File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/3a1318bd2e01dca34ec495f043ee78/.command.log
Size
45.1 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00598_B23MVV7LT4_1)
Attempt

Content

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/3a1318bd2e01dca34ec495f043ee78/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/7a22b2de962dca980c007eb2dc48d4/fi_workdir/tih_rna_sample_00598_B23MVV7LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/3a1318bd2e01dca34ec495f043ee78/.command.run
==> STAGING COMPLETE (3 inputs)

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: 4930
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4930
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:4930
  => 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: 
ARHGEF7--CCDC122	HAVANA	gene	4085	39179	.	+	.	FI_gene_label "ARHGEF7^ENSG00000102606.18"  ; ID "ARHGEF7--CCDC122^ARHGEF7^ENSG00000102606.18"  ; ccdsid "CCDS86361.1"  ; exon_id "ENSE00003799982.1"  ; exon_number 4 ; gene_id "ARHGEF7--CCDC122^ARHGEF7^ENSG00000102606.18"  ; gene_name ARHGEF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017357.11"  ; havana_transcript "OTTHUMT00000045805.3"  ; hgnc_id "HGNC:15607"  ; level 2 ; orig_coord_info "chr13,111217682,111217880,+"  ; protein_id "ENSP00000218789.5"  ; tag basic CCDS ; transcript_id "ARHGEF7--CCDC122^ENST00000218789.9"  ; transcript_name "ARHGEF7-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ARHGEF7--CCDC122	HAVANA	mRNA	4085	39179	.	+	.	FI_gene_label "ARHGEF7^ENSG00000102606.18"  ; ID "ARHGEF7--CCDC122^ENST00000218789.9"  ; Parent "ARHGEF7--CCDC122^ARHGEF7^ENSG00000102606.18"  ; ccdsid "CCDS86361.1"  ; exon_id "ENSE00003799982.1"  ; exon_number 4 ; gene_id "ARHGEF7--CCDC122^ARHGEF7^ENSG00000102606.18"  ; gene_name ARHGEF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017357.11"  ; havana_transcript "OTTHUMT00000045805.3"  ; hgnc_id "HGNC:15607"  ; level 2 ; orig_coord_info "chr13,111217682,111217880,+"  ; protein_id "ENSP00000218789.5"  ; tag basic CCDS ; transcript_id "ARHGEF7--CCDC122^ENST00000218789.9"  ; transcript_name "ARHGEF7-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ARHGEF7--CCDC122	HAVANA	gene	42186	53799	.	+	.	FI_gene_label "CCDC122^ENSG00000151773.13"  ; ID "ARHGEF7--CCDC122^CCDC122^ENSG00000151773.13"  ; ccdsid "CCDS9390.2"  ; exon_id "ENSE00003524812.1"  ; exon_number 3 ; gene_id "ARHGEF7--CCDC122^CCDC122^ENSG00000151773.13"  ; gene_name CCDC122 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017413.9"  ; havana_transcript "OTTHUMT00000276172.5"  ; hgnc_id "HGNC:26478"  ; level 2 ; orig_coord_info "chr13,43869331,43869376,-"  ; protein_id "ENSP00000407763.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGEF7--CCDC122^ENST00000444614.8"  ; transcript_name "CCDC122-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ARHGEF7--CCDC122	HAVANA	mRNA	42186	53799	.	+	.	FI_gene_label "CCDC122^ENSG00000151773.13"  ; ID "ARHGEF7--CCDC122^ENST00000444614.8"  ; Parent "ARHGEF7--CCDC122^CCDC122^ENSG00000151773.13"  ; ccdsid "CCDS9390.2"  ; exon_id "ENSE00003524812.1"  ; exon_number 3 ; gene_id "ARHGEF7--CCDC122^CCDC122^ENSG00000151773.13"  ; gene_name CCDC122 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017413.9"  ; havana_transcript "OTTHUMT00000276172.5"  ; hgnc_id "HGNC:26478"  ; level 2 ; orig_coord_info "chr13,43869331,43869376,-"  ; protein_id "ENSP00000407763.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGEF7--CCDC122^ENST00000444614.8"  ; transcript_name "CCDC122-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ARHGEF7--LACC1	HAVANA	gene	4085	39179	.	+	.	FI_gene_label "ARHGEF7^ENSG00000102606.18"  ; ID "ARHGEF7--LACC1^ARHGEF7^ENSG00000102606.18"  ; ccdsid "CCDS86361.1"  ; exon_id "ENSE00003799982.1"  ; exon_number 4 ; gene_id "ARHGEF7--LACC1^ARHGEF7^ENSG00000102606.18"  ; gene_name ARHGEF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017357.11"  ; havana_transcript "OTTHUMT00000045805.3"  ; hgnc_id "HGNC:15607"  ; level 2 ; orig_coord_info "chr13,111217682,111217880,+"  ; protein_id "ENSP00000218789.5"  ; tag basic CCDS ; transcript_id "ARHGEF7--LACC1^ENST00000218789.9"  ; transcript_name "ARHGEF7-201"  ; transcript_support_level 5 ; transcript_type protein_coding
