.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cIX-T1-TRNA-1_B23WHTKLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/4cc01f017a6033462e9e5b2afe7103/.command.log
Size: 50.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cIX-T1-TRNA-1_B23WHTKLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/6b4377a197facd366c297e0310f554/fi_workdir/659_cIX-T1-TRNA-1_B23WHTKLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/4cc01f017a6033462e9e5b2afe7103/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/4cc01f017a6033462e9e5b2afe7103/.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: 2526
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2526
=> 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:2526
  => 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: 
AC092807.3--DDAH1	HAVANA	gene	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1	HAVANA	mRNA	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^ENST00000284031.13"  ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP1--AC068051.1	HAVANA	gene	1001	13176	.	+	.	FI_gene_label "ARHGAP1^ENSG00000175220.12"  ; ID "ARHGAP1--AC068051.1^ARHGAP1^ENSG00000175220.12"  ; ccdsid "CCDS7922.1"  ; exon_id "ENSE00003641077.1"  ; exon_number 2 ; gene_id "ARHGAP1--AC068051.1^ARHGAP1^ENSG00000175220.12"  ; gene_name ARHGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166567.3"  ; havana_transcript "OTTHUMT00000390472.2"  ; hgnc_id "HGNC:673"  ; level 2 ; orig_coord_info "chr11,46695975,46696107,-"  ; protein_id "ENSP00000310491.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGAP1--AC068051.1^ENST00000311956.9"  ; transcript_name "ARHGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGAP1--AC068051.1	HAVANA	mRNA	1001	13176	.	+	.	FI_gene_label "ARHGAP1^ENSG00000175220.12"  ; ID "ARHGAP1--AC068051.1^ENST00000311956.9"  ; Parent "ARHGAP1--AC068051.1^ARHGAP1^ENSG00000175220.12"  ; ccdsid "CCDS7922.1"  ; exon_id "ENSE00003641077.1"  ; exon_number 2 ; gene_id "ARHGAP1--AC068051.1^ARHGAP1^ENSG00000175220.12"  ; gene_name ARHGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166567.3"  ; havana_transcript "OTTHUMT00000390472.2"  ; hgnc_id "HGNC:673"  ; level 2 ; orig_coord_info "chr11,46695975,46696107,-"  ; protein_id "ENSP00000310491.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGAP1--AC068051.1^ENST00000311956.9"  ; transcript_name "ARHGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CASC15--GRIA4	HAVANA	gene	100201	130450	.	+	.	FI_gene_label "GRIA4^ENSG00000152578.13"  ; ID "CASC15--GRIA4^GRIA4^ENSG00000152578.13"  ; ccdsid "CCDS8333.1"  ; exon_id "ENSE00003895763.1"  ; exon_number 2 ; gene_id "CASC15--GRIA4^GRIA4^ENSG00000152578.13"  ; gene_name GRIA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166236.5"  ; havana_transcript "OTTHUMT00000504290.2"  ; hgnc_id "HGNC:4574"  ; level 2 ; orig_coord_info "chr11,105610998,105611085,+"  ; protein_id "ENSP00000282499.5"  ; tag RNA_Seq_supported_only basic MANE_Select CCDS ; transcript_id "CASC15--GRIA4^ENST00000282499.10"  ; transcript_name "GRIA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
