.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00576_B23MVV7LT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/5614718ee02fc957f5822cd99b4a2b/.command.out
Size: 49.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00576_B23MVV7LT4_1)
Attempt
Content

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: 3273
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3273
=> 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:3273
  => 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: 
CCDC40--ENPP7	HAVANA	gene	1021	12850	.	+	.	FI_gene_label "CCDC40^ENSG00000141519.15"  ; ID "CCDC40--ENPP7^CCDC40^ENSG00000141519.15"  ; ccdsid "CCDS82212.1"  ; exon_id "ENSE00001871814.2"  ; exon_number 1 ; gene_id "CCDC40--ENPP7^CCDC40^ENSG00000141519.15"  ; gene_name CCDC40 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132707.5"  ; havana_transcript "OTTHUMT00000437423.1"  ; hgnc_id "HGNC:26090"  ; level 2 ; orig_coord_info "chr17,80036663,80036691,+"  ; protein_id "ENSP00000269318.5"  ; tag basic CCDS ; transcript_id "CCDC40--ENPP7^ENST00000269318.9"  ; transcript_name "CCDC40-201"  ; transcript_support_level 2 ; transcript_type protein_coding
CCDC40--ENPP7	HAVANA	mRNA	1021	12850	.	+	.	FI_gene_label "CCDC40^ENSG00000141519.15"  ; ID "CCDC40--ENPP7^ENST00000269318.9"  ; Parent "CCDC40--ENPP7^CCDC40^ENSG00000141519.15"  ; ccdsid "CCDS82212.1"  ; exon_id "ENSE00001871814.2"  ; exon_number 1 ; gene_id "CCDC40--ENPP7^CCDC40^ENSG00000141519.15"  ; gene_name CCDC40 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132707.5"  ; havana_transcript "OTTHUMT00000437423.1"  ; hgnc_id "HGNC:26090"  ; level 2 ; orig_coord_info "chr17,80036663,80036691,+"  ; protein_id "ENSP00000269318.5"  ; tag basic CCDS ; transcript_id "CCDC40--ENPP7^ENST00000269318.9"  ; transcript_name "CCDC40-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CCDC40--ENPP7	HAVANA	gene	30384	38560	.	+	.	FI_gene_label "ENPP7^ENSG00000182156.10"  ; ID "CCDC40--ENPP7^ENPP7^ENSG00000182156.10"  ; ccdsid "CCDS11763.1"  ; exon_id "ENSE00001297319.6"  ; exon_number 1 ; gene_id "CCDC40--ENPP7^ENPP7^ENSG00000182156.10"  ; gene_name ENPP7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177462.3"  ; havana_transcript "OTTHUMT00000437038.3"  ; hgnc_id "HGNC:23764"  ; level 2 ; orig_coord_info "chr17,79731140,79731392,+"  ; protein_id "ENSP00000332656.5"  ; tag upstream_ATG basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC40--ENPP7^ENST00000328313.10"  ; transcript_name "ENPP7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC40--ENPP7	HAVANA	mRNA	30384	38560	.	+	.	FI_gene_label "ENPP7^ENSG00000182156.10"  ; ID "CCDC40--ENPP7^ENST00000328313.10"  ; Parent "CCDC40--ENPP7^ENPP7^ENSG00000182156.10"  ; ccdsid "CCDS11763.1"  ; exon_id "ENSE00001297319.6"  ; exon_number 1 ; gene_id "CCDC40--ENPP7^ENPP7^ENSG00000182156.10"  ; gene_name ENPP7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177462.3"  ; havana_transcript "OTTHUMT00000437038.3"  ; hgnc_id "HGNC:23764"  ; level 2 ; orig_coord_info "chr17,79731140,79731392,+"  ; protein_id "ENSP00000332656.5"  ; tag upstream_ATG basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC40--ENPP7^ENST00000328313.10"  ; transcript_name "ENPP7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CU104787.1--KMT2C	HAVANA	gene	5927	79546	.	+	.	FI_gene_label "KMT2C^ENSG00000055609.20"  ; ID "CU104787.1--KMT2C^KMT2C^ENSG00000055609.20"  ; ccdsid "CCDS5931.1"  ; exon_id "ENSE00003850683.1"  ; exon_number 1 ; gene_id "CU104787.1--KMT2C^KMT2C^ENSG00000055609.20"  ; gene_name KMT2C ; gene_type protein_coding ; havana_gene "OTTHUMG00000150553.7"  ; havana_transcript "OTTHUMT00000318887.4"  ; hgnc_id "HGNC:13726"  ; level 2 ; orig_coord_info "chr7,152435626,152435786,-"  ; protein_id "ENSP00000262189.6"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CU104787.1--KMT2C^ENST00000262189.11"  ; transcript_name "KMT2C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CU104787.1--KMT2C	HAVANA	mRNA	5927	79546	.	