ARHGEF7--LACC1	HAVANA	mRNA	4085	39179	.	+	.	FI_gene_label "ARHGEF7^ENSG00000102606.18"  ; ID "ARHGEF7--LACC1^ENST00000218789.9"  ; Parent "ARHGEF7--LACC1^ARHGEF7^ENSG00000102606.18"  ; ccdsid "CCDS86361.1"  ; exon_id "ENSE00003799982.1"  ; exon_number 4 ; gene_id "ARHGEF7--LACC1^ARHGEF7^ENSG00000102606.18"  ; gene_name ARHGEF7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017357.11"  ; havana_transcript "OTTHUMT00000045805.3"  ; hgnc_id "HGNC:15607"  ; level 2 ; orig_coord_info "chr13,111217682,111217880,+"  ; protein_id "ENSP00000218789.5"  ; tag basic CCDS ; transcript_id "ARHGEF7--LACC1^ENST00000218789.9"  ; transcript_name "ARHGEF7-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ARHGEF7--LACC1	HAVANA	gene	42806	52302	.	+	.	FI_gene_label "LACC1^ENSG00000179630.11"  ; ID "ARHGEF7--LACC1^LACC1^ENSG00000179630.11"  ; ccdsid "CCDS9391.1"  ; exon_id "ENSE00001267830.1"  ; exon_number 2 ; gene_id "ARHGEF7--LACC1^LACC1^ENSG00000179630.11"  ; gene_name LACC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016826.5"  ; havana_transcript "OTTHUMT00000044726.4"  ; hgnc_id "HGNC:26789"  ; level 2 ; orig_coord_info "chr13,43880986,43881547,+"  ; protein_id "ENSP00000317619.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGEF7--LACC1^ENST00000325686.7"  ; transcript_name "LACC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGEF7--LACC1	HAVANA	mRNA	42806	52302	.	+	.	FI_gene_label "LACC1^ENSG00000179630.11"  ; ID "ARHGEF7--LACC1^ENST00000325686.7"  ; Parent "ARHGEF7--LACC1^LACC1^ENSG00000179630.11"  ; ccdsid "CCDS9391.1"  ; exon_id "ENSE00001267830.1"  ; exon_number 2 ; gene_id "ARHGEF7--LACC1^LACC1^ENSG00000179630.11"  ; gene_name LACC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016826.5"  ; havana_transcript "OTTHUMT00000044726.4"  ; hgnc_id "HGNC:26789"  ; level 2 ; orig_coord_info "chr13,43880986,43881547,+"  ; protein_id "ENSP00000317619.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGEF7--LACC1^ENST00000325686.7"  ; transcript_name "LACC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BMPR1B--UNC5C	HAVANA	gene	8163	19884	.	+	.	FI_gene_label "BMPR1B^ENSG00000138696.11"  ; ID "BMPR1B--UNC5C^BMPR1B^ENSG00000138696.11"  ; ccdsid "CCDS3642.1"  ; exon_id "ENSE00003894599.1"  ; exon_number 2 ; gene_id "BMPR1B--UNC5C^BMPR1B^ENSG00000138696.11"  ; gene_name BMPR1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130991.6"  ; havana_transcript "OTTHUMT00000363051.1"  ; hgnc_id "HGNC:1077"  ; level 2 ; orig_coord_info "chr4,95104425,95104567,+"  ; protein_id "ENSP00000264568.4"  ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "BMPR1B--UNC5C^ENST00000264568.8"  ; transcript_name "BMPR1B-201"  ; transcript_support_level 2 ; transcript_type protein_coding
BMPR1B--UNC5C	HAVANA	mRNA	8163	19884	.	+	.	FI_gene_label "BMPR1B^ENSG00000138696.11"  ; ID "BMPR1B--UNC5C^ENST00000264568.8"  ; Parent "BMPR1B--UNC5C^BMPR1B^ENSG00000138696.11"  ; ccdsid "CCDS3642.1"  ; exon_id "ENSE00003894599.1"  ; exon_number 2 ; gene_id "BMPR1B--UNC5C^BMPR1B^ENSG00000138696.11"  ; gene_name BMPR1B ; gene_type protein_coding ; havana_gene "OTTHUMG00000130991.6"  ; havana_transcript "OTTHUMT00000363051.1"  ; hgnc_id "HGNC:1077"  ; level 2 ; orig_coord_info "chr4,95104425,95104567,+"  ; protein_id "ENSP00000264568.4"  ; tag alternative_5_UTR basic appris_principal_4 CCDS ; transcript_id "BMPR1B--UNC5C^ENST00000264568.8"  ; transcript_name "BMPR1B-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