CASC15--GRIA4	HAVANA	mRNA	100201	130450	.	+	.	FI_gene_label "GRIA4^ENSG00000152578.13"  ; ID "CASC15--GRIA4^ENST00000282499.10"  ; Parent "CASC15--GRIA4^GRIA4^ENSG00000152578.13"  ; ccdsid "CCDS8333.1"  ; exon_id "ENSE00003895763.1"  ; exon_number 2 ; gene_id "CASC15--GRIA4^GRIA4^ENSG00000152578.13"  ; gene_name GRIA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166236.5"  ; havana_transcript "OTTHUMT00000504290.2"  ; hgnc_id "HGNC:4574"  ; level 2 ; orig_coord_info "chr11,105610998,105611085,+"  ; protein_id "ENSP00000282499.5"  ; tag RNA_Seq_supported_only basic MANE_Select CCDS ; transcript_id "CASC15--GRIA4^ENST00000282499.10"  ; transcript_name "GRIA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MDH1--PAUPAR	HAVANA	gene	1355	13918	.	+	.	FI_gene_label "MDH1^ENSG00000014641.21"  ; ID "MDH1--PAUPAR^MDH1^ENSG00000014641.21"  ; ccdsid "CCDS1874.1"  ; exon_id "ENSE00003559734.2"  ; exon_number 1 ; gene_id "MDH1--PAUPAR^MDH1^ENSG00000014641.21"  ; gene_name MDH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129512.14"  ; havana_transcript "OTTHUMT00000251687.2"  ; hgnc_id "HGNC:6970"  ; level 2 ; orig_coord_info "chr2,63589044,63589046,+"  ; protein_id "ENSP00000233114.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MDH1--PAUPAR^ENST00000233114.13"  ; transcript_name "MDH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MDH1--PAUPAR	HAVANA	mRNA	1355	13918	.	+	.	FI_gene_label "MDH1^ENSG00000014641.21"  ; ID "MDH1--PAUPAR^ENST00000233114.13"  ; Parent "MDH1--PAUPAR^MDH1^ENSG00000014641.21"  ; ccdsid "CCDS1874.1"  ; exon_id "ENSE00003559734.2"  ; exon_number 1 ; gene_id "MDH1--PAUPAR^MDH1^ENSG00000014641.21"  ; gene_name MDH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129512.14"  ; havana_transcript "OTTHUMT00000251687.2"  ; hgnc_id "HGNC:6970"  ; level 2 ; orig_coord_info "chr2,63589044,63589046,+"  ; protein_id "ENSP00000233114.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MDH1--PAUPAR^ENST00000233114.13"  ; transcript_name "MDH1-201"  ; 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: 
PCDHA11--PCDHA13	HAVANA	gene	7419	15859	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHA13	HAVANA	mRNA	7419	15859	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA11--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHA13	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHA13	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHA13^ENST00000616325.1"  ; Parent "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC1	HAVANA	gene	7419	17434	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC1	HAVANA	mRNA	7419	17434	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA11--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC1	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC1	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC1^ENST00000616325.1"  ; Parent "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC2	HAVANA	gene	7425	18160	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC2	HAVANA	mRNA	7425	18160	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA11--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA11--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 "PCDHA11--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA11--PCDHAC2	HAVANA	gene	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC2	HAVANA	mRNA	1001	4418	.	+	.	FI_gene_label "PCDHA11^ENSG00000249158.7"  ; ID "PCDHA11--PCDHAC2^ENST00000616325.1"  ; Parent "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; ccdsid "CCDS75326.1"  ; exon_id "ENSE00003719125.1"  ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7"  ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3"  ; havana_transcript "OTTHUMT00000477577.1"  ; hgnc_id "HGNC:8665"  ; level 2 ; orig_coord_info "chr5,140869104,140871533,+"  ; protein_id "ENSP00000482503.1"  ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1"  ; transcript_name "PCDHA11-202"  ; transcript_support_level NA ; 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: 
