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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/b682ccadbf844b961aa4dc1813606f/.command.log
Size: 44.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_bUW-T1-TRNA-1_B23WHTKLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/b682ccadbf844b961aa4dc1813606f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/b3b0bda5c86f4db19c4feacf537fa2/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/b682ccadbf844b961aa4dc1813606f/.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: 3526
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3526
=> 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:3526
  => 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: 
AGAP1--SH3BP4	HAVANA	gene	1001	37685	.	+	.	FI_gene_label "AGAP1^ENSG00000157985.19"  ; ID "AGAP1--SH3BP4^AGAP1^ENSG00000157985.19"  ; ccdsid "CCDS33408.1"  ; exon_id "ENSE00003848629.1"  ; exon_number 1 ; gene_id "AGAP1--SH3BP4^AGAP1^ENSG00000157985.19"  ; gene_name AGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133293.7"  ; havana_transcript "OTTHUMT00000257076.3"  ; hgnc_id "HGNC:16922"  ; level 2 ; orig_coord_info "chr2,235494687,235494849,+"  ; protein_id "ENSP00000307634.7"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "AGAP1--SH3BP4^ENST00000304032.13"  ; transcript_name "AGAP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AGAP1--SH3BP4	HAVANA	mRNA	1001	37685	.	+	.	FI_gene_label "AGAP1^ENSG00000157985.19"  ; ID "AGAP1--SH3BP4^ENST00000304032.13"  ; Parent "AGAP1--SH3BP4^AGAP1^ENSG00000157985.19"  ; ccdsid "CCDS33408.1"  ; exon_id "ENSE00003848629.1"  ; exon_number 1 ; gene_id "AGAP1--SH3BP4^AGAP1^ENSG00000157985.19"  ; gene_name AGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133293.7"  ; havana_transcript "OTTHUMT00000257076.3"  ; hgnc_id "HGNC:16922"  ; level 2 ; orig_coord_info "chr2,235494687,235494849,+"  ; protein_id "ENSP00000307634.7"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "AGAP1--SH3BP4^ENST00000304032.13"  ; transcript_name "AGAP1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
AGAP1--SH3BP4	HAVANA	gene	42885	58440	.	+	.	FI_gene_label "SH3BP4^ENSG00000130147.16"  ; ID "AGAP1--SH3BP4^SH3BP4^ENSG00000130147.16"  ; ccdsid "CCDS2513.1"  ; exon_id "ENSE00001589692.1"  ; exon_number 3 ; gene_id "AGAP1--SH3BP4^SH3BP4^ENSG00000130147.16"  ; gene_name SH3BP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133292.5"  ; havana_transcript "OTTHUMT00000329764.1"  ; hgnc_id "HGNC:10826"  ; level 2 ; orig_coord_info "chr2,235035003,235035120,+"  ; protein_id "ENSP00000340237.4"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "AGAP1--SH3BP4^ENST00000344528.8"  ; transcript_name "SH3BP4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AGAP1--SH3BP4	HAVANA	mRNA	42885	58440	.	+	.	FI_gene_label "SH3BP4^ENSG00000130147.16"  ; ID "AGAP1--SH3BP4^ENST00000344528.8"  ; Parent "AGAP1--SH3BP4^SH3BP4^ENSG00000130147.16"  ; ccdsid "CCDS2513.1"  ; exon_id "ENSE00001589692.1"  ; exon_number 3 ; gene_id "AGAP1--SH3BP4^SH3BP4^ENSG00000130147.16"  ; gene_name SH3BP4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133292.5"  ; havana_transcript "OTTHUMT00000329764.1"  ; hgnc_id "HGNC:10826"  ; level 2 ; orig_coord_info "chr2,235035003,235035120,+"  ; protein_id "ENSP00000340237.4"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "AGAP1--SH3BP4^ENST00000344528.8"  ; transcript_name "SH3BP4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AL669831.4--SEPTIN14	HAVANA	gene	8876	22423	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