BMPR1B--UNC5C	HAVANA	gene	26749	53625	.	+	.	FI_gene_label "UNC5C^ENSG00000182168.15"  ; ID "BMPR1B--UNC5C^UNC5C^ENSG00000182168.15"  ; ccdsid "CCDS3643.1"  ; exon_id "ENSE00003849916.1"  ; exon_number 1 ; gene_id "BMPR1B--UNC5C^UNC5C^ENSG00000182168.15"  ; gene_name UNC5C ; gene_type protein_coding ; havana_gene "OTTHUMG00000130989.5"  ; havana_transcript "OTTHUMT00000253607.2"  ; hgnc_id "HGNC:12569"  ; level 2 ; orig_coord_info "chr4,95548734,95548857,-"  ; protein_id "ENSP00000406022.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BMPR1B--UNC5C^ENST00000453304.6"  ; transcript_name "UNC5C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BMPR1B--UNC5C	HAVANA	mRNA	26749	53625	.	+	.	FI_gene_label "UNC5C^ENSG00000182168.15"  ; ID "BMPR1B--UNC5C^ENST00000453304.6"  ; Parent "BMPR1B--UNC5C^UNC5C^ENSG00000182168.15"  ; ccdsid "CCDS3643.1"  ; exon_id "ENSE00003849916.1"  ; exon_number 1 ; gene_id "BMPR1B--UNC5C^UNC5C^ENSG00000182168.15"  ; gene_name UNC5C ; gene_type protein_coding ; havana_gene "OTTHUMG00000130989.5"  ; havana_transcript "OTTHUMT00000253607.2"  ; hgnc_id "HGNC:12569"  ; level 2 ; orig_coord_info "chr4,95548734,95548857,-"  ; protein_id "ENSP00000406022.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BMPR1B--UNC5C^ENST00000453304.6"  ; transcript_name "UNC5C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
C1QTNF3--AMACR	HAVANA	gene	1001	8952	.	+	.	FI_gene_label "C1QTNF3^ENSG00000082196.21"  ; ID "C1QTNF3--AMACR^C1QTNF3^ENSG00000082196.21"  ; ccdsid "CCDS3904.1"  ; exon_id "ENSE00001898423.1"  ; exon_number 1 ; gene_id "C1QTNF3--AMACR^C1QTNF3^ENSG00000082196.21"  ; gene_name C1QTNF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090735.5"  ; havana_transcript "OTTHUMT00000207469.1"  ; hgnc_id "HGNC:14326"  ; level 2 ; orig_coord_info "chr5,34043042,34043125,-"  ; protein_id "ENSP00000231338.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "C1QTNF3--AMACR^ENST00000231338.7"  ; transcript_name "C1QTNF3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
C1QTNF3--AMACR	HAVANA	mRNA	1001	8952	.	+	.	FI_gene_label "C1QTNF3^ENSG00000082196.21"  ; ID "C1QTNF3--AMACR^ENST00000231338.7"  ; Parent "C1QTNF3--AMACR^C1QTNF3^ENSG00000082196.21"  ; ccdsid "CCDS3904.1"  ; exon_id "ENSE00001898423.1"  ; exon_number 1 ; gene_id "C1QTNF3--AMACR^C1QTNF3^ENSG00000082196.21"  ; gene_name C1QTNF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090735.5"  ; havana_transcript "OTTHUMT00000207469.1"  ; hgnc_id "HGNC:14326"  ; level 2 ; orig_coord_info "chr5,34043042,34043125,-"  ; protein_id "ENSP00000231338.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "C1QTNF3--AMACR^ENST00000231338.7"  ; transcript_name "C1QTNF3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
C1QTNF3--AMACR	HAVANA	gene	13602	24394	.	+	.	FI_gene_label "AMACR^ENSG00000242110.8"  ; ID "C1QTNF3--AMACR^AMACR^ENSG00000242110.8"  ; ccdsid "CCDS3902.1"  ; exon_id "ENSE00001953485.2"  ; exon_number 1 ; gene_id "C1QTNF3--AMACR^AMACR^ENSG00000242110.8"  ; gene_name AMACR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090734.3"  ; havana_transcript "OTTHUMT00000207467.2"  ; hgnc_id "HGNC:451"  ; level 2 ; orig_coord_info "chr5,34007773,34008019,-"  ; protein_id "ENSP00000334424.6"  ; tag basic MANE_Select CCDS ; transcript_id "C1QTNF3--AMACR^ENST00000335606.11"  ; transcript_name "AMACR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
