.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/b7ebc5d86a930488656a1f00fbf491/.command.out
Size: 51.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt
Content

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: 4015
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4015
=> 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:4015
  => 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: 
AC015911.9--SLFN12L	HAVANA	gene	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L	HAVANA	mRNA	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^ENST00000260908.12"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CBL--DACH2	HAVANA	gene	1042	23816	.	+	.	FI_gene_label "CBL^ENSG00000110395.7"  ; ID "CBL--DACH2^CBL^ENSG00000110395.7"  ; ccdsid "CCDS8418.1"  ; exon_id "ENSE00001240819.5"  ; exon_number 1 ; gene_id "CBL--DACH2^CBL^ENSG00000110395.7"  ; gene_name CBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000166170.7"  ; havana_transcript "OTTHUMT00000388219.6"  ; hgnc_id "HGNC:1541"  ; level 2 ; orig_coord_info "chr11,119206418,119206612,+"  ; protein_id "ENSP00000264033.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CBL--DACH2^ENST00000264033.6"  ; transcript_name "CBL-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CBL--DACH2	HAVANA	mRNA	1042	23816	.	+	.	FI_gene_label "CBL^ENSG00000110395.7"  ; ID "CBL--DACH2^ENST00000264033.6"  ; Parent "CBL--DACH2^CBL^ENSG00000110395.7"  ; ccdsid "CCDS8418.1"  ; exon_id "ENSE00001240819.5"  ; exon_number 1 ; gene_id "CBL--DACH2^CBL^ENSG00000110395.7"  ; gene_name CBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000166170.7"  ; havana_transcript "OTTHUMT00000388219.6"  ; hgnc_id "HGNC:1541"  ; level 2 ; orig_coord_info "chr11,119206418,119206612,+"  ; protein_id "ENSP00000264033.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CBL--DACH2^ENST00000264033.6"  ; transcript_name "CBL-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CBL--DACH2	HAVANA	gene	28326	48468	.	+	.	FI_gene_label "DACH2^ENSG00000126733.21"  ; ID "CBL--DACH2^DACH2^ENSG00000126733.21"  ; ccdsid "CCDS14455.1"  ; exon_id "ENSE00003844511.1"  ; exon_number 1 ; gene_id "CBL--DACH2^DACH2^ENSG00000126733.21"  ; gene_name DACH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021944.4"  ; havana_transcript "OTTHUMT00000359266.2"  ; hgnc_id "HGNC:16814"  ; level 2 ; orig_coord_info "chrX,86148621,86149108,+"  ; protein_id "ENSP00000362217.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CBL--DACH2^ENST00000373125.9"  ; transcript_name "DACH2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CBL--DACH2	HAVANA	mRNA	28326	48468	.	+	.	FI_gene_label "DACH2^ENSG00000126733.21"  ; ID "CBL--DACH2^ENST00000373125.9"  ; Parent "CBL--DACH2^DACH2^ENSG00000126733.21"  ; ccdsid "CCDS14455.1"  ; exon_id "ENSE00003844511.1"  ; exon_number 1 ; gene_id "CBL--DACH2^DACH2^ENSG00000126733.21"  ; gene_name DACH2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021944.4"  ; havana_transcript "OTTHUMT00000359266.2"  ; hgnc_id "HGNC:16814"  ; level 2 ; orig_coord_info "chrX,86148621,86149108,+"  ; protein_id "ENSP00000362217.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CBL--DACH2^ENST00000373125.9"  ; transcript_name "DACH2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COL1A1--SLC45A4	HAVANA	gene	25435	34927	.	+	.	FI_gene_label "SLC45A4^ENSG00000022567.10"  ; ID "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; ccdsid "CCDS34948.1"  ; exon_id "ENSE00001475008.1"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; gene_name SLC45A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164393.4"  ; havana_transcript "OTTHUMT00000378571.3"  ; hgnc_id "HGNC:29196"  ; level 2 ; orig_coord_info "chr8,141228179,141228266,-"  ; protein_id "ENSP00000024061.