File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/69b0ea6fbcdfbee845f13d6dcb5933/.command.out
Size
49.1 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00088_23H5VFLT4_s02)
Attempt

Content

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

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 2735
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2735
=> 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:2735
  => 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: 
AC009396.1--NAA30	HAVANA	gene	6837	13812	.	+	.	FI_gene_label "NAA30^ENSG00000139977.14"  ; ID "AC009396.1--NAA30^NAA30^ENSG00000139977.14"  ; exon_id "ENSE00002442052.1"  ; exon_number 1 ; gene_id "AC009396.1--NAA30^NAA30^ENSG00000139977.14"  ; gene_name NAA30 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171311.2"  ; havana_transcript "OTTHUMT00000412927.1"  ; hgnc_id "HGNC:19844"  ; level 1 ; orig_coord_info "chr14,57391301,57391506,+"  ; protein_id "ENSP00000298406.6"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "AC009396.1--NAA30^ENST00000298406.6"  ; transcript_name "NAA30-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC009396.1--NAA30	HAVANA	mRNA	6837	13812	.	+	.	FI_gene_label "NAA30^ENSG00000139977.14"  ; ID "AC009396.1--NAA30^ENST00000298406.6"  ; Parent "AC009396.1--NAA30^NAA30^ENSG00000139977.14"  ; exon_id "ENSE00002442052.1"  ; exon_number 1 ; gene_id "AC009396.1--NAA30^NAA30^ENSG00000139977.14"  ; gene_name NAA30 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171311.2"  ; havana_transcript "OTTHUMT00000412927.1"  ; hgnc_id "HGNC:19844"  ; level 1 ; orig_coord_info "chr14,57391301,57391506,+"  ; protein_id "ENSP00000298406.6"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "AC009396.1--NAA30^ENST00000298406.6"  ; transcript_name "NAA30-201"  ; transcript_support_level 1 ; transcript_type protein_coding
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: 
BAG4--AC084024.4	HAVANA	gene	1323	9259	.	+	.	FI_gene_label "BAG4^ENSG00000156735.11"  ; ID "BAG4--AC084024.4^BAG4^ENSG00000156735.11"  ; ccdsid "CCDS6104.1"  ; exon_id "ENSE00002093149.2"  ; exon_number 1 ; gene_id "BAG4--AC084024.4^BAG4^ENSG00000156735.11"  ; gene_name BAG4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164064.3"  ; havana_transcript "OTTHUMT00000377038.3"  ; hgnc_id "HGNC:940"  ; level 2 ; orig_coord_info "chr8,38176870,38177139,+"  ; protein_id "ENSP00000287322.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BAG4--AC084024.4^ENST00000287322.5"  ; transcript_name "BAG4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BAG4--AC084024.4	HAVANA	mRNA	1323	9259	.	+	.	FI_gene_label "BAG4^ENSG00000156735.11"  ; ID "BAG4--AC084024.4^ENST00000287322.5"  ; Parent "BAG4--AC084024.4^BAG4^ENSG00000156735.11"  ; ccdsid "CCDS6104.1"  ; exon_id "ENSE00002093149.2"  ; exon_number 1 ; gene_id "BAG4--AC084024.4^BAG4^ENSG00000156735.11"  ; gene_name BAG4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164064.3"  ; havana_transcript "OTTHUMT00000377038.3"  ; hgnc_id "HGNC:940"  ; level 2 ; orig_coord_info "chr8,38176870,38177139,+"  ; protein_id "ENSP00000287322.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BAG4--AC084024.4^ENST00000287322.5"  ; transcript_name "BAG4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B	HAVANA	mRNA	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^ENST00000308284.10"  ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GALNT8--CEP128	HAVANA	gene	24876	39369	.	+	.	