C1QTNF3--AMACR	HAVANA	mRNA	13602	24394	.	+	.	FI_gene_label "AMACR^ENSG00000242110.8"  ; ID "C1QTNF3--AMACR^ENST00000335606.11"  ; Parent "C1QTNF3--AMACR^AMACR^ENSG00000242110.8"  ; ccdsid "CCDS3902.1"  ; exon_id "ENSE00001953485.2"  ; exon_number 1 ; gene_id "C1QTNF3--AMACR^AMACR^ENSG00000242110.8"  ; gene_name AMACR ; gene_type protein_coding ; havana_gene "OTTHUMG00000090734.3"  ; havana_transcript "OTTHUMT00000207467.2"  ; hgnc_id "HGNC:451"  ; level 2 ; orig_coord_info "chr5,34007773,34008019,-"  ; protein_id "ENSP00000334424.6"  ; tag basic MANE_Select CCDS ; transcript_id "C1QTNF3--AMACR^ENST00000335606.11"  ; transcript_name "AMACR-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GPC1--LINC01937	HAVANA	gene	1001	14710	.	+	.	FI_gene_label "GPC1^ENSG00000063660.9"  ; ID "GPC1--LINC01937^GPC1^ENSG00000063660.9"  ; ccdsid "CCDS2534.1"  ; exon_id "ENSE00001259907.4"  ; exon_number 1 ; gene_id "GPC1--LINC01937^GPC1^ENSG00000063660.9"  ; gene_name GPC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133349.7"  ; havana_transcript "OTTHUMT00000257179.5"  ; hgnc_id "HGNC:4449"  ; level 2 ; orig_coord_info "chr2,240435919,240436084,+"  ; protein_id "ENSP00000264039.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPC1--LINC01937^ENST00000264039.7"  ; transcript_name "GPC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GPC1--LINC01937	HAVANA	mRNA	1001	14710	.	+	.	FI_gene_label "GPC1^ENSG00000063660.9"  ; ID "GPC1--LINC01937^ENST00000264039.7"  ; Parent "GPC1--LINC01937^GPC1^ENSG00000063660.9"  ; ccdsid "CCDS2534.1"  ; exon_id "ENSE00001259907.4"  ; exon_number 1 ; gene_id "GPC1--LINC01937^GPC1^ENSG00000063660.9"  ; gene_name GPC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133349.7"  ; havana_transcript "OTTHUMT00000257179.5"  ; hgnc_id "HGNC:4449"  ; level 2 ; orig_coord_info "chr2,240435919,240436084,+"  ; protein_id "ENSP00000264039.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPC1--LINC01937^ENST00000264039.7"  ; transcript_name "GPC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
JMJD1C--FRMD4A	HAVANA	gene	49512	77321	.	+	.	FI_gene_label "FRMD4A^ENSG00000151474.23"  ; ID "JMJD1C--FRMD4A^FRMD4A^ENSG00000151474.23"  ; exon_id "ENSE00001699048.1"  ; exon_number 1 ; gene_id "JMJD1C--FRMD4A^FRMD4A^ENSG00000151474.23"  ; gene_name FRMD4A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017708.10"  ; havana_transcript "OTTHUMT00000046891.2"  ; hgnc_id "HGNC:25491"  ; level 2 ; orig_coord_info "chr10,13971656,13971799,-"  ; protein_id "ENSP00000264546.6"  ; tag CAGE_supported_TSS mRNA_end_NF cds_end_NF ; transcript_id "JMJD1C--FRMD4A^ENST00000264546.10"  ; transcript_name "FRMD4A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
JMJD1C--FRMD4A	HAVANA	mRNA	49512	77321	.	+	.	FI_gene_label "FRMD4A^ENSG00000151474.23"  ; ID "JMJD1C--FRMD4A^ENST00000264546.10"  ; Parent "JMJD1C--FRMD4A^FRMD4A^ENSG00000151474.23"  ; exon_id "ENSE00001699048.1"  ; exon_number 1 ; gene_id "JMJD1C--FRMD4A^FRMD4A^ENSG00000151474.23"  ; gene_name FRMD4A ; gene_type protein_coding ; havana_gene "OTTHUMG00000017708.10"  ; havana_transcript "OTTHUMT00000046891.2"  ; hgnc_id "HGNC:25491"  ; level 2 ; orig_coord_info "chr10,13971656,13971799,-"  ; protein_id "ENSP00000264546.6"  ; tag CAGE_supported_TSS mRNA_end_NF cds_end_NF ; transcript_id "JMJD1C--FRMD4A^ENST00000264546.10"  ; transcript_name "FRMD4A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