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000024061.7"  ; transcript_name "SLC45A4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COL1A1--SLC45A4	HAVANA	mRNA	25435	34927	.	+	.	FI_gene_label "SLC45A4^ENSG00000022567.10"  ; ID "COL1A1--SLC45A4^ENST00000024061.7"  ; Parent "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; ccdsid "CCDS34948.1"  ; exon_id "ENSE00001475008.1"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; gene_name SLC45A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164393.4"  ; havana_transcript "OTTHUMT00000378571.3"  ; hgnc_id "HGNC:29196"  ; level 2 ; orig_coord_info "chr8,141228179,141228266,-"  ; protein_id "ENSP00000024061.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000024061.7"  ; transcript_name "SLC45A4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COL1A1--SLC45A4	HAVANA	gene	1002	18313	.	+	.	FI_gene_label "COL1A1^ENSG00000108821.14"  ; ID "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; ccdsid "CCDS11561.1"  ; exon_id "ENSE00003500023.2"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; gene_name COL1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148674.9"  ; havana_transcript "OTTHUMT00000309036.3"  ; hgnc_id "HGNC:2197"  ; level 2 ; orig_coord_info "chr17,50201411,50201513,-"  ; protein_id "ENSP00000225964.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000225964.10"  ; transcript_name "COL1A1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COL1A1--SLC45A4	HAVANA	mRNA	1002	18313	.	+	.	FI_gene_label "COL1A1^ENSG00000108821.14"  ; ID "COL1A1--SLC45A4^ENST00000225964.10"  ; Parent "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; ccdsid "CCDS11561.1"  ; exon_id "ENSE00003500023.2"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; gene_name COL1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148674.9"  ; havana_transcript "OTTHUMT00000309036.3"  ; hgnc_id "HGNC:2197"  ; level 2 ; orig_coord_info "chr17,50201411,50201513,-"  ; protein_id "ENSP00000225964.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000225964.10"  ; transcript_name "COL1A1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IQGAP1--SEMA4B	HAVANA	gene	1001	41690	.	+	.	FI_gene_label "IQGAP1^ENSG00000140575.13"  ; ID "IQGAP1--SEMA4B^IQGAP1^ENSG00000140575.13"  ; ccdsid "CCDS10362.1"  ; exon_id "ENSE00001304261.8"  ; exon_number 1 ; gene_id "IQGAP1--SEMA4B^IQGAP1^ENSG00000140575.13"  ; gene_name IQGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149832.6"  ; havana_transcript "OTTHUMT00000313493.2"  ; hgnc_id "HGNC:6110"  ; level 2 ; orig_coord_info "chr15,90388342,90388396,+"  ; protein_id "ENSP00000268182.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IQGAP1--SEMA4B^ENST00000268182.10"  ; transcript_name "IQGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IQGAP1--SEMA4B	HAVANA	mRNA	1001	41690	.	+	.	FI_gene_label "IQGAP1^ENSG00000140575.13"  ; ID "IQGAP1--SEMA4B^ENST00000268182.10"  ; Parent "IQGAP1--SEMA4B^IQGAP1^ENSG00000140575.13"  ; ccdsid "CCDS10362.1"  ; exon_id "ENSE00001304261.8"  ; exon_number 1 ; gene_id "IQGAP1--SEMA4B^IQGAP1^ENSG00000140575.13"  ; gene_name IQGAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149832.6"  ; havana_transcript "OTTHUMT00000313493.2"  ; hgnc_id "HGNC:6110"  ; level 2 ; orig_coord_info "chr15,90388342,90388396,+"  ; protein_id "ENSP00000268182.