TNFAIP8L3--CYP19A1	HAVANA	gene	1001	5614	.	+	.	FI_gene_label "TNFAIP8L3^ENSG00000183578.8"  ; ID "TNFAIP8L3--CYP19A1^TNFAIP8L3^ENSG00000183578.8"  ; ccdsid "CCDS32241.1"  ; exon_id "ENSE00001486468.1"  ; exon_number 1 ; gene_id "TNFAIP8L3--CYP19A1^TNFAIP8L3^ENSG00000183578.8"  ; gene_name TNFAIP8L3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172460.5"  ; havana_transcript "OTTHUMT00000418661.1"  ; hgnc_id "HGNC:20620"  ; level 2 ; orig_coord_info "chr15,51105005,51105176,-"  ; protein_id "ENSP00000328016.5"  ; tag basic CCDS ; transcript_id "TNFAIP8L3--CYP19A1^ENST00000327536.5"  ; transcript_name "TNFAIP8L3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TNFAIP8L3--CYP19A1	HAVANA	mRNA	1001	5614	.	+	.	FI_gene_label "TNFAIP8L3^ENSG00000183578.8"  ; ID "TNFAIP8L3--CYP19A1^ENST00000327536.5"  ; Parent "TNFAIP8L3--CYP19A1^TNFAIP8L3^ENSG00000183578.8"  ; ccdsid "CCDS32241.1"  ; exon_id "ENSE00001486468.1"  ; exon_number 1 ; gene_id "TNFAIP8L3--CYP19A1^TNFAIP8L3^ENSG00000183578.8"  ; gene_name TNFAIP8L3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172460.5"  ; havana_transcript "OTTHUMT00000418661.1"  ; hgnc_id "HGNC:20620"  ; level 2 ; orig_coord_info "chr15,51105005,51105176,-"  ; protein_id "ENSP00000328016.5"  ; tag basic CCDS ; transcript_id "TNFAIP8L3--CYP19A1^ENST00000327536.5"  ; transcript_name "TNFAIP8L3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TNFAIP8L3--CYP19A1	HAVANA	gene	8620	32660	.	+	.	FI_gene_label "CYP19A1^ENSG00000137869.15"  ; ID "TNFAIP8L3--CYP19A1^CYP19A1^ENSG00000137869.15"  ; ccdsid "CCDS10139.1"  ; exon_id "ENSE00001621872.1"  ; exon_number 2 ; gene_id "TNFAIP8L3--CYP19A1^CYP19A1^ENSG00000137869.15"  ; gene_name CYP19A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131747.7"  ; havana_transcript "OTTHUMT00000254669.2"  ; hgnc_id "HGNC:2594"  ; level 2 ; orig_coord_info "chr15,51242768,51242912,-"  ; protein_id "ENSP00000379683.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNFAIP8L3--CYP19A1^ENST00000396402.6"  ; transcript_name "CYP19A1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TNFAIP8L3--CYP19A1	HAVANA	mRNA	8620	32660	.	+	.	FI_gene_label "CYP19A1^ENSG00000137869.15"  ; ID "TNFAIP8L3--CYP19A1^ENST00000396402.6"  ; Parent "TNFAIP8L3--CYP19A1^CYP19A1^ENSG00000137869.15"  ; ccdsid "CCDS10139.1"  ; exon_id "ENSE00001621872.1"  ; exon_number 2 ; gene_id "TNFAIP8L3--CYP19A1^CYP19A1^ENSG00000137869.15"  ; gene_name CYP19A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131747.7"  ; havana_transcript "OTTHUMT00000254669.2"  ; hgnc_id "HGNC:2594"  ; level 2 ; orig_coord_info "chr15,51242768,51242912,-"  ; protein_id "ENSP00000379683.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNFAIP8L3--CYP19A1^ENST00000396402.6"  ; transcript_name "CYP19A1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TNS1--ALK	HAVANA	gene	8232	56093	.	+	.	