JMJD1C--FRMD4A	HAVANA	gene	14813	30669	.	+	.	FI_gene_label "JMJD1C^ENSG00000171988.19"  ; ID "JMJD1C--FRMD4A^JMJD1C^ENSG00000171988.19"  ; exon_id "ENSE00001605128.1"  ; exon_number 1 ; gene_id "JMJD1C--FRMD4A^JMJD1C^ENSG00000171988.19"  ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7"  ; havana_transcript "OTTHUMT00000048250.1"  ; hgnc_id "HGNC:12313"  ; level 1 ; orig_coord_info "chr10,63206595,63207725,-"  ; protein_id "ENSP00000335929.5"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "JMJD1C--FRMD4A^ENST00000327520.7"  ; transcript_name "JMJD1C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
JMJD1C--FRMD4A	HAVANA	mRNA	14813	30669	.	+	.	FI_gene_label "JMJD1C^ENSG00000171988.19"  ; ID "JMJD1C--FRMD4A^ENST00000327520.7"  ; Parent "JMJD1C--FRMD4A^JMJD1C^ENSG00000171988.19"  ; exon_id "ENSE00001605128.1"  ; exon_number 1 ; gene_id "JMJD1C--FRMD4A^JMJD1C^ENSG00000171988.19"  ; gene_name JMJD1C ; gene_type protein_coding ; havana_gene "OTTHUMG00000018311.7"  ; havana_transcript "OTTHUMT00000048250.1"  ; hgnc_id "HGNC:12313"  ; level 1 ; orig_coord_info "chr10,63206595,63207725,-"  ; protein_id "ENSP00000335929.5"  ; tag mRNA_start_NF cds_start_NF exp_conf ; transcript_id "JMJD1C--FRMD4A^ENST00000327520.7"  ; transcript_name "JMJD1C-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	7417	15704	.	+	.	FI_gene_label "KLRK1^ENSG00000213809.9"  ; ID "KLRC4--KLRK1^ENST00000240618.11"  ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; ccdsid "CCDS8623.1"  ; exon_id "ENSE00003640305.1"  ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9"  ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3"  ; havana_transcript "OTTHUMT00000400269.2"  ; hgnc_id "HGNC:18788"  ; level 2 ; orig_coord_info "chr12,10388771,10388810,-"  ; protein_id "ENSP00000240618.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11"  ; transcript_name "KLRK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KLRC4--KLRK1	HAVANA	gene	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1	HAVANA	mRNA	1001	3376	.	+	.	FI_gene_label "KLRC4^ENSG00000183542.5"  ; ID "KLRC4--KLRK1^ENST00000309384.2"  ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; ccdsid "CCDS8624.1"  ; exon_id "ENSE00001145174.1"  ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5"  ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2"  ; havana_transcript "OTTHUMT00000400108.2"  ; hgnc_id "HGNC:6377"  ; level 2 ; orig_coord_info "chr12,10409389,10409575,-"  ; protein_id "ENSP00000310216.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2"  ; transcript_name "KLRC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NEDD4L--HSPA13	HAVANA	gene	1436	72667	.	+	.	FI_gene_label "NEDD4L^ENSG00000049759.20"  ; ID "NEDD4L--HSPA13^NEDD4L^ENSG00000049759.20"  ; exon_id "ENSE00002934128.1"  ; exon_number 1 ; gene_id "NEDD4L--HSPA13^NEDD4L^ENSG00000049759.20"  ; gene_name NEDD4L ; gene_type protein_coding ; havana_gene "OTTHUMG00000179875.12"  ; havana_transcript "OTTHUMT00000449050.2"  ; hgnc_id "HGNC:7728"  ; level 1 ; orig_coord_info "chr18,58044661,58044708,+"  ; protein_id "ENSP00000256830.8"  ; tag basic exp_conf ; transcript_id "NEDD4L--HSPA13^ENST00000256830.13"  ; transcript_name "NEDD4L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
NEDD4L--HSPA13	HAVANA	mRNA	1436	72667	.	+	.	FI_gene_label "NEDD4L^ENSG00000049759.20"  ; ID "NEDD4L--HSPA13^ENST00000256830.13"  ; Parent "NEDD4L--HSPA13^NEDD4L^ENSG00000049759.20"  ; exon_id "ENSE00002934128.1"  ; exon_number 1 ; gene_id "NEDD4L--HSPA13^NEDD4L^ENSG00000049759.20"  ; gene_name NEDD4L ; gene_type protein_coding ; havana_gene "OTTHUMG00000179875.12"  ; havana_transcript "OTTHUMT00000449050.2"  ; hgnc_id "HGNC:7728"  ; level 1 ; orig_coord_info "chr18,58044661,58044708,+"  ; protein_id "ENSP00000256830.8"  ; tag basic exp_conf ; transcript_id "NEDD4L--HSPA13^ENST00000256830.13"  ; transcript_name "NEDD4L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