+	.	FI_gene_label "KMT2C^ENSG00000055609.20"  ; ID "CU104787.1--KMT2C^ENST00000262189.11"  ; Parent "CU104787.1--KMT2C^KMT2C^ENSG00000055609.20"  ; ccdsid "CCDS5931.1"  ; exon_id "ENSE00003850683.1"  ; exon_number 1 ; gene_id "CU104787.1--KMT2C^KMT2C^ENSG00000055609.20"  ; gene_name KMT2C ; gene_type protein_coding ; havana_gene "OTTHUMG00000150553.7"  ; havana_transcript "OTTHUMT00000318887.4"  ; hgnc_id "HGNC:13726"  ; level 2 ; orig_coord_info "chr7,152435626,152435786,-"  ; protein_id "ENSP00000262189.6"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CU104787.1--KMT2C^ENST00000262189.11"  ; transcript_name "KMT2C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FBXO42--OSTCP2	HAVANA	gene	1001	17155	.	+	.	FI_gene_label "FBXO42^ENSG00000037637.11"  ; ID "FBXO42--OSTCP2^FBXO42^ENSG00000037637.11"  ; ccdsid "CCDS30613.1"  ; exon_id "ENSE00001467565.1"  ; exon_number 2 ; gene_id "FBXO42--OSTCP2^FBXO42^ENSG00000037637.11"  ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3"  ; havana_transcript "OTTHUMT00000006285.2"  ; hgnc_id "HGNC:29249"  ; level 2 ; orig_coord_info "chr1,16315169,16315418,-"  ; protein_id "ENSP00000364742.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--OSTCP2^ENST00000375592.8"  ; transcript_name "FBXO42-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FBXO42--OSTCP2	HAVANA	mRNA	1001	17155	.	+	.	FI_gene_label "FBXO42^ENSG00000037637.11"  ; ID "FBXO42--OSTCP2^ENST00000375592.8"  ; Parent "FBXO42--OSTCP2^FBXO42^ENSG00000037637.11"  ; ccdsid "CCDS30613.1"  ; exon_id "ENSE00001467565.1"  ; exon_number 2 ; gene_id "FBXO42--OSTCP2^FBXO42^ENSG00000037637.11"  ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3"  ; havana_transcript "OTTHUMT00000006285.2"  ; hgnc_id "HGNC:29249"  ; level 2 ; orig_coord_info "chr1,16315169,16315418,-"  ; protein_id "ENSP00000364742.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--OSTCP2^ENST00000375592.8"  ; transcript_name "FBXO42-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FBXO42--TRNP1	HAVANA	gene	1001	17155	.	+	.	FI_gene_label "FBXO42^ENSG00000037637.11"  ; ID "FBXO42--TRNP1^FBXO42^ENSG00000037637.11"  ; ccdsid "CCDS30613.1"  ; exon_id "ENSE00001467565.1"  ; exon_number 2 ; gene_id "FBXO42--TRNP1^FBXO42^ENSG00000037637.11"  ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3"  ; havana_transcript "OTTHUMT00000006285.2"  ; hgnc_id "HGNC:29249"  ; level 2 ; orig_coord_info "chr1,16315169,16315418,-"  ; protein_id "ENSP00000364742.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--TRNP1^ENST00000375592.8"  ; transcript_name "FBXO42-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FBXO42--TRNP1	HAVANA	mRNA	1001	17155	.	+	.	FI_gene_label "FBXO42^ENSG00000037637.11"  ; ID "FBXO42--TRNP1^ENST00000375592.8"  ; Parent "FBXO42--TRNP1^FBXO42^ENSG00000037637.11"  ; ccdsid "CCDS30613.1"  ; exon_id "ENSE00001467565.1"  ; exon_number 2 ; gene_id "FBXO42--TRNP1^FBXO42^ENSG00000037637.11"  ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3"  ; havana_transcript "OTTHUMT00000006285.2"  ; hgnc_id "HGNC:29249"  ; level 2 ; orig_coord_info "chr1,16315169,16315418,-"  ; protein_id "ENSP00000364742.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--TRNP1^ENST00000375592.8"  ; transcript_name "FBXO42-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FBXO42--TRNP1	HAVANA	gene	20156	23134	.	+	.	FI_gene_label "TRNP1^ENSG00000253368.4"  ; ID "FBXO42--TRNP1^TRNP1^ENSG00000253368.4"  ; ccdsid "CCDS41289.1"  ; exon_id "ENSE00002107275.2"  ; exon_number 1 ; gene_id "FBXO42--TRNP1^TRNP1^ENSG00000253368.4"  ; gene_name TRNP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000004277.5"  ; havana_transcript "OTTHUMT00000012346.4"  ; hgnc_id "HGNC:34348"  ; level 2 ; orig_coord_info "chr1,26993787,26994467,+"  ; protein_id "ENSP00000429216.2"  ; tag NMD_exception basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--TRNP1^ENST00000522111.3"  ; transcript_name "TRNP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FBXO42--TRNP1	HAVANA	mRNA	20156	23134	.	