AL669831.4--SEPTIN14	HAVANA	mRNA	8876	22423	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.4--SEPTIN14^ENST00000388975.4"  ; Parent "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ARMCX2--BTK	HAVANA	gene	9923	27240	.	+	.	FI_gene_label "BTK^ENSG00000010671.16"  ; ID "ARMCX2--BTK^BTK^ENSG00000010671.16"  ; ccdsid "CCDS14482.1"  ; exon_id "ENSE00003687319.1"  ; exon_number 2 ; gene_id "ARMCX2--BTK^BTK^ENSG00000010671.16"  ; gene_name BTK ; gene_type protein_coding ; havana_gene "OTTHUMG00000022022.2"  ; havana_transcript "OTTHUMT00000057532.2"  ; hgnc_id "HGNC:1133"  ; level 2 ; orig_coord_info "chrX,101375144,101375284,-"  ; protein_id "ENSP00000308176.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARMCX2--BTK^ENST00000308731.8"  ; transcript_name "BTK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARMCX2--BTK	HAVANA	mRNA	9923	27240	.	+	.	FI_gene_label "BTK^ENSG00000010671.16"  ; ID "ARMCX2--BTK^ENST00000308731.8"  ; Parent "ARMCX2--BTK^BTK^ENSG00000010671.16"  ; ccdsid "CCDS14482.1"  ; exon_id "ENSE00003687319.1"  ; exon_number 2 ; gene_id "ARMCX2--BTK^BTK^ENSG00000010671.16"  ; gene_name BTK ; gene_type protein_coding ; havana_gene "OTTHUMG00000022022.2"  ; havana_transcript "OTTHUMT00000057532.2"  ; hgnc_id "HGNC:1133"  ; level 2 ; orig_coord_info "chrX,101375144,101375284,-"  ; protein_id "ENSP00000308176.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARMCX2--BTK^ENST00000308731.8"  ; transcript_name "BTK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARMCX2--BTK	HAVANA	gene	1007	5570	.	+	.	FI_gene_label "ARMCX2^ENSG00000184867.14"  ; ID "ARMCX2--BTK^ARMCX2^ENSG00000184867.14"  ; ccdsid "CCDS14490.1"  ; exon_id "ENSE00001347589.3"  ; exon_number 5 ; gene_id "ARMCX2--BTK^ARMCX2^ENSG00000184867.14"  ; gene_name ARMCX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022038.4"  ; havana_transcript "OTTHUMT00000057586.1"  ; hgnc_id "HGNC:16869"  ; level 2 ; orig_coord_info "chrX,101655693,101657588,-"  ; protein_id "ENSP00000331662.5"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ARMCX2--BTK^ENST00000328766.9"  ; transcript_name "ARMCX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARMCX2--BTK	HAVANA	mRNA	1007	5570	.	+	.	FI_gene_label "ARMCX2^ENSG00000184867.14"  ; ID "ARMCX2--BTK^ENST00000328766.9"  ; Parent "ARMCX2--BTK^ARMCX2^ENSG00000184867.14"  ; ccdsid "CCDS14490.1"  ; exon_id "ENSE00001347589.3"  ; exon_number 5 ; gene_id "ARMCX2--BTK^ARMCX2^ENSG00000184867.14"  ; gene_name ARMCX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022038.4"  ; havana_transcript "OTTHUMT00000057586.1"  ; hgnc_id "HGNC:16869"  ; level 2 ; orig_coord_info "chrX,101655693,101657588,-"  ; protein_id "ENSP00000331662.5"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "ARMCX2--BTK^ENST00000328766.9"  ; transcript_name "ARMCX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCDC6--RET	HAVANA	gene	1001	16128	.	+	.	FI_gene_label "CCDC6^ENSG00000108091.11"  ; ID "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; ccdsid "CCDS7257.1"  ; exon_id "ENSE00001950758.3"  ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3"  ; havana_transcript "OTTHUMT00000048176.3"  ; hgnc_id "HGNC:18782"  ; level 2 ; orig_coord_info "chr10,59906122,59906424,-"  ; protein_id "ENSP00000263102.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7"  ; transcript_name "CCDC6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET	HAVANA	mRNA	1001	16128	.	+	.	FI_gene_label "CCDC6^ENSG00000108091.11"  ; ID "CCDC6--RET^ENST00000263102.7"  ; Parent "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; ccdsid "CCDS7257.1"  ; exon_id "ENSE00001950758.3"  ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3"  ; havana_transcript "OTTHUMT00000048176.3"  ; hgnc_id "HGNC:18782"  ; level 2 ; orig_coord_info "chr10,59906122,59906424,-"  ; protein_id "ENSP00000263102.