.3"  ; exon_number 1 ; gene_id "RNF216--EIF2AK1^EIF2AK1^ENSG00000086232.13"  ; gene_name EIF2AK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090689.15"  ; havana_transcript "OTTHUMT00000207373.4"  ; hgnc_id "HGNC:24921"  ; level 2 ; orig_coord_info "chr7,6058966,6059083,-"  ; protein_id "ENSP00000199389.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNF216--EIF2AK1^ENST00000199389.11"  ; transcript_name "EIF2AK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RNF216--EIF2AK1	HAVANA	mRNA	34260	53063	.	+	.	FI_gene_label "EIF2AK1^ENSG00000086232.13"  ; ID "RNF216--EIF2AK1^ENST00000199389.11"  ; Parent "RNF216--EIF2AK1^EIF2AK1^ENSG00000086232.13"  ; ccdsid "CCDS5345.1"  ; exon_id "ENSE00001634941.3"  ; exon_number 1 ; gene_id "RNF216--EIF2AK1^EIF2AK1^ENSG00000086232.13"  ; gene_name EIF2AK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090689.15"  ; havana_transcript "OTTHUMT00000207373.4"  ; hgnc_id "HGNC:24921"  ; level 2 ; orig_coord_info "chr7,6058966,6059083,-"  ; protein_id "ENSP00000199389.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNF216--EIF2AK1^ENST00000199389.11"  ; transcript_name "EIF2AK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RNF216--EIF2AK1	HAVANA	gene	6827	28611	.	+	.	FI_gene_label "RNF216^ENSG00000011275.19"  ; ID "RNF216--EIF2AK1^RNF216^ENSG00000011275.19"  ; exon_id "ENSE00001422787.1"  ; exon_number 1 ; gene_id "RNF216--EIF2AK1^RNF216^ENSG00000011275.19"  ; gene_name RNF216 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155500.4"  ; havana_transcript "OTTHUMT00000340377.1"  ; hgnc_id "HGNC:21698"  ; level 2 ; orig_coord_info "chr7,5761003,5761069,-"  ; protein_id "ENSP00000374550.4"  ; transcript_id "RNF216--EIF2AK1^ENST00000389900.8"  ; transcript_name "RNF216-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
RNF216--EIF2AK1	HAVANA	mRNA	6827	28611	.	+	.	FI_gene_label "RNF216^ENSG00000011275.19"  ; ID "RNF216--EIF2AK1^ENST00000389900.8"  ; Parent "RNF216--EIF2AK1^RNF216^ENSG00000011275.19"  ; exon_id "ENSE00001422787.1"  ; exon_number 1 ; gene_id "RNF216--EIF2AK1^RNF216^ENSG00000011275.19"  ; gene_name RNF216 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155500.4"  ; havana_transcript "OTTHUMT00000340377.1"  ; hgnc_id "HGNC:21698"  ; level 2 ; orig_coord_info "chr7,5761003,5761069,-"  ; protein_id "ENSP00000374550.4"  ; transcript_id "RNF216--EIF2AK1^ENST00000389900.8"  ; transcript_name "RNF216-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
RPN2--SPATA5	HAVANA	gene	1921	21709	.	+	.	FI_gene_label "RPN2^ENSG00000118705.17"  ; ID "RPN2--SPATA5^RPN2^ENSG00000118705.17"  ; ccdsid "CCDS13291.1"  ; exon_id "ENSE00001369190.4"  ; exon_number 1 ; gene_id "RPN2--SPATA5^RPN2^ENSG00000118705.17"  ; gene_name RPN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032409.6"  ; havana_transcript "OTTHUMT00000079076.4"  ; hgnc_id "HGNC:10382"  ; level 2 ; orig_coord_info "chr20,37179357,37179369,+"  ; protein_id "ENSP00000237530.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RPN2--SPATA5^ENST00000237530.11"  ; transcript_name "RPN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RPN2--SPATA5	HAVANA	mRNA	1921	21709	.	+	.	FI_gene_label "RPN2^ENSG00000118705.17"  ; ID "RPN2--SPATA5^ENST00000237530.11"  ; Parent "RPN2--SPATA5^RPN2^ENSG00000118705.17"  ; ccdsid "CCDS13291.1"  ; exon_id "ENSE00001369190.4"  ; exon_number 1 ; gene_id "RPN2--SPATA5^RPN2^ENSG00000118705.17"  ; gene_name RPN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032409.6"  ; havana_transcript "OTTHUMT00000079076.4"  ; hgnc_id "HGNC:10382"  ; level 2 ; orig_coord_info "chr20,37179357,37179369,+"  ; protein_id "ENSP00000237530.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RPN2--SPATA5^ENST00000237530.11"  ; transcript_name "RPN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RPN2--SPATA5	HAVANA	gene	24718	49969	.	+	.	FI_gene_label "SPATA5^ENSG00000145375.9"  ; ID "RPN2--SPATA5^SPATA5^ENSG00000145375.9"  ; ccdsid "CCDS3730.1"  ; exon_id "ENSE00001895453.2"  ; exon_number 1 ; gene_id "RPN2--SPATA5^SPATA5^ENSG00000145375.9"  ; gene_name SPATA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133074.5"  ; havana_transcript "OTTHUMT00000256714.3"  ; hgnc_id "HGNC:18119"  ; level 2 ; orig_coord_info "chr4,122923143,122923305,+"  ; protein_id "ENSP00000274008.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RPN2--SPATA5^ENST00000274008.5"  ; transcript_name "SPATA5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RPN2--SPATA5	HAVANA	mRNA	24718	49969	.	