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IQGAP1--SEMA4B^ENST00000268182.10"  ; transcript_name "IQGAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IQGAP1--SEMA4B	HAVANA	gene	45833	64207	.	+	.	FI_gene_label "SEMA4B^ENSG00000185033.14"  ; ID "IQGAP1--SEMA4B^SEMA4B^ENSG00000185033.14"  ; ccdsid "CCDS45347.1"  ; exon_id "ENSE00001289963.3"  ; exon_number 2 ; gene_id "IQGAP1--SEMA4B^SEMA4B^ENSG00000185033.14"  ; gene_name SEMA4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000172096.6"  ; havana_transcript "OTTHUMT00000416809.1"  ; hgnc_id "HGNC:10730"  ; level 2 ; orig_coord_info "chr15,90201579,90201735,+"  ; protein_id "ENSP00000332204.6"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "IQGAP1--SEMA4B^ENST00000332496.10"  ; transcript_name "SEMA4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IQGAP1--SEMA4B	HAVANA	mRNA	45833	64207	.	+	.	FI_gene_label "SEMA4B^ENSG00000185033.14"  ; ID "IQGAP1--SEMA4B^ENST00000332496.10"  ; Parent "IQGAP1--SEMA4B^SEMA4B^ENSG00000185033.14"  ; ccdsid "CCDS45347.1"  ; exon_id "ENSE00001289963.3"  ; exon_number 2 ; gene_id "IQGAP1--SEMA4B^SEMA4B^ENSG00000185033.14"  ; gene_name SEMA4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000172096.6"  ; havana_transcript "OTTHUMT00000416809.1"  ; hgnc_id "HGNC:10730"  ; level 2 ; orig_coord_info "chr15,90201579,90201735,+"  ; protein_id "ENSP00000332204.6"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "IQGAP1--SEMA4B^ENST00000332496.10"  ; transcript_name "SEMA4B-201"  ; transcript_support_level 1 ; 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: 
LTBP3--GANAB	HAVANA	gene	1572	17918	.	+	.	FI_gene_label "LTBP3^ENSG00000168056.17"  ; ID "LTBP3--GANAB^LTBP3^ENSG00000168056.17"  ; ccdsid "CCDS44647.1"  ; exon_id "ENSE00001603933.3"  ; exon_number 1 ; gene_id "LTBP3--GANAB^LTBP3^ENSG00000168056.17"  ; gene_name LTBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166575.7"  ; havana_transcript "OTTHUMT00000390538.2"  ; hgnc_id "HGNC:6716"  ; level 2 ; orig_coord_info "chr11,65557629,65557959,-"  ; protein_id "ENSP00000301873.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LTBP3--GANAB^ENST00000301873.11"  ; transcript_name "LTBP3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
LTBP3--GANAB	HAVANA	mRNA	1572	17918	.	+	.	FI_gene_label "LTBP3^ENSG00000168056.17"  ; ID "LTBP3--GANAB^ENST00000301873.11"  ; Parent "LTBP3--GANAB^LTBP3^ENSG00000168056.17"  ; ccdsid "CCDS44647.1"  ; exon_id "ENSE00001603933.3"  ; exon_number 1 ; gene_id "LTBP3--GANAB^LTBP3^ENSG00000168056.17"  ; gene_name LTBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166575.7"  ; havana_transcript "OTTHUMT00000390538.2"  ; hgnc_id "HGNC:6716"  ; level 2 ; orig_coord_info "chr11,65557629,65557959,-"  ; protein_id "ENSP00000301873.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LTBP3--GANAB^ENST00000301873.11"  ; transcript_name "LTBP3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
LTBP3--GANAB	HAVANA	gene	21030	33549	.	+	.	FI_gene_label "GANAB^ENSG00000089597.18"  ; ID "LTBP3--GANAB^GANAB^ENSG00000089597.18"  ; ccdsid "CCDS41656.1"  ; exon_id "ENSE00002175558.1"  ; exon_number 1 ; gene_id "LTBP3--GANAB^GANAB^ENSG00000089597.18"  ; gene_name GANAB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167696.7"  ; havana_transcript "OTTHUMT00000395688.2"  ; hgnc_id "HGNC:4138"  ; level 2 ; orig_coord_info "chr11,62646562,62646599,-"  ; protein_id "ENSP00000340466.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "LTBP3--GANAB^ENST00000346178.8"  ; transcript_name "GANAB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LTBP3--GANAB	HAVANA	mRNA	21030	33549	.	