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7"  ; transcript_name "CCDC6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCDC6--RET	HAVANA	gene	19134	39754	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "CCDC6--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET	HAVANA	mRNA	19134	39754	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "CCDC6--RET^ENST00000340058.6"  ; Parent "CCDC6--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6"  ; transcript_name "RET-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: 
CYB5R3--NDUFA6	HAVANA	gene	1001	14475	.	+	.	FI_gene_label "CYB5R3^ENSG00000100243.21"  ; ID "CYB5R3--NDUFA6^CYB5R3^ENSG00000100243.21"  ; ccdsid "CCDS33658.1"  ; exon_id "ENSE00001892790.2"  ; exon_number 1 ; gene_id "CYB5R3--NDUFA6^CYB5R3^ENSG00000100243.21"  ; gene_name CYB5R3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150745.7"  ; havana_transcript "OTTHUMT00000320439.2"  ; hgnc_id "HGNC:2873"  ; level 2 ; orig_coord_info "chr22,42649295,42649315,-"  ; protein_id "ENSP00000338461.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CYB5R3--NDUFA6^ENST00000352397.10"  ; transcript_name "CYB5R3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CYB5R3--NDUFA6	HAVANA	mRNA	1001	14475	.	+	.	FI_gene_label "CYB5R3^ENSG00000100243.21"  ; ID "CYB5R3--NDUFA6^ENST00000352397.10"  ; Parent "CYB5R3--NDUFA6^CYB5R3^ENSG00000100243.21"  ; ccdsid "CCDS33658.1"  ; exon_id "ENSE00001892790.2"  ; exon_number 1 ; gene_id "CYB5R3--NDUFA6^CYB5R3^ENSG00000100243.21"  ; gene_name CYB5R3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150745.7"  ; havana_transcript "OTTHUMT00000320439.2"  ; hgnc_id "HGNC:2873"  ; level 2 ; orig_coord_info "chr22,42649295,42649315,-"  ; protein_id "ENSP00000338461.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CYB5R3--NDUFA6^ENST00000352397.10"  ; transcript_name "CYB5R3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CYB5R3--NDUFA6	HAVANA	gene	18755	19974	.	+	.	FI_gene_label "NDUFA6^ENSG00000184983.11"  ; ID "CYB5R3--NDUFA6^NDUFA6^ENSG00000184983.11"  ; exon_id "ENSE00001919192.1"  ; exon_number 1 ; gene_id "CYB5R3--NDUFA6^NDUFA6^ENSG00000184983.11"  ; gene_name NDUFA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151287.6"  ; havana_transcript "OTTHUMT00000322090.2"  ; hgnc_id "HGNC:7690"  ; level 2 ; orig_coord_info "chr22,42087060,42087143,-"  ; protein_id "ENSP00000473478.1"  ; tag RP_supported_TIS basic ; transcript_id "CYB5R3--NDUFA6^ENST00000470753.1"  ; transcript_name "NDUFA6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
CYB5R3--NDUFA6	HAVANA	mRNA	18755	19974	.	+	.	FI_gene_label "NDUFA6^ENSG00000184983.11"  ; ID "CYB5R3--NDUFA6^ENST00000470753.1"  ; Parent "CYB5R3--NDUFA6^NDUFA6^ENSG00000184983.11"  ; exon_id "ENSE00001919192.1"  ; exon_number 1 ; gene_id "CYB5R3--NDUFA6^NDUFA6^ENSG00000184983.11"  ; gene_name NDUFA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151287.6"  ; havana_transcript "OTTHUMT00000322090.2"  ; hgnc_id "HGNC:7690"  ; level 2 ; orig_coord_info "chr22,42087060,42087143,-"  ; protein_id "ENSP00000473478.1"  ; tag RP_supported_TIS basic ; transcript_id "CYB5R3--NDUFA6^ENST00000470753.1"  ; transcript_name "NDUFA6-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