FI_gene_label "TNS1^ENSG00000079308.19"  ; ID "TNS1--ALK^TNS1^ENSG00000079308.19"  ; ccdsid "CCDS2407.1"  ; exon_id "ENSE00003622889.1"  ; exon_number 6 ; gene_id "TNS1--ALK^TNS1^ENSG00000079308.19"  ; gene_name TNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133056.10"  ; havana_transcript "OTTHUMT00000256672.2"  ; hgnc_id "HGNC:11973"  ; level 2 ; orig_coord_info "chr2,217897798,217897965,-"  ; protein_id "ENSP00000171887.4"  ; tag basic CCDS ; transcript_id "TNS1--ALK^ENST00000171887.8"  ; transcript_name "TNS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TNS1--ALK	HAVANA	mRNA	8232	56093	.	+	.	FI_gene_label "TNS1^ENSG00000079308.19"  ; ID "TNS1--ALK^ENST00000171887.8"  ; Parent "TNS1--ALK^TNS1^ENSG00000079308.19"  ; ccdsid "CCDS2407.1"  ; exon_id "ENSE00003622889.1"  ; exon_number 6 ; gene_id "TNS1--ALK^TNS1^ENSG00000079308.19"  ; gene_name TNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133056.10"  ; havana_transcript "OTTHUMT00000256672.2"  ; hgnc_id "HGNC:11973"  ; level 2 ; orig_coord_info "chr2,217897798,217897965,-"  ; protein_id "ENSP00000171887.4"  ; tag basic CCDS ; transcript_id "TNS1--ALK^ENST00000171887.8"  ; transcript_name "TNS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TNS1--ALK	HAVANA	gene	59295	94299	.	+	.	FI_gene_label "ALK^ENSG00000171094.18"  ; ID "TNS1--ALK^ALK^ENSG00000171094.18"  ; ccdsid "CCDS33172.1"  ; exon_id "ENSE00001794937.2"  ; exon_number 1 ; gene_id "TNS1--ALK^ALK^ENSG00000171094.18"  ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4"  ; havana_transcript "OTTHUMT00000324994.2"  ; hgnc_id "HGNC:427"  ; level 2 ; orig_coord_info "chr2,29919993,29920659,-"  ; protein_id "ENSP00000373700.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS1--ALK^ENST00000389048.8"  ; transcript_name "ALK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TNS1--ALK	HAVANA	mRNA	59295	94299	.	+	.	FI_gene_label "ALK^ENSG00000171094.18"  ; ID "TNS1--ALK^ENST00000389048.8"  ; Parent "TNS1--ALK^ALK^ENSG00000171094.18"  ; ccdsid "CCDS33172.1"  ; exon_id "ENSE00001794937.2"  ; exon_number 1 ; gene_id "TNS1--ALK^ALK^ENSG00000171094.18"  ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4"  ; havana_transcript "OTTHUMT00000324994.2"  ; hgnc_id "HGNC:427"  ; level 2 ; orig_coord_info "chr2,29919993,29920659,-"  ; protein_id "ENSP00000373700.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS1--ALK^ENST00000389048.8"  ; transcript_name "ALK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^ENST00000225576.7"  ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^ENST00000619038.5"  ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC092807.3--DDAH1	HAVANA	gene	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1	HAVANA	RNA	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^ENST00000467530.5"  ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
ARHGAP1--AC068051.1	HAVANA	gene	16177	24040	.	+	.	FI_gene_label "AC068051.1^ENSG00000197585.10"  ; ID "ARHGAP1--AC068051.1^AC068051.1^ENSG00000197585.10"  ; exon_id "ENSE00001732962.1"  ; exon_number 1 ; gene_id "ARHGAP1--AC068051.1^AC068051.1^ENSG00000197585.10"  ; gene_name "AC068051.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000154823.3"  ; havana_transcript "OTTHUMT00000337270.2"  ; level 2 ; orig_coord_info "chr2,214684115,214684246,-"  ; transcript_id "ARHGAP1--AC068051.1^ENST00000412896.5"  ; transcript_name "AC068051.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