FI_gene_label "CEP128^ENSG00000100629.17"  ; ID "GALNT8--CEP128^CEP128^ENSG00000100629.17"  ; exon_id "ENSE00003508511.1"  ; exon_number 3 ; gene_id "GALNT8--CEP128^CEP128^ENSG00000100629.17"  ; gene_name CEP128 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171442.5"  ; havana_transcript "OTTHUMT00000413420.1"  ; hgnc_id "HGNC:20359"  ; level 2 ; orig_coord_info "chr14,80916401,80916547,-"  ; protein_id "ENSP00000216517.6"  ; tag basic appris_alternative_2 ; transcript_id "GALNT8--CEP128^ENST00000216517.10"  ; transcript_name "CEP128-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GALNT8--CEP128	HAVANA	mRNA	24876	39369	.	+	.	FI_gene_label "CEP128^ENSG00000100629.17"  ; ID "GALNT8--CEP128^ENST00000216517.10"  ; Parent "GALNT8--CEP128^CEP128^ENSG00000100629.17"  ; exon_id "ENSE00003508511.1"  ; exon_number 3 ; gene_id "GALNT8--CEP128^CEP128^ENSG00000100629.17"  ; gene_name CEP128 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171442.5"  ; havana_transcript "OTTHUMT00000413420.1"  ; hgnc_id "HGNC:20359"  ; level 2 ; orig_coord_info "chr14,80916401,80916547,-"  ; protein_id "ENSP00000216517.6"  ; tag basic appris_alternative_2 ; transcript_id "GALNT8--CEP128^ENST00000216517.10"  ; transcript_name "CEP128-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GALNT8--CEP128	HAVANA	gene	1001	13346	.	+	.	FI_gene_label "GALNT8^ENSG00000130035.9"  ; ID "GALNT8--CEP128^GALNT8^ENSG00000130035.9"  ; ccdsid "CCDS8533.1"  ; exon_id "ENSE00000893107.3"  ; exon_number 1 ; gene_id "GALNT8--CEP128^GALNT8^ENSG00000130035.9"  ; gene_name GALNT8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166188.6"  ; havana_transcript "OTTHUMT00000388277.3"  ; hgnc_id "HGNC:4130"  ; level 1 ; orig_coord_info "chr12,4720678,4720888,+"  ; protein_id "ENSP00000252318.2"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "GALNT8--CEP128^ENST00000252318.7"  ; transcript_name "GALNT8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GALNT8--CEP128	HAVANA	mRNA	1001	13346	.	+	.	FI_gene_label "GALNT8^ENSG00000130035.9"  ; ID "GALNT8--CEP128^ENST00000252318.7"  ; Parent "GALNT8--CEP128^GALNT8^ENSG00000130035.9"  ; ccdsid "CCDS8533.1"  ; exon_id "ENSE00000893107.3"  ; exon_number 1 ; gene_id "GALNT8--CEP128^GALNT8^ENSG00000130035.9"  ; gene_name GALNT8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166188.6"  ; havana_transcript "OTTHUMT00000388277.3"  ; hgnc_id "HGNC:4130"  ; level 1 ; orig_coord_info "chr12,4720678,4720888,+"  ; protein_id "ENSP00000252318.2"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "GALNT8--CEP128^ENST00000252318.7"  ; transcript_name "GALNT8-201"  ; transcript_support_level 1 ; 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: 
PEF1--COL16A1	HAVANA	gene	15750	23884	.	+	.	FI_gene_label "COL16A1^ENSG00000084636.18"  ; ID "PEF1--COL16A1^COL16A1^ENSG00000084636.18"  ; exon_id "ENSE00001634687.1"  ; exon_number 1 ; gene_id "PEF1--COL16A1^COL16A1^ENSG00000084636.18"  ; gene_name COL16A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003883.24"  ; havana_transcript "OTTHUMT00000091414.2"  ; hgnc_id "HGNC:2193"  ; level 2 ; orig_coord_info "chr1,31696963,31697010,-"  ; protein_id "ENSP00000362771.4"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "PEF1--COL16A1^ENST00000373667.4"  ; transcript_name "COL16A1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PEF1--COL16A1	HAVANA	mRNA	15750	23884	.	+	.	