EIF3E--RSPO2	HAVANA	gene	23210	53212	.	+	.	FI_gene_label "EIF3E^ENSG00000104408.11"  ; ID "EIF3E--RSPO2^EIF3E^ENSG00000104408.11"  ; ccdsid "CCDS6308.1"  ; exon_id "ENSE00003671921.1"  ; exon_number 1 ; gene_id "EIF3E--RSPO2^EIF3E^ENSG00000104408.11"  ; gene_name EIF3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000164858.7"  ; havana_transcript "OTTHUMT00000380612.3"  ; hgnc_id "HGNC:3277"  ; level 2 ; orig_coord_info "chr8,108248613,108248702,-"  ; protein_id "ENSP00000220849.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF3E--RSPO2^ENST00000220849.10"  ; transcript_name "EIF3E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EIF3E--RSPO2	HAVANA	mRNA	23210	53212	.	+	.	FI_gene_label "EIF3E^ENSG00000104408.11"  ; ID "EIF3E--RSPO2^ENST00000220849.10"  ; Parent "EIF3E--RSPO2^EIF3E^ENSG00000104408.11"  ; ccdsid "CCDS6308.1"  ; exon_id "ENSE00003671921.1"  ; exon_number 1 ; gene_id "EIF3E--RSPO2^EIF3E^ENSG00000104408.11"  ; gene_name EIF3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000164858.7"  ; havana_transcript "OTTHUMT00000380612.3"  ; hgnc_id "HGNC:3277"  ; level 2 ; orig_coord_info "chr8,108248613,108248702,-"  ; protein_id "ENSP00000220849.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF3E--RSPO2^ENST00000220849.10"  ; transcript_name "EIF3E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EIF3E--RSPO2	HAVANA	gene	61623	73686	.	+	.	FI_gene_label "RSPO2^ENSG00000147655.12"  ; ID "EIF3E--RSPO2^RSPO2^ENSG00000147655.12"  ; ccdsid "CCDS6307.1"  ; exon_id "ENSE00001378581.2"  ; exon_number 2 ; gene_id "EIF3E--RSPO2^RSPO2^ENSG00000147655.12"  ; gene_name RSPO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164893.4"  ; havana_transcript "OTTHUMT00000380830.2"  ; hgnc_id "HGNC:28583"  ; level 2 ; orig_coord_info "chr8,108082545,108082638,-"  ; protein_id "ENSP00000276659.5"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF3E--RSPO2^ENST00000276659.10"  ; transcript_name "RSPO2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EIF3E--RSPO2	HAVANA	mRNA	61623	73686	.	+	.	FI_gene_label "RSPO2^ENSG00000147655.12"  ; ID "EIF3E--RSPO2^ENST00000276659.10"  ; Parent "EIF3E--RSPO2^RSPO2^ENSG00000147655.12"  ; ccdsid "CCDS6307.1"  ; exon_id "ENSE00001378581.2"  ; exon_number 2 ; gene_id "EIF3E--RSPO2^RSPO2^ENSG00000147655.12"  ; gene_name RSPO2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164893.4"  ; havana_transcript "OTTHUMT00000380830.2"  ; hgnc_id "HGNC:28583"  ; level 2 ; orig_coord_info "chr8,108082545,108082638,-"  ; protein_id "ENSP00000276659.5"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF3E--RSPO2^ENST00000276659.10"  ; transcript_name "RSPO2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MANBA--AC098487.1	HAVANA	gene	1062	34457	.	+	.	FI_gene_label "MANBA^ENSG00000109323.11"  ; ID "MANBA--AC098487.1^MANBA^ENSG00000109323.11"  ; exon_id "ENSE00002066732.1"  ; exon_number 1 ; gene_id "MANBA--AC098487.1^MANBA^ENSG00000109323.11"  ; gene_name MANBA ; gene_type protein_coding ; havana_gene "OTTHUMG00000131123.14"  ; havana_transcript "OTTHUMT00000363561.1"  ; hgnc_id "HGNC:6831"  ; level 2 ; orig_coord_info "chr4,102760718,102760894,-"  ; protein_id "ENSP00000427322.1"  ; tag basic ; transcript_id "MANBA--AC098487.1^ENST00000505239.1"  ; transcript_name "MANBA-201"  ; transcript_support_level 2 ; transcript_type protein_coding
MANBA--AC098487.1	HAVANA	mRNA	1062	34457	.	+	.	FI_gene_label "MANBA^ENSG00000109323.11"  ; ID "MANBA--AC098487.1^ENST00000505239.1"  ; Parent "MANBA--AC098487.1^MANBA^ENSG00000109323.11"  ; exon_id "ENSE00002066732.1"  ; exon_number 1 ; gene_id "MANBA--AC098487.1^MANBA^ENSG00000109323.11"  ; gene_name MANBA ; gene_type protein_coding ; havana_gene "OTTHUMG00000131123.14"  ; havana_transcript "OTTHUMT00000363561.1"  ; hgnc_id "HGNC:6831"  ; level 2 ; orig_coord_info "chr4,102760718,102760894,-"  ; protein_id "ENSP00000427322.1"  ; tag basic ; transcript_id "MANBA--AC098487.1^ENST00000505239.1"  ; transcript_name "MANBA-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