+	.	FI_gene_label "GANAB^ENSG00000089597.18"  ; ID "LTBP3--GANAB^ENST00000346178.8"  ; Parent "LTBP3--GANAB^GANAB^ENSG00000089597.18"  ; ccdsid "CCDS41656.1"  ; exon_id "ENSE00002175558.1"  ; exon_number 1 ; gene_id "LTBP3--GANAB^GANAB^ENSG00000089597.18"  ; gene_name GANAB ; gene_type protein_coding ; havana_gene "OTTHUMG00000167696.7"  ; havana_transcript "OTTHUMT00000395688.2"  ; hgnc_id "HGNC:4138"  ; level 2 ; orig_coord_info "chr11,62646562,62646599,-"  ; protein_id "ENSP00000340466.4"  ; tag basic appris_principal_1 CCDS ; transcript_id "LTBP3--GANAB^ENST00000346178.8"  ; transcript_name "GANAB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RAPGEF6--AC087239.1	HAVANA	gene	1121	42012	.	+	.	FI_gene_label "RAPGEF6^ENSG00000158987.22"  ; ID "RAPGEF6--AC087239.1^RAPGEF6^ENSG00000158987.22"  ; ccdsid "CCDS54900.1"  ; exon_id "ENSE00001781777.1"  ; exon_number 1 ; gene_id "RAPGEF6--AC087239.1^RAPGEF6^ENSG00000158987.22"  ; gene_name RAPGEF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162683.7"  ; havana_transcript "OTTHUMT00000370064.1"  ; hgnc_id "HGNC:20655"  ; level 2 ; orig_coord_info "chr5,131634962,131635030,-"  ; protein_id "ENSP00000296859.6"  ; tag basic appris_principal_4 CCDS ; transcript_id "RAPGEF6--AC087239.1^ENST00000296859.10"  ; transcript_name "RAPGEF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAPGEF6--AC087239.1	HAVANA	mRNA	1121	42012	.	+	.	FI_gene_label "RAPGEF6^ENSG00000158987.22"  ; ID "RAPGEF6--AC087239.1^ENST00000296859.10"  ; Parent "RAPGEF6--AC087239.1^RAPGEF6^ENSG00000158987.22"  ; ccdsid "CCDS54900.1"  ; exon_id "ENSE00001781777.1"  ; exon_number 1 ; gene_id "RAPGEF6--AC087239.1^RAPGEF6^ENSG00000158987.22"  ; gene_name RAPGEF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162683.7"  ; havana_transcript "OTTHUMT00000370064.1"  ; hgnc_id "HGNC:20655"  ; level 2 ; orig_coord_info "chr5,131634962,131635030,-"  ; protein_id "ENSP00000296859.6"  ; tag basic appris_principal_4 CCDS ; transcript_id "RAPGEF6--AC087239.1^ENST00000296859.10"  ; transcript_name "RAPGEF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RAPGEF6--KRAS	HAVANA	gene	47658	60495	.	+	.	FI_gene_label "KRAS^ENSG00000133703.13"  ; ID "RAPGEF6--KRAS^KRAS^ENSG00000133703.13"  ; ccdsid "CCDS8703.1"  ; exon_id "ENSE00000936617.1"  ; exon_number 2 ; gene_id "RAPGEF6--KRAS^KRAS^ENSG00000133703.13"  ; gene_name KRAS ; gene_type protein_coding ; havana_gene "OTTHUMG00000171193.4"  ; havana_transcript "OTTHUMT00000412232.4"  ; hgnc_id "HGNC:6407"  ; level 2 ; orig_coord_info "chr12,25245274,25245384,-"  ; protein_id "ENSP00000256078.5"  ; tag RNA_Seq_supported_only basic appris_alternative_1 CCDS ; transcript_id "RAPGEF6--KRAS^ENST00000256078.10"  ; transcript_name "KRAS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAPGEF6--KRAS	HAVANA	mRNA	47658	60495	.	+	.	FI_gene_label "KRAS^ENSG00000133703.13"  ; ID "RAPGEF6--KRAS^ENST00000256078.10"  ; Parent "RAPGEF6--KRAS^KRAS^ENSG00000133703.13"  ; ccdsid "CCDS8703.1"  ; exon_id "ENSE00000936617.1"  ; exon_number 2 ; gene_id "RAPGEF6--KRAS^KRAS^ENSG00000133703.13"  ; gene_name KRAS ; gene_type protein_coding ; havana_gene "OTTHUMG00000171193.4"  ; havana_transcript "OTTHUMT00000412232.4"  ; hgnc_id "HGNC:6407"  ; level 2 ; orig_coord_info "chr12,25245274,25245384,-"  ; protein_id "ENSP00000256078.5"  ; tag RNA_Seq_supported_only basic appris_alternative_1 CCDS ; transcript_id "RAPGEF6--KRAS^ENST00000256078.10"  ; transcript_name "KRAS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RAPGEF6--KRAS	HAVANA	gene	1121	42012	.	