FI_gene_label "COL16A1^ENSG00000084636.18"  ; ID "PEF1--COL16A1^ENST00000373667.4"  ; Parent "PEF1--COL16A1^COL16A1^ENSG00000084636.18"  ; exon_id "ENSE00001634687.1"  ; exon_number 1 ; gene_id "PEF1--COL16A1^COL16A1^ENSG00000084636.18"  ; gene_name COL16A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003883.24"  ; havana_transcript "OTTHUMT00000091414.2"  ; hgnc_id "HGNC:2193"  ; level 2 ; orig_coord_info "chr1,31696963,31697010,-"  ; protein_id "ENSP00000362771.4"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "PEF1--COL16A1^ENST00000373667.4"  ; transcript_name "COL16A1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PEF1--COL16A1	HAVANA	gene	1021	7260	.	+	.	FI_gene_label "PEF1^ENSG00000162517.13"  ; ID "PEF1--COL16A1^PEF1^ENSG00000162517.13"  ; ccdsid "CCDS345.1"  ; exon_id "ENSE00001838580.2"  ; exon_number 1 ; gene_id "PEF1--COL16A1^PEF1^ENSG00000162517.13"  ; gene_name PEF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003877.3"  ; havana_transcript "OTTHUMT00000011046.2"  ; hgnc_id "HGNC:30009"  ; level 2 ; orig_coord_info "chr1,31644841,31644864,-"  ; protein_id "ENSP00000362807.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PEF1--COL16A1^ENST00000373703.5"  ; transcript_name "PEF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PEF1--COL16A1	HAVANA	mRNA	1021	7260	.	+	.	FI_gene_label "PEF1^ENSG00000162517.13"  ; ID "PEF1--COL16A1^ENST00000373703.5"  ; Parent "PEF1--COL16A1^PEF1^ENSG00000162517.13"  ; ccdsid "CCDS345.1"  ; exon_id "ENSE00001838580.2"  ; exon_number 1 ; gene_id "PEF1--COL16A1^PEF1^ENSG00000162517.13"  ; gene_name PEF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000003877.3"  ; havana_transcript "OTTHUMT00000011046.2"  ; hgnc_id "HGNC:30009"  ; level 2 ; orig_coord_info "chr1,31644841,31644864,-"  ; protein_id "ENSP00000362807.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PEF1--COL16A1^ENST00000373703.5"  ; transcript_name "PEF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PMS2P6--CCDC146	HAVANA	gene	9058	29425	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P6--CCDC146	HAVANA	mRNA	9058	29425	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P6--CCDC146^ENST00000285871.5"  ; Parent "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SRP54--TTC6	HAVANA	gene	2036	23297	.	+	.	FI_gene_label "SRP54^ENSG00000100883.13"  ; ID "SRP54--TTC6^SRP54^ENSG00000100883.13"  ; ccdsid "CCDS9652.1"  ; exon_id "ENSE00003906262.1"  ; exon_number 2 ; gene_id "SRP54--TTC6^SRP54^ENSG00000100883.13"  ; gene_name SRP54 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140214.6"  ; havana_transcript "OTTHUMT00000504331.2"  ; hgnc_id "HGNC:11301"  ; level 2 ; orig_coord_info "chr14,34996710,34996787,+"  ; protein_id "ENSP00000216774.6"  ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRP54--TTC6^ENST00000216774.11"  ; transcript_name "SRP54-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SRP54--TTC6	HAVANA	mRNA	2036	23297	.	+	.	FI_gene_label "SRP54^ENSG00000100883.13"  ; ID "SRP54--TTC6^ENST00000216774.11"  ; Parent "SRP54--TTC6^SRP54^ENSG00000100883.13"  ; ccdsid "CCDS9652.1"  ; exon_id "ENSE00003906262.1"  ; exon_number 2 ; gene_id "SRP54--TTC6^SRP54^ENSG00000100883.13"  ; gene_name SRP54 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140214.6"  ; havana_transcript "OTTHUMT00000504331.2"  ; hgnc_id "HGNC:11301"  ; level 2 ; orig_coord_info "chr14,34996710,34996787,+"  ; protein_id "ENSP00000216774.6"  ; tag RNA_Seq_supported_only basic MANE_Select appris_principal_1 CCDS ; transcript_id "SRP54--TTC6^ENST00000216774.11"  ; transcript_name "SRP54-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SRP54--TTC6	ENSEMBL	gene	51053	67040	.	