SLCO1B3--SLCO1B7	ENSEMBL	gene	3179	19485	.	+	.	FI_gene_label "SLCO1B3^ENSG00000111700.13"  ; ID "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; ccdsid "CCDS8684.1"  ; exon_id "ENSE00003727652.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5"  ; hgnc_id "HGNC:10961"  ; level 3 ; orig_coord_info "chr12,20815739,20815822,+"  ; protein_id "ENSP00000261196.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; transcript_name "SLCO1B3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLCO1B3--SLCO1B7	ENSEMBL	mRNA	3179	19485	.	+	.	FI_gene_label "SLCO1B3^ENSG00000111700.13"  ; ID "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; Parent "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; ccdsid "CCDS8684.1"  ; exon_id "ENSE00003727652.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B3^ENSG00000111700.13"  ; gene_name SLCO1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169011.5"  ; hgnc_id "HGNC:10961"  ; level 3 ; orig_coord_info "chr12,20815739,20815822,+"  ; protein_id "ENSP00000261196.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "SLCO1B3--SLCO1B7^ENST00000261196.6"  ; transcript_name "SLCO1B3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^ENST00000326270.13"  ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^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: 
TXNRD2--GNB1L	HAVANA	gene	29384	41811	.	+	.	FI_gene_label "GNB1L^ENSG00000185838.14"  ; ID "TXNRD2--GNB1L^GNB1L^ENSG00000185838.14"  ; ccdsid "CCDS13768.1"  ; exon_id "ENSE00001297632.2"  ; exon_number 3 ; gene_id "TXNRD2--GNB1L^GNB1L^ENSG00000185838.14"  ; gene_name GNB1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000150279.4"  ; havana_transcript "OTTHUMT00000075202.2"  ; hgnc_id "HGNC:4397"  ; level 2 ; orig_coord_info "chr22,19821228,19821355,-"  ; protein_id "ENSP00000331313.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNRD2--GNB1L^ENST00000329517.11"  ; transcript_name "GNB1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TXNRD2--GNB1L	HAVANA	mRNA	29384	41811	.	+	.	FI_gene_label "GNB1L^ENSG00000185838.14"  ; ID "TXNRD2--GNB1L^ENST00000329517.11"  ; Parent "TXNRD2--GNB1L^GNB1L^ENSG00000185838.14"  ; ccdsid "CCDS13768.1"  ; exon_id "ENSE00001297632.2"  ; exon_number 3 ; gene_id "TXNRD2--GNB1L^GNB1L^ENSG00000185838.14"  ; gene_name GNB1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000150279.4"  ; havana_transcript "OTTHUMT00000075202.2"  ; hgnc_id "HGNC:4397"  ; level 2 ; orig_coord_info "chr22,19821228,19821355,-"  ; protein_id "ENSP00000331313.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TXNRD2--GNB1L^ENST00000329517.11"  ; transcript_name "GNB1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TXNRD2--GNB1L	HAVANA	gene	1017	16347	.	+	.	FI_gene_label "TXNRD2^ENSG00000184470.21"  ; ID "TXNRD2--GNB1L^TXNRD2^ENSG00000184470.21"  ; ccdsid "CCDS63402.1"  ; exon_id "ENSE00001543323.2"  ; exon_number 1 ; gene_id "TXNRD2--GNB1L^TXNRD2^ENSG00000184470.21"  ; gene_name TXNRD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149975.8"  ; havana_transcript "OTTHUMT00000488472.1"  ; hgnc_id "HGNC:18155"  ; level 2 ; orig_coord_info "chr22,19941701,19941803,-"  ; protein_id "ENSP00000334451.9"  ; tag basic CCDS ; transcript_id "TXNRD2--GNB1L^ENST00000334363.14"  ; transcript_name "TXNRD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TXNRD2--GNB1L	HAVANA	mRNA	1017	16347	.	