NEDD4L--HSPA13	HAVANA	gene	80973	88917	.	+	.	FI_gene_label "HSPA13^ENSG00000155304.6"  ; ID "NEDD4L--HSPA13^HSPA13^ENSG00000155304.6"  ; ccdsid "CCDS13567.1"  ; exon_id "ENSE00001020226.6"  ; exon_number 1 ; gene_id "NEDD4L--HSPA13^HSPA13^ENSG00000155304.6"  ; gene_name HSPA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074261.2"  ; havana_transcript "OTTHUMT00000157815.2"  ; hgnc_id "HGNC:11375"  ; level 2 ; orig_coord_info "chr21,14383095,14383119,-"  ; protein_id "ENSP00000285667.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NEDD4L--HSPA13^ENST00000285667.4"  ; transcript_name "HSPA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NEDD4L--HSPA13	HAVANA	mRNA	80973	88917	.	+	.	FI_gene_label "HSPA13^ENSG00000155304.6"  ; ID "NEDD4L--HSPA13^ENST00000285667.4"  ; Parent "NEDD4L--HSPA13^HSPA13^ENSG00000155304.6"  ; ccdsid "CCDS13567.1"  ; exon_id "ENSE00001020226.6"  ; exon_number 1 ; gene_id "NEDD4L--HSPA13^HSPA13^ENSG00000155304.6"  ; gene_name HSPA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074261.2"  ; havana_transcript "OTTHUMT00000157815.2"  ; hgnc_id "HGNC:11375"  ; level 2 ; orig_coord_info "chr21,14383095,14383119,-"  ; protein_id "ENSP00000285667.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NEDD4L--HSPA13^ENST00000285667.4"  ; transcript_name "HSPA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PIAS2--RIT2	HAVANA	gene	2641	26137	.	+	.	FI_gene_label "PIAS2^ENSG00000078043.16"  ; ID "PIAS2--RIT2^PIAS2^ENSG00000078043.16"  ; ccdsid "CCDS32825.1"  ; exon_id "ENSE00001355821.1"  ; exon_number 1 ; gene_id "PIAS2--RIT2^PIAS2^ENSG00000078043.16"  ; gene_name PIAS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179301.8"  ; havana_transcript "OTTHUMT00000445658.2"  ; hgnc_id "HGNC:17311"  ; level 2 ; orig_coord_info "chr18,46917322,46917345,-"  ; protein_id "ENSP00000317163.6"  ; tag basic appris_alternative_1 CCDS ; transcript_id "PIAS2--RIT2^ENST00000324794.11"  ; transcript_name "PIAS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PIAS2--RIT2	HAVANA	mRNA	2641	26137	.	+	.	FI_gene_label "PIAS2^ENSG00000078043.16"  ; ID "PIAS2--RIT2^ENST00000324794.11"  ; Parent "PIAS2--RIT2^PIAS2^ENSG00000078043.16"  ; ccdsid "CCDS32825.1"  ; exon_id "ENSE00001355821.1"  ; exon_number 1 ; gene_id "PIAS2--RIT2^PIAS2^ENSG00000078043.16"  ; gene_name PIAS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179301.8"  ; havana_transcript "OTTHUMT00000445658.2"  ; hgnc_id "HGNC:17311"  ; level 2 ; orig_coord_info "chr18,46917322,46917345,-"  ; protein_id "ENSP00000317163.6"  ; tag basic appris_alternative_1 CCDS ; transcript_id "PIAS2--RIT2^ENST00000324794.11"  ; transcript_name "PIAS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PIAS2--RIT2	HAVANA	gene	39938	49976	.	+	.	FI_gene_label "RIT2^ENSG00000152214.14"  ; ID "PIAS2--RIT2^RIT2^ENSG00000152214.14"  ; ccdsid "CCDS11921.1"  ; exon_id "ENSE00003844024.1"  ; exon_number 1 ; gene_id "PIAS2--RIT2^RIT2^ENSG00000152214.14"  ; gene_name RIT2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132611.7"  ; havana_transcript "OTTHUMT00000255852.2"  ; hgnc_id "HGNC:10017"  ; level 2 ; orig_coord_info "chr18,43115417,43115519,-"  ; protein_id "ENSP00000321805.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PIAS2--RIT2^ENST00000326695.10"  ; transcript_name "RIT2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PIAS2--RIT2	HAVANA	mRNA	39938	49976	.	+	.	FI_gene_label "RIT2^ENSG00000152214.14"  ; ID "PIAS2--RIT2^ENST00000326695.10"  ; Parent "PIAS2--RIT2^RIT2^ENSG00000152214.14"  ; ccdsid "CCDS11921.1"  ; exon_id "ENSE00003844024.1"  ; exon_number 1 ; gene_id "PIAS2--RIT2^RIT2^ENSG00000152214.14"  ; gene_name RIT2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132611.7"  ; havana_transcript "OTTHUMT00000255852.2"  ; hgnc_id "HGNC:10017"  ; level 2 ; orig_coord_info "chr18,43115417,43115519,-"  ; protein_id "ENSP00000321805.