+	.	FI_gene_label "RAPGEF6^ENSG00000158987.22"  ; ID "RAPGEF6--KRAS^RAPGEF6^ENSG00000158987.22"  ; ccdsid "CCDS54900.1"  ; exon_id "ENSE00001781777.1"  ; exon_number 1 ; gene_id "RAPGEF6--KRAS^RAPGEF6^ENSG00000158987.22"  ; gene_name RAPGEF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162683.7"  ; havana_transcript "OTTHUMT00000370064.1"  ; hgnc_id "HGNC:20655"  ; level 2 ; orig_coord_info "chr5,131634962,131635030,-"  ; protein_id "ENSP00000296859.6"  ; tag basic appris_principal_4 CCDS ; transcript_id "RAPGEF6--KRAS^ENST00000296859.10"  ; transcript_name "RAPGEF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAPGEF6--KRAS	HAVANA	mRNA	1121	42012	.	+	.	FI_gene_label "RAPGEF6^ENSG00000158987.22"  ; ID "RAPGEF6--KRAS^ENST00000296859.10"  ; Parent "RAPGEF6--KRAS^RAPGEF6^ENSG00000158987.22"  ; ccdsid "CCDS54900.1"  ; exon_id "ENSE00001781777.1"  ; exon_number 1 ; gene_id "RAPGEF6--KRAS^RAPGEF6^ENSG00000158987.22"  ; gene_name RAPGEF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162683.7"  ; havana_transcript "OTTHUMT00000370064.1"  ; hgnc_id "HGNC:20655"  ; level 2 ; orig_coord_info "chr5,131634962,131635030,-"  ; protein_id "ENSP00000296859.6"  ; tag basic appris_principal_4 CCDS ; transcript_id "RAPGEF6--KRAS^ENST00000296859.10"  ; transcript_name "RAPGEF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RIMKLB--AP000442.1	ENSEMBL	gene	2965	14982	.	+	.	FI_gene_label "RIMKLB^ENSG00000166532.16"  ; ID "RIMKLB--AP000442.1^RIMKLB^ENSG00000166532.16"  ; ccdsid "CCDS41748.1"  ; exon_id "ENSE00003587193.1"  ; exon_number 3 ; gene_id "RIMKLB--AP000442.1^RIMKLB^ENSG00000166532.16"  ; gene_name RIMKLB ; gene_type protein_coding ; havana_gene "OTTHUMG00000168197.4"  ; hgnc_id "HGNC:29228"  ; level 3 ; orig_coord_info "chr12,8713867,8714041,+"  ; protein_id "ENSP00000350136.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "RIMKLB--AP000442.1^ENST00000357529.7"  ; transcript_name "RIMKLB-202"  ; transcript_support_level 5 ; transcript_type protein_coding
RIMKLB--AP000442.1	ENSEMBL	mRNA	2965	14982	.	+	.	FI_gene_label "RIMKLB^ENSG00000166532.16"  ; ID "RIMKLB--AP000442.1^ENST00000357529.7"  ; Parent "RIMKLB--AP000442.1^RIMKLB^ENSG00000166532.16"  ; ccdsid "CCDS41748.1"  ; exon_id "ENSE00003587193.1"  ; exon_number 3 ; gene_id "RIMKLB--AP000442.1^RIMKLB^ENSG00000166532.16"  ; gene_name RIMKLB ; gene_type protein_coding ; havana_gene "OTTHUMG00000168197.4"  ; hgnc_id "HGNC:29228"  ; level 3 ; orig_coord_info "chr12,8713867,8714041,+"  ; protein_id "ENSP00000350136.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "RIMKLB--AP000442.1^ENST00000357529.7"  ; transcript_name "RIMKLB-202"  ; transcript_support_level 5 ; 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: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^ENST00000225576.7"  ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^ENST00000619038.5"  ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZFP64--RPL36P1	HAVANA	gene	2114	11281	.	+	.	FI_gene_label "ZFP64^ENSG00000020256.20"  ; ID "ZFP64--RPL36P1^ZFP64^ENSG00000020256.20"  ; ccdsid "CCDS13440.1"  ; exon_id "ENSE00001455426.1"  ; exon_number 1 ; gene_id "ZFP64--RPL36P1^ZFP64^ENSG00000020256.20"  ; gene_name ZFP64 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032756.3"  ; havana_transcript "OTTHUMT00000079744.1"  ; hgnc_id "HGNC:15940"  ; level 2 ; orig_coord_info "chr20,52191591,52191636,-"  ; protein_id "ENSP00000216923.4"  ; tag basic MANE_Select CCDS ; transcript_id "ZFP64--RPL36P1^ENST00000216923.5"  ; transcript_name "ZFP64-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZFP64--RPL36P1	HAVANA	mRNA	2114	11281	.	