+	.	FI_gene_label "TXNRD2^ENSG00000184470.21"  ; ID "TXNRD2--GNB1L^ENST00000334363.14"  ; Parent "TXNRD2--GNB1L^TXNRD2^ENSG00000184470.21"  ; ccdsid "CCDS63402.1"  ; exon_id "ENSE00001543323.2"  ; exon_number 1 ; gene_id "TXNRD2--GNB1L^TXNRD2^ENSG00000184470.21"  ; gene_name TXNRD2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149975.8"  ; havana_transcript "OTTHUMT00000488472.1"  ; hgnc_id "HGNC:18155"  ; level 2 ; orig_coord_info "chr22,19941701,19941803,-"  ; protein_id "ENSP00000334451.9"  ; tag basic CCDS ; transcript_id "TXNRD2--GNB1L^ENST00000334363.14"  ; transcript_name "TXNRD2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
UPF1--AC011447.3	HAVANA	gene	1001	23784	.	+	.	FI_gene_label "UPF1^ENSG00000005007.13"  ; ID "UPF1--AC011447.3^UPF1^ENSG00000005007.13"  ; ccdsid "CCDS12386.1"  ; exon_id "ENSE00001123172.8"  ; exon_number 1 ; gene_id "UPF1--AC011447.3^UPF1^ENSG00000005007.13"  ; gene_name UPF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183025.2"  ; havana_transcript "OTTHUMT00000464683.1"  ; hgnc_id "HGNC:9962"  ; level 2 ; orig_coord_info "chr19,18832210,18832440,+"  ; protein_id "ENSP00000262803.5"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "UPF1--AC011447.3^ENST00000262803.10"  ; transcript_name "UPF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
UPF1--AC011447.3	HAVANA	mRNA	1001	23784	.	+	.	FI_gene_label "UPF1^ENSG00000005007.13"  ; ID "UPF1--AC011447.3^ENST00000262803.10"  ; Parent "UPF1--AC011447.3^UPF1^ENSG00000005007.13"  ; ccdsid "CCDS12386.1"  ; exon_id "ENSE00001123172.8"  ; exon_number 1 ; gene_id "UPF1--AC011447.3^UPF1^ENSG00000005007.13"  ; gene_name UPF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183025.2"  ; havana_transcript "OTTHUMT00000464683.1"  ; hgnc_id "HGNC:9962"  ; level 2 ; orig_coord_info "chr19,18832210,18832440,+"  ; protein_id "ENSP00000262803.5"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "UPF1--AC011447.3^ENST00000262803.10"  ; transcript_name "UPF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AL669831.4--SEPTIN14	HAVANA	gene	1001	5872	.	+	.	FI_gene_label "AL669831.4^ENSG00000230092.7"  ; ID "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; exon_id "ENSE00001746491.1"  ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; gene_name "AL669831.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3"  ; havana_transcript "OTTHUMT00000448550.2"  ; level 2 ; orig_coord_info "chr1,817373,817712,-"  ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4"  ; transcript_name "AL669831.4-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
AL669831.4--SEPTIN14	HAVANA	RNA	1001	5872	.	+	.	FI_gene_label "AL669831.4^ENSG00000230092.7"  ; ID "AL669831.4--SEPTIN14^ENST00000447500.4"  ; Parent "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; exon_id "ENSE00001746491.1"  ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; gene_name "AL669831.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3"  ; havana_transcript "OTTHUMT00000448550.2"  ; level 2 ; orig_coord_info "chr1,817373,817712,-"  ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4"  ; transcript_name "AL669831.4-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
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: 
MANBA--AC098487.1	HAVANA	gene	39797	42842	.	+	.	FI_gene_label "AC098487.1^ENSG00000248161.5"  ; ID "MANBA--AC098487.1^AC098487.1^ENSG00000248161.5"  ; exon_id "ENSE00002028515.1"  ; exon_number 1 ; gene_id "MANBA--AC098487.1^AC098487.1^ENSG00000248161.5"  ; gene_name "AC098487.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000131122.10"  ; havana_transcript "OTTHUMT00000363754.1"  ; level 2 ; orig_coord_info "chr4,102431062,102431249,-"  ; tag dotter_confirmed ; transcript_id "MANBA--AC098487.1^ENST00000502883.5"  ; transcript_name "AC098487.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