+	.	FI_gene_label "SPATA5^ENSG00000145375.9"  ; ID "RPN2--SPATA5^ENST00000274008.5"  ; Parent "RPN2--SPATA5^SPATA5^ENSG00000145375.9"  ; ccdsid "CCDS3730.1"  ; exon_id "ENSE00001895453.2"  ; exon_number 1 ; gene_id "RPN2--SPATA5^SPATA5^ENSG00000145375.9"  ; gene_name SPATA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133074.5"  ; havana_transcript "OTTHUMT00000256714.3"  ; hgnc_id "HGNC:18119"  ; level 2 ; orig_coord_info "chr4,122923143,122923305,+"  ; protein_id "ENSP00000274008.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RPN2--SPATA5^ENST00000274008.5"  ; transcript_name "SPATA5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
UBR4--MINDY3	HAVANA	gene	96584	114310	.	+	.	FI_gene_label "MINDY3^ENSG00000148481.14"  ; ID "UBR4--MINDY3^MINDY3^ENSG00000148481.14"  ; ccdsid "CCDS7110.1"  ; exon_id "ENSE00001285483.5"  ; exon_number 1 ; gene_id "UBR4--MINDY3^MINDY3^ENSG00000148481.14"  ; gene_name MINDY3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017734.4"  ; havana_transcript "OTTHUMT00000046990.3"  ; hgnc_id "HGNC:23578"  ; level 2 ; orig_coord_info "chr10,15860206,15860299,-"  ; protein_id "ENSP00000277632.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "UBR4--MINDY3^ENST00000277632.8"  ; transcript_name "MINDY3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
UBR4--MINDY3	HAVANA	mRNA	96584	114310	.	+	.	FI_gene_label "MINDY3^ENSG00000148481.14"  ; ID "UBR4--MINDY3^ENST00000277632.8"  ; Parent "UBR4--MINDY3^MINDY3^ENSG00000148481.14"  ; ccdsid "CCDS7110.1"  ; exon_id "ENSE00001285483.5"  ; exon_number 1 ; gene_id "UBR4--MINDY3^MINDY3^ENSG00000148481.14"  ; gene_name MINDY3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017734.4"  ; havana_transcript "OTTHUMT00000046990.3"  ; hgnc_id "HGNC:23578"  ; level 2 ; orig_coord_info "chr10,15860206,15860299,-"  ; protein_id "ENSP00000277632.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "UBR4--MINDY3^ENST00000277632.8"  ; transcript_name "MINDY3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
UBR4--MINDY3	HAVANA	gene	60021	66647	.	+	.	FI_gene_label "UBR4^ENSG00000127481.15"  ; ID "UBR4--MINDY3^UBR4^ENSG00000127481.15"  ; exon_id "ENSE00003662944.1"  ; exon_number 2 ; gene_id "UBR4--MINDY3^UBR4^ENSG00000127481.15"  ; gene_name UBR4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002498.6"  ; havana_transcript "OTTHUMT00000007089.2"  ; hgnc_id "HGNC:30313"  ; level 2 ; orig_coord_info "chr1,19117221,19117288,-"  ; protein_id "ENSP00000364366.3"  ; tag basic ; transcript_id "UBR4--MINDY3^ENST00000375218.3"  ; transcript_name "UBR4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
UBR4--MINDY3	HAVANA	mRNA	60021	66647	.	+	.	FI_gene_label "UBR4^ENSG00000127481.15"  ; ID "UBR4--MINDY3^ENST00000375218.3"  ; Parent "UBR4--MINDY3^UBR4^ENSG00000127481.15"  ; exon_id "ENSE00003662944.1"  ; exon_number 2 ; gene_id "UBR4--MINDY3^UBR4^ENSG00000127481.15"  ; gene_name UBR4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002498.6"  ; havana_transcript "OTTHUMT00000007089.2"  ; hgnc_id "HGNC:30313"  ; level 2 ; orig_coord_info "chr1,19117221,19117288,-"  ; protein_id "ENSP00000364366.3"  ; tag basic ; transcript_id "UBR4--MINDY3^ENST00000375218.3"  ; transcript_name "UBR4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
IGH-@-ext--ARL4D	SuperLocus-ext	gene	1001	1292341	.	+	.	FI_gene_label "IGH-@-ext^IGH-.g@-ext"  ; ID "IGH-@-ext--ARL4D^IGH-@-ext^IGH-.g@-ext"  ; gene_id "IGH-@-ext--ARL4D^IGH-@-ext^IGH-.g@-ext"  ; gene_name "IGH-@-ext"  ; orig_coord_info "chr14,105583731,106875071,+"  ; transcript_id "IGH-@-ext--ARL4D^IGH-.t@-ext" 
IGH-@-ext--ARL4D	SuperLocus-ext	RNA	1001	1292341	.	+	.	FI_gene_label "IGH-@-ext^IGH-.g@-ext"  ; ID "IGH-@-ext--ARL4D^IGH-.t@-ext"  ; Parent "IGH-@-ext--ARL4D^IGH-@-ext^IGH-.g@-ext"  ; gene_id "IGH-@-ext--ARL4D^IGH-@-ext^IGH-.g@-ext"  ; gene_name "IGH-@-ext"  ; orig_coord_info "chr14,105583731,106875071,+"  ; transcript_id "IGH-@-ext--ARL4D^IGH-.t@-ext" 
166 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 ------------------------------
218 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------

------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

------------------------ Check12: all level1 locations -------------------------
We fixed 16 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

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


GFF3 file parsed