+	.	FI_gene_label "TTC6^ENSG00000139865.16"  ; ID "SRP54--TTC6^TTC6^ENSG00000139865.16"  ; exon_id "ENSE00003549424.1"  ; exon_number 2 ; gene_id "SRP54--TTC6^TTC6^ENSG00000139865.16"  ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8"  ; hgnc_id "HGNC:19739"  ; level 3 ; orig_coord_info "chr14,37796310,37796370,+"  ; protein_id "ENSP00000267368.7"  ; tag basic ; transcript_id "SRP54--TTC6^ENST00000267368.11"  ; transcript_name "TTC6-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SRP54--TTC6	ENSEMBL	mRNA	51053	67040	.	+	.	FI_gene_label "TTC6^ENSG00000139865.16"  ; ID "SRP54--TTC6^ENST00000267368.11"  ; Parent "SRP54--TTC6^TTC6^ENSG00000139865.16"  ; exon_id "ENSE00003549424.1"  ; exon_number 2 ; gene_id "SRP54--TTC6^TTC6^ENSG00000139865.16"  ; gene_name TTC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157369.8"  ; hgnc_id "HGNC:19739"  ; level 3 ; orig_coord_info "chr14,37796310,37796370,+"  ; protein_id "ENSP00000267368.7"  ; tag basic ; transcript_id "SRP54--TTC6^ENST00000267368.11"  ; transcript_name "TTC6-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; 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: 
WIPF2--NRXN3	HAVANA	gene	47142	69852	.	+	.	FI_gene_label "NRXN3^ENSG00000021645.20"  ; ID "WIPF2--NRXN3^NRXN3^ENSG00000021645.20"  ; ccdsid "CCDS9871.1"  ; exon_id "ENSE00002455959.1"  ; exon_number 1 ; gene_id "WIPF2--NRXN3^NRXN3^ENSG00000021645.20"  ; gene_name NRXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171502.7"  ; havana_transcript "OTTHUMT00000413791.2"  ; hgnc_id "HGNC:8010"  ; level 2 ; orig_coord_info "chr14,79280292,79280538,+"  ; protein_id "ENSP00000281127.7"  ; tag basic CCDS ; transcript_id "WIPF2--NRXN3^ENST00000281127.11"  ; transcript_name "NRXN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
WIPF2--NRXN3	HAVANA	mRNA	47142	69852	.	+	.	FI_gene_label "NRXN3^ENSG00000021645.20"  ; ID "WIPF2--NRXN3^ENST00000281127.11"  ; Parent "WIPF2--NRXN3^NRXN3^ENSG00000021645.20"  ; ccdsid "CCDS9871.1"  ; exon_id "ENSE00002455959.1"  ; exon_number 1 ; gene_id "WIPF2--NRXN3^NRXN3^ENSG00000021645.20"  ; gene_name NRXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171502.7"  ; havana_transcript "OTTHUMT00000413791.2"  ; hgnc_id "HGNC:8010"  ; level 2 ; orig_coord_info "chr14,79280292,79280538,+"  ; protein_id "ENSP00000281127.7"  ; tag basic CCDS ; transcript_id "WIPF2--NRXN3^ENST00000281127.11"  ; transcript_name "NRXN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
WIPF2--NRXN3	HAVANA	gene	1001	16889	.	+	.	FI_gene_label "WIPF2^ENSG00000171475.14"  ; ID "WIPF2--NRXN3^WIPF2^ENSG00000171475.14"  ; ccdsid "CCDS11364.1"  ; exon_id "ENSE00003596032.1"  ; exon_number 2 ; gene_id "WIPF2--NRXN3^WIPF2^ENSG00000171475.14"  ; gene_name WIPF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133331.4"  ; havana_transcript "OTTHUMT00000257157.2"  ; hgnc_id "HGNC:30923"  ; level 2 ; orig_coord_info "chr17,40256460,40256522,+"  ; protein_id "ENSP00000320924.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WIPF2--NRXN3^ENST00000323571.9"  ; transcript_name "WIPF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