+	.	FI_gene_label "ZFP64^ENSG00000020256.20"  ; ID "ZFP64--RPL36P1^ENST00000216923.5"  ; Parent "ZFP64--RPL36P1^ZFP64^ENSG00000020256.20"  ; ccdsid "CCDS13440.1"  ; exon_id "ENSE00001455426.1"  ; exon_number 1 ; gene_id "ZFP64--RPL36P1^ZFP64^ENSG00000020256.20"  ; gene_name ZFP64 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032756.3"  ; havana_transcript "OTTHUMT00000079744.1"  ; hgnc_id "HGNC:15940"  ; level 2 ; orig_coord_info "chr20,52191591,52191636,-"  ; protein_id "ENSP00000216923.4"  ; tag basic MANE_Select CCDS ; transcript_id "ZFP64--RPL36P1^ENST00000216923.5"  ; transcript_name "ZFP64-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZFP64--TSHZ2	HAVANA	gene	2114	11281	.	+	.	FI_gene_label "ZFP64^ENSG00000020256.20"  ; ID "ZFP64--TSHZ2^ZFP64^ENSG00000020256.20"  ; ccdsid "CCDS13440.1"  ; exon_id "ENSE00001455426.1"  ; exon_number 1 ; gene_id "ZFP64--TSHZ2^ZFP64^ENSG00000020256.20"  ; gene_name ZFP64 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032756.3"  ; havana_transcript "OTTHUMT00000079744.1"  ; hgnc_id "HGNC:15940"  ; level 2 ; orig_coord_info "chr20,52191591,52191636,-"  ; protein_id "ENSP00000216923.4"  ; tag basic MANE_Select CCDS ; transcript_id "ZFP64--TSHZ2^ENST00000216923.5"  ; transcript_name "ZFP64-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZFP64--TSHZ2	HAVANA	mRNA	2114	11281	.	+	.	FI_gene_label "ZFP64^ENSG00000020256.20"  ; ID "ZFP64--TSHZ2^ENST00000216923.5"  ; Parent "ZFP64--TSHZ2^ZFP64^ENSG00000020256.20"  ; ccdsid "CCDS13440.1"  ; exon_id "ENSE00001455426.1"  ; exon_number 1 ; gene_id "ZFP64--TSHZ2^ZFP64^ENSG00000020256.20"  ; gene_name ZFP64 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032756.3"  ; havana_transcript "OTTHUMT00000079744.1"  ; hgnc_id "HGNC:15940"  ; level 2 ; orig_coord_info "chr20,52191591,52191636,-"  ; protein_id "ENSP00000216923.4"  ; tag basic MANE_Select CCDS ; transcript_id "ZFP64--TSHZ2^ENST00000216923.5"  ; transcript_name "ZFP64-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZFP64--TSHZ2	ENSEMBL	gene	26920	31012	.	+	.	FI_gene_label "TSHZ2^ENSG00000182463.16"  ; ID "ZFP64--TSHZ2^TSHZ2^ENSG00000182463.16"  ; exon_id "ENSE00003593980.2"  ; exon_number 1 ; gene_id "ZFP64--TSHZ2^TSHZ2^ENSG00000182463.16"  ; gene_name TSHZ2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033058.9"  ; hgnc_id "HGNC:13010"  ; level 3 ; orig_coord_info "chr20,53185646,53185676,+"  ; protein_id "ENSP00000333114.5"  ; tag basic ; transcript_id "ZFP64--TSHZ2^ENST00000329613.7"  ; transcript_name "TSHZ2-201"  ; transcript_support_level 4 ; transcript_type protein_coding
ZFP64--TSHZ2	ENSEMBL	mRNA	26920	31012	.	+	.	FI_gene_label "TSHZ2^ENSG00000182463.16"  ; ID "ZFP64--TSHZ2^ENST00000329613.7"  ; Parent "ZFP64--TSHZ2^TSHZ2^ENSG00000182463.16"  ; exon_id "ENSE00003593980.2"  ; exon_number 1 ; gene_id "ZFP64--TSHZ2^TSHZ2^ENSG00000182463.16"  ; gene_name TSHZ2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033058.9"  ; hgnc_id "HGNC:13010"  ; level 3 ; orig_coord_info "chr20,53185646,53185676,+"  ; protein_id "ENSP00000333114.5"  ; tag basic ; transcript_id "ZFP64--TSHZ2^ENST00000329613.7"  ; transcript_name "TSHZ2-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