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PIAS2--RIT2^ENST00000326695.10"  ; transcript_name "RIT2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PPP1R12A--SYT1	HAVANA	gene	40251	63785	.	+	.	FI_gene_label "SYT1^ENSG00000067715.14"  ; ID "PPP1R12A--SYT1^SYT1^ENSG00000067715.14"  ; ccdsid "CCDS9017.1"  ; exon_id "ENSE00001164727.3"  ; exon_number 4 ; gene_id "PPP1R12A--SYT1^SYT1^ENSG00000067715.14"  ; gene_name SYT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000134326.5"  ; havana_transcript "OTTHUMT00000259415.2"  ; hgnc_id "HGNC:11509"  ; level 2 ; orig_coord_info "chr12,79217520,79217685,+"  ; protein_id "ENSP00000261205.4"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "PPP1R12A--SYT1^ENST00000261205.9"  ; transcript_name "SYT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PPP1R12A--SYT1	HAVANA	mRNA	40251	63785	.	+	.	FI_gene_label "SYT1^ENSG00000067715.14"  ; ID "PPP1R12A--SYT1^ENST00000261205.9"  ; Parent "PPP1R12A--SYT1^SYT1^ENSG00000067715.14"  ; ccdsid "CCDS9017.1"  ; exon_id "ENSE00001164727.3"  ; exon_number 4 ; gene_id "PPP1R12A--SYT1^SYT1^ENSG00000067715.14"  ; gene_name SYT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000134326.5"  ; havana_transcript "OTTHUMT00000259415.2"  ; hgnc_id "HGNC:11509"  ; level 2 ; orig_coord_info "chr12,79217520,79217685,+"  ; protein_id "ENSP00000261205.4"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "PPP1R12A--SYT1^ENST00000261205.9"  ; transcript_name "SYT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PPP1R12A--SYT1	ENSEMBL	gene	1006	36469	.	+	.	FI_gene_label "PPP1R12A^ENSG00000058272.19"  ; ID "PPP1R12A--SYT1^PPP1R12A^ENSG00000058272.19"  ; ccdsid "CCDS44947.1"  ; exon_id "ENSE00001628888.1"  ; exon_number 2 ; gene_id "PPP1R12A--SYT1^PPP1R12A^ENSG00000058272.19"  ; gene_name PPP1R12A ; gene_type protein_coding ; havana_gene "OTTHUMG00000170100.7"  ; hgnc_id "HGNC:7618"  ; level 3 ; orig_coord_info "chr12,79934695,79934931,-"  ; protein_id "ENSP00000261207.5"  ; tag basic appris_principal_3 CCDS ; transcript_id "PPP1R12A--SYT1^ENST00000261207.9"  ; transcript_name "PPP1R12A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PPP1R12A--SYT1	ENSEMBL	mRNA	1006	36469	.	+	.	FI_gene_label "PPP1R12A^ENSG00000058272.19"  ; ID "PPP1R12A--SYT1^ENST00000261207.9"  ; Parent "PPP1R12A--SYT1^PPP1R12A^ENSG00000058272.19"  ; ccdsid "CCDS44947.1"  ; exon_id "ENSE00001628888.1"  ; exon_number 2 ; gene_id "PPP1R12A--SYT1^PPP1R12A^ENSG00000058272.19"  ; gene_name PPP1R12A ; gene_type protein_coding ; havana_gene "OTTHUMG00000170100.7"  ; hgnc_id "HGNC:7618"  ; level 3 ; orig_coord_info "chr12,79934695,79934931,-"  ; protein_id "ENSP00000261207.5"  ; tag basic appris_principal_3 CCDS ; transcript_id "PPP1R12A--SYT1^ENST00000261207.9"  ; transcript_name "PPP1R12A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
RUNDC1--ADGRD1	HAVANA	gene	11949	53243	.	+	.	FI_gene_label "ADGRD1^ENSG00000111452.13"  ; ID "RUNDC1--ADGRD1^ADGRD1^ENSG00000111452.13"  ; ccdsid "CCDS9272.1"  ; exon_id "ENSE00003636799.1"  ; exon_number 1 ; gene_id "RUNDC1--ADGRD1^ADGRD1^ENSG00000111452.13"  ; gene_name ADGRD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168339.5"  ; havana_transcript "OTTHUMT00000399356.2"  ; hgnc_id "HGNC:19893"  ; level 2 ; orig_coord_info "chr12,130954466,130954531,+"  ; protein_id "ENSP00000261654.5"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "RUNDC1--ADGRD1^ENST00000261654.10"  ; transcript_name "ADGRD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RUNDC1--ADGRD1	HAVANA	mRNA	11949	53243	.	