WIPF2--NRXN3	HAVANA	mRNA	1001	16889	.	+	.	FI_gene_label "WIPF2^ENSG00000171475.14"  ; ID "WIPF2--NRXN3^ENST00000323571.9"  ; Parent "WIPF2--NRXN3^WIPF2^ENSG00000171475.14"  ; ccdsid "CCDS11364.1"  ; exon_id "ENSE00003596032.1"  ; exon_number 2 ; gene_id "WIPF2--NRXN3^WIPF2^ENSG00000171475.14"  ; gene_name WIPF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133331.4"  ; havana_transcript "OTTHUMT00000257157.2"  ; hgnc_id "HGNC:30923"  ; level 2 ; orig_coord_info "chr17,40256460,40256522,+"  ; protein_id "ENSP00000320924.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WIPF2--NRXN3^ENST00000323571.9"  ; transcript_name "WIPF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZCCHC14--LSM1	ENSEMBL	gene	2171	19711	.	+	.	FI_gene_label "ZCCHC14^ENSG00000140948.13"  ; ID "ZCCHC14--LSM1^ZCCHC14^ENSG00000140948.13"  ; ccdsid "CCDS10961.1"  ; exon_id "ENSE00001826524.2"  ; exon_number 1 ; gene_id "ZCCHC14--LSM1^ZCCHC14^ENSG00000140948.13"  ; gene_name ZCCHC14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137655.4"  ; hgnc_id "HGNC:24134"  ; level 3 ; orig_coord_info "chr16,87491669,87491827,-"  ; protein_id "ENSP00000268616.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "ZCCHC14--LSM1^ENST00000268616.9"  ; transcript_name "ZCCHC14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZCCHC14--LSM1	ENSEMBL	mRNA	2171	19711	.	+	.	FI_gene_label "ZCCHC14^ENSG00000140948.13"  ; ID "ZCCHC14--LSM1^ENST00000268616.9"  ; Parent "ZCCHC14--LSM1^ZCCHC14^ENSG00000140948.13"  ; ccdsid "CCDS10961.1"  ; exon_id "ENSE00001826524.2"  ; exon_number 1 ; gene_id "ZCCHC14--LSM1^ZCCHC14^ENSG00000140948.13"  ; gene_name ZCCHC14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137655.4"  ; hgnc_id "HGNC:24134"  ; level 3 ; orig_coord_info "chr16,87491669,87491827,-"  ; protein_id "ENSP00000268616.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "ZCCHC14--LSM1^ENST00000268616.9"  ; transcript_name "ZCCHC14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZCCHC14--LSM1	HAVANA	gene	22949	28335	.	+	.	FI_gene_label "LSM1^ENSG00000175324.10"  ; ID "ZCCHC14--LSM1^LSM1^ENSG00000175324.10"  ; ccdsid "CCDS6103.1"  ; exon_id "ENSE00002099181.2"  ; exon_number 1 ; gene_id "ZCCHC14--LSM1^LSM1^ENSG00000175324.10"  ; gene_name LSM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164051.2"  ; havana_transcript "OTTHUMT00000376965.2"  ; hgnc_id "HGNC:20472"  ; level 2 ; orig_coord_info "chr8,38176275,38176320,-"  ; protein_id "ENSP00000310596.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZCCHC14--LSM1^ENST00000311351.9"  ; transcript_name "LSM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZCCHC14--LSM1	HAVANA	mRNA	22949	28335	.	+	.	FI_gene_label "LSM1^ENSG00000175324.10"  ; ID "ZCCHC14--LSM1^ENST00000311351.9"  ; Parent "ZCCHC14--LSM1^LSM1^ENSG00000175324.10"  ; ccdsid "CCDS6103.1"  ; exon_id "ENSE00002099181.2"  ; exon_number 1 ; gene_id "ZCCHC14--LSM1^LSM1^ENSG00000175324.10"  ; gene_name LSM1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164051.2"  ; havana_transcript "OTTHUMT00000376965.2"  ; hgnc_id "HGNC:20472"  ; level 2 ; orig_coord_info "chr8,38176275,38176320,-"  ; protein_id "ENSP00000310596.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZCCHC14--LSM1^ENST00000311351.9"  ; transcript_name "LSM1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC009396.1--NAA30	HAVANA	gene	1001	3079	.	+	.	FI_gene_label "AC009396.1^ENSG00000258478.1"  ; ID "AC009396.1--NAA30^AC009396.1^ENSG00000258478.1"  ; exon_id "ENSE00002484191.1"  ; exon_number 1 ; gene_id "AC009396.1--NAA30^AC009396.1^ENSG00000258478.1"  ; gene_name "AC009396.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000171515.1"  ; havana_transcript "OTTHUMT00000413835.1"  ; level 2 ; orig_coord_info "chr14,78753724,78753878,-"  ; tag basic ; transcript_id "AC009396.1--NAA30^ENST00000553628.1"  ; transcript_name "AC009396.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