ZPR1--APOA1	HAVANA	gene	1017	13921	.	+	.	FI_gene_label "ZPR1^ENSG00000109917.11"  ; ID "ZPR1--APOA1^ZPR1^ENSG00000109917.11"  ; ccdsid "CCDS8375.1"  ; exon_id "ENSE00001294966.6"  ; exon_number 1 ; gene_id "ZPR1--APOA1^ZPR1^ENSG00000109917.11"  ; gene_name ZPR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000046114.10"  ; havana_transcript "OTTHUMT00000106283.4"  ; hgnc_id "HGNC:13051"  ; level 2 ; orig_coord_info "chr11,116787820,116787990,-"  ; protein_id "ENSP00000227322.3"  ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZPR1--APOA1^ENST00000227322.8"  ; transcript_name "ZPR1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZPR1--APOA1	HAVANA	mRNA	1017	13921	.	+	.	FI_gene_label "ZPR1^ENSG00000109917.11"  ; ID "ZPR1--APOA1^ENST00000227322.8"  ; Parent "ZPR1--APOA1^ZPR1^ENSG00000109917.11"  ; ccdsid "CCDS8375.1"  ; exon_id "ENSE00001294966.6"  ; exon_number 1 ; gene_id "ZPR1--APOA1^ZPR1^ENSG00000109917.11"  ; gene_name ZPR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000046114.10"  ; havana_transcript "OTTHUMT00000106283.4"  ; hgnc_id "HGNC:13051"  ; level 2 ; orig_coord_info "chr11,116787820,116787990,-"  ; protein_id "ENSP00000227322.3"  ; tag 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZPR1--APOA1^ENST00000227322.8"  ; transcript_name "ZPR1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZPR1--APOA1	HAVANA	gene	16922	18793	.	+	.	FI_gene_label "APOA1^ENSG00000118137.10"  ; ID "ZPR1--APOA1^APOA1^ENSG00000118137.10"  ; ccdsid "CCDS8378.1"  ; exon_id "ENSE00001255973.1"  ; exon_number 2 ; gene_id "ZPR1--APOA1^APOA1^ENSG00000118137.10"  ; gene_name APOA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000046112.5"  ; havana_transcript "OTTHUMT00000106281.2"  ; hgnc_id "HGNC:600"  ; level 2 ; orig_coord_info "chr11,116837345,116837387,-"  ; protein_id "ENSP00000236850.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZPR1--APOA1^ENST00000236850.5"  ; transcript_name "APOA1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZPR1--APOA1	HAVANA	mRNA	16922	18793	.	+	.	FI_gene_label "APOA1^ENSG00000118137.10"  ; ID "ZPR1--APOA1^ENST00000236850.5"  ; Parent "ZPR1--APOA1^APOA1^ENSG00000118137.10"  ; ccdsid "CCDS8378.1"  ; exon_id "ENSE00001255973.1"  ; exon_number 2 ; gene_id "ZPR1--APOA1^APOA1^ENSG00000118137.10"  ; gene_name APOA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000046112.5"  ; havana_transcript "OTTHUMT00000106281.2"  ; hgnc_id "HGNC:600"  ; level 2 ; orig_coord_info "chr11,116837345,116837387,-"  ; protein_id "ENSP00000236850.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZPR1--APOA1^ENST00000236850.5"  ; transcript_name "APOA1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC015911.9--SLFN12L	HAVANA	gene	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L	HAVANA	RNA	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^ENST00000650652.2"  ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AC015911.9--SLFN12L	ENSEMBL	gene	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
AC015911.9--SLFN12L	ENSEMBL	RNA	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^ENST00000675965.1"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
L1 and L2 created: 
RAPGEF6--AC087239.1	HAVANA	gene	47651	48222	.	+	.	FI_gene_label "AC087239.1^ENSG00000278743.1"  ; ID "RAPGEF6--AC087239.1^AC087239.1^ENSG00000278743.1"  ; exon_id "ENSE00003724254.1"  ; exon_number 1 ; gene_id "RAPGEF6--AC087239.1^AC087239.1^ENSG00000278743.1"  ; gene_name "AC087239.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000187136.1"  ; havana_transcript "OTTHUMT00000474472.1"  ; level 2 ; orig_coord_info "chr12,25385670,25386241,-"  ; tag basic ; transcript_id "RAPGEF6--AC087239.1^ENST00000622671.1"  ; transcript_name "AC087239.1-201"  ; transcript_support_level NA ; transcript_type lncRNA