ARHGAP1--AC068051.1	HAVANA	RNA	16177	24040	.	+	.	FI_gene_label "AC068051.1^ENSG00000197585.10"  ; ID "ARHGAP1--AC068051.1^ENST00000412896.5"  ; Parent "ARHGAP1--AC068051.1^AC068051.1^ENSG00000197585.10"  ; exon_id "ENSE00001732962.1"  ; exon_number 1 ; gene_id "ARHGAP1--AC068051.1^AC068051.1^ENSG00000197585.10"  ; gene_name "AC068051.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000154823.3"  ; havana_transcript "OTTHUMT00000337270.2"  ; level 2 ; orig_coord_info "chr2,214684115,214684246,-"  ; transcript_id "ARHGAP1--AC068051.1^ENST00000412896.5"  ; transcript_name "AC068051.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
CASC15--GRIA4	HAVANA	gene	18078	66802	.	+	.	FI_gene_label "CASC15^ENSG00000272168.8"  ; ID "CASC15--GRIA4^CASC15^ENSG00000272168.8"  ; exon_id "ENSE00003696426.1"  ; exon_number 1 ; gene_id "CASC15--GRIA4^CASC15^ENSG00000272168.8"  ; gene_name CASC15 ; gene_type lncRNA ; havana_gene "OTTHUMG00000014345.88"  ; havana_transcript "OTTHUMT00000470987.2"  ; hgnc_id "HGNC:28245"  ; level 2 ; orig_coord_info "chr6,21898720,21898784,+"  ; tag basic ; transcript_id "CASC15--GRIA4^ENST00000444265.6"  ; transcript_name "CASC15-201"  ; transcript_support_level 1 ; transcript_type lncRNA
CASC15--GRIA4	HAVANA	RNA	18078	66802	.	+	.	FI_gene_label "CASC15^ENSG00000272168.8"  ; ID "CASC15--GRIA4^ENST00000444265.6"  ; Parent "CASC15--GRIA4^CASC15^ENSG00000272168.8"  ; exon_id "ENSE00003696426.1"  ; exon_number 1 ; gene_id "CASC15--GRIA4^CASC15^ENSG00000272168.8"  ; gene_name CASC15 ; gene_type lncRNA ; havana_gene "OTTHUMG00000014345.88"  ; havana_transcript "OTTHUMT00000470987.2"  ; hgnc_id "HGNC:28245"  ; level 2 ; orig_coord_info "chr6,21898720,21898784,+"  ; tag basic ; transcript_id "CASC15--GRIA4^ENST00000444265.6"  ; transcript_name "CASC15-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
MDH1--PAUPAR	HAVANA	gene	19576	26684	.	+	.	FI_gene_label "PAUPAR^ENSG00000281880.2"  ; ID "MDH1--PAUPAR^PAUPAR^ENSG00000281880.2"  ; exon_id "ENSE00002067491.1"  ; exon_number 1 ; gene_id "MDH1--PAUPAR^PAUPAR^ENSG00000281880.2"  ; gene_name PAUPAR ; gene_type lncRNA ; havana_gene "OTTHUMG00000189576.2"  ; havana_transcript "OTTHUMT00000493869.2"  ; hgnc_id "HGNC:49670"  ; level 2 ; orig_coord_info "chr11,31816566,31816639,+"  ; transcript_id "MDH1--PAUPAR^ENST00000506388.2"  ; transcript_name "PAUPAR-201"  ; transcript_support_level 1 ; transcript_type lncRNA
MDH1--PAUPAR	HAVANA	RNA	19576	26684	.	+	.	FI_gene_label "PAUPAR^ENSG00000281880.2"  ; ID "MDH1--PAUPAR^ENST00000506388.2"  ; Parent "MDH1--PAUPAR^PAUPAR^ENSG00000281880.2"  ; exon_id "ENSE00002067491.1"  ; exon_number 1 ; gene_id "MDH1--PAUPAR^PAUPAR^ENSG00000281880.2"  ; gene_name PAUPAR ; gene_type lncRNA ; havana_gene "OTTHUMG00000189576.2"  ; havana_transcript "OTTHUMT00000493869.2"  ; hgnc_id "HGNC:49670"  ; level 2 ; orig_coord_info "chr11,31816566,31816639,+"  ; transcript_id "MDH1--PAUPAR^ENST00000506388.2"  ; transcript_name "PAUPAR-201"  ; transcript_support_level 1 ; transcript_type lncRNA
277 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 ------------------------------
285 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 13 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