AC009396.1--NAA30	HAVANA	RNA	1001	3079	.	+	.	FI_gene_label "AC009396.1^ENSG00000258478.1"  ; ID "AC009396.1--NAA30^ENST00000553628.1"  ; Parent "AC009396.1--NAA30^AC009396.1^ENSG00000258478.1"  ; exon_id "ENSE00002484191.1"  ; exon_number 1 ; gene_id "AC009396.1--NAA30^AC009396.1^ENSG00000258478.1"  ; gene_name "AC009396.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000171515.1"  ; havana_transcript "OTTHUMT00000413835.1"  ; level 2 ; orig_coord_info "chr14,78753724,78753878,-"  ; tag basic ; transcript_id "AC009396.1--NAA30^ENST00000553628.1"  ; transcript_name "AC009396.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
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: 
BAG4--AC084024.4	HAVANA	gene	12260	15561	.	+	.	FI_gene_label "AC084024.4^ENSG00000285632.1"  ; ID "BAG4--AC084024.4^AC084024.4^ENSG00000285632.1"  ; exon_id "ENSE00003833787.1"  ; exon_number 1 ; gene_id "BAG4--AC084024.4^AC084024.4^ENSG00000285632.1"  ; gene_name "AC084024.4"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000193104.1"  ; havana_transcript "OTTHUMT00000500148.1"  ; level 2 ; orig_coord_info "chr8,38231661,38231695,-"  ; tag basic ; transcript_id "BAG4--AC084024.4^ENST00000648284.1"  ; transcript_name "AC084024.4-201"  ; transcript_type lncRNA
BAG4--AC084024.4	HAVANA	RNA	12260	15561	.	+	.	FI_gene_label "AC084024.4^ENSG00000285632.1"  ; ID "BAG4--AC084024.4^ENST00000648284.1"  ; Parent "BAG4--AC084024.4^AC084024.4^ENSG00000285632.1"  ; exon_id "ENSE00003833787.1"  ; exon_number 1 ; gene_id "BAG4--AC084024.4^AC084024.4^ENSG00000285632.1"  ; gene_name "AC084024.4"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000193104.1"  ; havana_transcript "OTTHUMT00000500148.1"  ; level 2 ; orig_coord_info "chr8,38231661,38231695,-"  ; tag basic ; transcript_id "BAG4--AC084024.4^ENST00000648284.1"  ; transcript_name "AC084024.4-201"  ; transcript_type lncRNA
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B	HAVANA	RNA	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^ENST00000462729.2"  ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created: 
PMS2P6--CCDC146	HAVANA	gene	1001	5876	.	+	.	FI_gene_label "PMS2P6^ENSG00000174384.9"  ; ID "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; exon_id "ENSE00002441642.1"  ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2"  ; havana_transcript "OTTHUMT00000347345.2"  ; hgnc_id "HGNC:33514"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,73093657,73093796,+"  ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5"  ; transcript_name "PMS2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
PMS2P6--CCDC146	HAVANA	RNA	1001	5876	.	+	.	FI_gene_label "PMS2P6^ENSG00000174384.9"  ; ID "PMS2P6--CCDC146^ENST00000333674.5"  ; Parent "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; exon_id "ENSE00002441642.1"  ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2"  ; havana_transcript "OTTHUMT00000347345.2"  ; hgnc_id "HGNC:33514"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,73093657,73093796,+"  ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5"  ; transcript_name "PMS2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
211 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 ------------------------------
381 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 22 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