RAPGEF6--AC087239.1	HAVANA	RNA	47651	48222	.	+	.	FI_gene_label "AC087239.1^ENSG00000278743.1"  ; ID "RAPGEF6--AC087239.1^ENST00000622671.1"  ; Parent "RAPGEF6--AC087239.1^AC087239.1^ENSG00000278743.1"  ; exon_id "ENSE00003724254.1"  ; exon_number 1 ; gene_id "RAPGEF6--AC087239.1^AC087239.1^ENSG00000278743.1"  ; gene_name "AC087239.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000187136.1"  ; havana_transcript "OTTHUMT00000474472.1"  ; level 2 ; orig_coord_info "chr12,25385670,25386241,-"  ; tag basic ; transcript_id "RAPGEF6--AC087239.1^ENST00000622671.1"  ; transcript_name "AC087239.1-201"  ; transcript_support_level NA ; transcript_type lncRNA
L1 and L2 created: 
RIMKLB--AP000442.1	HAVANA	gene	24985	28971	.	+	.	FI_gene_label "AP000442.1^ENSG00000255139.2"  ; ID "RIMKLB--AP000442.1^AP000442.1^ENSG00000255139.2"  ; exon_id "ENSE00002186231.1"  ; exon_number 1 ; gene_id "RIMKLB--AP000442.1^AP000442.1^ENSG00000255139.2"  ; gene_name "AP000442.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000167345.3"  ; havana_transcript "OTTHUMT00000394239.1"  ; level 1 ; orig_coord_info "chr11,59616429,59616474,+"  ; tag basic exp_conf ; transcript_id "RIMKLB--AP000442.1^ENST00000531108.1"  ; transcript_name "AP000442.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
RIMKLB--AP000442.1	HAVANA	RNA	24985	28971	.	+	.	FI_gene_label "AP000442.1^ENSG00000255139.2"  ; ID "RIMKLB--AP000442.1^ENST00000531108.1"  ; Parent "RIMKLB--AP000442.1^AP000442.1^ENSG00000255139.2"  ; exon_id "ENSE00002186231.1"  ; exon_number 1 ; gene_id "RIMKLB--AP000442.1^AP000442.1^ENSG00000255139.2"  ; gene_name "AP000442.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000167345.3"  ; havana_transcript "OTTHUMT00000394239.1"  ; level 1 ; orig_coord_info "chr11,59616429,59616474,+"  ; tag basic exp_conf ; transcript_id "RIMKLB--AP000442.1^ENST00000531108.1"  ; transcript_name "AP000442.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
ZFP64--RPL36P1	HAVANA	gene	24581	24805	.	+	.	FI_gene_label "RPL36P1^ENSG00000230636.1"  ; ID "ZFP64--RPL36P1^RPL36P1^ENSG00000230636.1"  ; exon_id "ENSE00001723768.1"  ; exon_number 1 ; gene_id "ZFP64--RPL36P1^RPL36P1^ENSG00000230636.1"  ; gene_name RPL36P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000032761.1"  ; havana_transcript "OTTHUMT00000079754.1"  ; hgnc_id "HGNC:16338"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr20,52890162,52890386,+"  ; tag basic ; transcript_id "ZFP64--RPL36P1^ENST00000419720.1"  ; transcript_name "RPL36P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
ZFP64--RPL36P1	HAVANA	RNA	24581	24805	.	+	.	FI_gene_label "RPL36P1^ENSG00000230636.1"  ; ID "ZFP64--RPL36P1^ENST00000419720.1"  ; Parent "ZFP64--RPL36P1^RPL36P1^ENSG00000230636.1"  ; exon_id "ENSE00001723768.1"  ; exon_number 1 ; gene_id "ZFP64--RPL36P1^RPL36P1^ENSG00000230636.1"  ; gene_name RPL36P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000032761.1"  ; havana_transcript "OTTHUMT00000079754.1"  ; hgnc_id "HGNC:16338"  ; level 2 ; ont "PGO:0000004"  ; orig_coord_info "chr20,52890162,52890386,+"  ; tag basic ; transcript_id "ZFP64--RPL36P1^ENST00000419720.1"  ; transcript_name "RPL36P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
282 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 1 seconds -------------------------------

----------------------------- Check10: check utrs ------------------------------
540 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 23 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
                  ------ End checks (done in 1 second) ------                   


GFF3 file parsed