MANBA--AC098487.1	HAVANA	RNA	39797	42842	.	+	.	FI_gene_label "AC098487.1^ENSG00000248161.5"  ; ID "MANBA--AC098487.1^ENST00000502883.5"  ; Parent "MANBA--AC098487.1^AC098487.1^ENSG00000248161.5"  ; exon_id "ENSE00002028515.1"  ; exon_number 1 ; gene_id "MANBA--AC098487.1^AC098487.1^ENSG00000248161.5"  ; gene_name "AC098487.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000131122.10"  ; havana_transcript "OTTHUMT00000363754.1"  ; level 2 ; orig_coord_info "chr4,102431062,102431249,-"  ; tag dotter_confirmed ; transcript_id "MANBA--AC098487.1^ENST00000502883.5"  ; transcript_name "AC098487.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
SLCO1B3--SLCO1B7	HAVANA	gene	34392	35949	.	+	.	FI_gene_label "SLCO1B7^ENSG00000205754.12"  ; ID "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; exon_id "ENSE00002290527.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3"  ; havana_transcript "OTTHUMT00000402068.1"  ; hgnc_id "HGNC:32934"  ; level 2 ; orig_coord_info "chr12,21067351,21067383,+"  ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; transcript_name "SLCO1B7-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
SLCO1B3--SLCO1B7	HAVANA	RNA	34392	35949	.	+	.	FI_gene_label "SLCO1B7^ENSG00000205754.12"  ; ID "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; Parent "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; exon_id "ENSE00002290527.1"  ; exon_number 1 ; gene_id "SLCO1B3--SLCO1B7^SLCO1B7^ENSG00000205754.12"  ; gene_name SLCO1B7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000169045.3"  ; havana_transcript "OTTHUMT00000402068.1"  ; hgnc_id "HGNC:32934"  ; level 2 ; orig_coord_info "chr12,21067351,21067383,+"  ; transcript_id "SLCO1B3--SLCO1B7^ENST00000541784.1"  ; transcript_name "SLCO1B7-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A	HAVANA	RNA	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^ENST00000437428.3"  ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
UPF1--AC011447.3	HAVANA	gene	30125	36749	.	+	.	FI_gene_label "AC011447.3^ENSG00000267383.7"  ; ID "UPF1--AC011447.3^AC011447.3^ENSG00000267383.7"  ; exon_id "ENSE00002836707.1"  ; exon_number 1 ; gene_id "UPF1--AC011447.3^AC011447.3^ENSG00000267383.7"  ; gene_name "AC011447.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000180742.4"  ; havana_transcript "OTTHUMT00000452861.1"  ; level 2 ; orig_coord_info "chr19,20238288,20238460,-"  ; transcript_id "UPF1--AC011447.3^ENST00000585498.1"  ; transcript_name "AC011447.3-204"  ; transcript_support_level 2 ; transcript_type lncRNA
UPF1--AC011447.3	HAVANA	RNA	30125	36749	.	+	.	FI_gene_label "AC011447.3^ENSG00000267383.7"  ; ID "UPF1--AC011447.3^ENST00000585498.1"  ; Parent "UPF1--AC011447.3^AC011447.3^ENSG00000267383.7"  ; exon_id "ENSE00002836707.1"  ; exon_number 1 ; gene_id "UPF1--AC011447.3^AC011447.3^ENSG00000267383.7"  ; gene_name "AC011447.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000180742.4"  ; havana_transcript "OTTHUMT00000452861.1"  ; level 2 ; orig_coord_info "chr19,20238288,20238460,-"  ; transcript_id "UPF1--AC011447.3^ENST00000585498.1"  ; transcript_name "AC011447.3-204"  ; transcript_support_level 2 ; transcript_type lncRNA
266 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 ------------------------------
594 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