+	.	FI_gene_label "ADGRD1^ENSG00000111452.13"  ; ID "RUNDC1--ADGRD1^ENST00000261654.10"  ; Parent "RUNDC1--ADGRD1^ADGRD1^ENSG00000111452.13"  ; ccdsid "CCDS9272.1"  ; exon_id "ENSE00003636799.1"  ; exon_number 1 ; gene_id "RUNDC1--ADGRD1^ADGRD1^ENSG00000111452.13"  ; gene_name ADGRD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168339.5"  ; havana_transcript "OTTHUMT00000399356.2"  ; hgnc_id "HGNC:19893"  ; level 2 ; orig_coord_info "chr12,130954466,130954531,+"  ; protein_id "ENSP00000261654.5"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "RUNDC1--ADGRD1^ENST00000261654.10"  ; transcript_name "ADGRD1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RUNDC1--ADGRD1	HAVANA	gene	1001	8948	.	+	.	FI_gene_label "RUNDC1^ENSG00000198863.7"  ; ID "RUNDC1--ADGRD1^RUNDC1^ENSG00000198863.7"  ; ccdsid "CCDS11448.1"  ; exon_id "ENSE00001212104.2"  ; exon_number 1 ; gene_id "RUNDC1--ADGRD1^RUNDC1^ENSG00000198863.7"  ; gene_name RUNDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180659.1"  ; havana_transcript "OTTHUMT00000452464.1"  ; hgnc_id "HGNC:25418"  ; level 2 ; orig_coord_info "chr17,42980577,42981074,+"  ; protein_id "ENSP00000354622.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "RUNDC1--ADGRD1^ENST00000361677.5"  ; transcript_name "RUNDC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RUNDC1--ADGRD1	HAVANA	mRNA	1001	8948	.	+	.	FI_gene_label "RUNDC1^ENSG00000198863.7"  ; ID "RUNDC1--ADGRD1^ENST00000361677.5"  ; Parent "RUNDC1--ADGRD1^RUNDC1^ENSG00000198863.7"  ; ccdsid "CCDS11448.1"  ; exon_id "ENSE00001212104.2"  ; exon_number 1 ; gene_id "RUNDC1--ADGRD1^RUNDC1^ENSG00000198863.7"  ; gene_name RUNDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180659.1"  ; havana_transcript "OTTHUMT00000452464.1"  ; hgnc_id "HGNC:25418"  ; level 2 ; orig_coord_info "chr17,42980577,42981074,+"  ; protein_id "ENSP00000354622.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "RUNDC1--ADGRD1^ENST00000361677.5"  ; transcript_name "RUNDC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; 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: 
GPC1--LINC01937	HAVANA	gene	19904	21456	.	+	.	FI_gene_label "LINC01937^ENSG00000234279.2"  ; ID "GPC1--LINC01937^LINC01937^ENSG00000234279.2"  ; exon_id "ENSE00001730393.1"  ; exon_number 1 ; gene_id "GPC1--LINC01937^LINC01937^ENSG00000234279.2"  ; gene_name LINC01937 ; gene_type lncRNA ; havana_gene "OTTHUMG00000152851.2"  ; havana_transcript "OTTHUMT00000328260.1"  ; hgnc_id "HGNC:52760"  ; level 1 ; orig_coord_info "chr2,238720324,238720421,+"  ; tag exp_conf ; transcript_id "GPC1--LINC01937^ENST00000448543.1"  ; transcript_name "LINC01937-201"  ; transcript_support_level 4 ; transcript_type lncRNA
GPC1--LINC01937	HAVANA	RNA	19904	21456	.	+	.	FI_gene_label "LINC01937^ENSG00000234279.2"  ; ID "GPC1--LINC01937^ENST00000448543.1"  ; Parent "GPC1--LINC01937^LINC01937^ENSG00000234279.2"  ; exon_id "ENSE00001730393.1"  ; exon_number 1 ; gene_id "GPC1--LINC01937^LINC01937^ENSG00000234279.2"  ; gene_name LINC01937 ; gene_type lncRNA ; havana_gene "OTTHUMG00000152851.2"  ; havana_transcript "OTTHUMT00000328260.1"  ; hgnc_id "HGNC:52760"  ; level 1 ; orig_coord_info "chr2,238720324,238720421,+"  ; tag exp_conf ; transcript_id "GPC1--LINC01937^ENST00000448543.1"  ; transcript_name "LINC01937-201"  ; transcript_support_level 4 ; 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
311 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 ------------------------------
648 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 1 seconds -------------------------------
                  ------ End checks (done in 1 second) ------                   


GFF3 file parsed