+	.	FI_gene_label "TRNP1^ENSG00000253368.4"  ; ID "FBXO42--TRNP1^ENST00000522111.3"  ; Parent "FBXO42--TRNP1^TRNP1^ENSG00000253368.4"  ; ccdsid "CCDS41289.1"  ; exon_id "ENSE00002107275.2"  ; exon_number 1 ; gene_id "FBXO42--TRNP1^TRNP1^ENSG00000253368.4"  ; gene_name TRNP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000004277.5"  ; havana_transcript "OTTHUMT00000012346.4"  ; hgnc_id "HGNC:34348"  ; level 2 ; orig_coord_info "chr1,26993787,26994467,+"  ; protein_id "ENSP00000429216.2"  ; tag NMD_exception basic MANE_Select appris_principal_1 CCDS ; transcript_id "FBXO42--TRNP1^ENST00000522111.3"  ; transcript_name "TRNP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KHDRBS3--ZFAT	HAVANA	gene	1001	18198	.	+	.	FI_gene_label "KHDRBS3^ENSG00000131773.14"  ; ID "KHDRBS3--ZFAT^KHDRBS3^ENSG00000131773.14"  ; ccdsid "CCDS6374.1"  ; exon_id "ENSE00001722982.2"  ; exon_number 1 ; gene_id "KHDRBS3--ZFAT^KHDRBS3^ENSG00000131773.14"  ; gene_name KHDRBS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164164.5"  ; havana_transcript "OTTHUMT00000377529.2"  ; hgnc_id "HGNC:18117"  ; level 2 ; orig_coord_info "chr8,135457867,135457954,+"  ; protein_id "ENSP00000348108.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KHDRBS3--ZFAT^ENST00000355849.10"  ; transcript_name "KHDRBS3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KHDRBS3--ZFAT	HAVANA	mRNA	1001	18198	.	+	.	FI_gene_label "KHDRBS3^ENSG00000131773.14"  ; ID "KHDRBS3--ZFAT^ENST00000355849.10"  ; Parent "KHDRBS3--ZFAT^KHDRBS3^ENSG00000131773.14"  ; ccdsid "CCDS6374.1"  ; exon_id "ENSE00001722982.2"  ; exon_number 1 ; gene_id "KHDRBS3--ZFAT^KHDRBS3^ENSG00000131773.14"  ; gene_name KHDRBS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164164.5"  ; havana_transcript "OTTHUMT00000377529.2"  ; hgnc_id "HGNC:18117"  ; level 2 ; orig_coord_info "chr8,135457867,135457954,+"  ; protein_id "ENSP00000348108.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KHDRBS3--ZFAT^ENST00000355849.10"  ; transcript_name "KHDRBS3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KHDRBS3--ZFAT	HAVANA	gene	23702	52396	.	+	.	FI_gene_label "ZFAT^ENSG00000066827.16"  ; ID "KHDRBS3--ZFAT^ZFAT^ENSG00000066827.16"  ; ccdsid "CCDS47924.1"  ; exon_id "ENSE00003841474.1"  ; exon_number 1 ; gene_id "KHDRBS3--ZFAT^ZFAT^ENSG00000066827.16"  ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3"  ; havana_transcript "OTTHUMT00000378272.2"  ; hgnc_id "HGNC:19899"  ; level 2 ; orig_coord_info "chr8,134712845,134712863,-"  ; protein_id "ENSP00000367069.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "KHDRBS3--ZFAT^ENST00000377838.8"  ; transcript_name "ZFAT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KHDRBS3--ZFAT	HAVANA	mRNA	23702	52396	.	+	.	FI_gene_label "ZFAT^ENSG00000066827.16"  ; ID "KHDRBS3--ZFAT^ENST00000377838.8"  ; Parent "KHDRBS3--ZFAT^ZFAT^ENSG00000066827.16"  ; ccdsid "CCDS47924.1"  ; exon_id "ENSE00003841474.1"  ; exon_number 1 ; gene_id "KHDRBS3--ZFAT^ZFAT^ENSG00000066827.16"  ; gene_name ZFAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000164321.3"  ; havana_transcript "OTTHUMT00000378272.2"  ; hgnc_id "HGNC:19899"  ; level 2 ; orig_coord_info "chr8,134712845,134712863,-"  ; protein_id "ENSP00000367069.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "KHDRBS3--ZFAT^ENST00000377838.8"  ; transcript_name "ZFAT-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PAFAH1B3--GSK3A	HAVANA	gene	8325	18727	.	+	.	FI_gene_label "GSK3A^ENSG00000105723.13"  ; ID "PAFAH1B3--GSK3A^GSK3A^ENSG00000105723.13"  ; ccdsid "CCDS12599.1"  ; exon_id "ENSE00001053028.4"  ; exon_number 1 ; gene_id "PAFAH1B3--GSK3A^GSK3A^ENSG00000105723.13"  ; gene_name GSK3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150722.3"  ; havana_transcript "OTTHUMT00000319782.3"  ; hgnc_id "HGNC:4616"  ; level 2 ; orig_coord_info "chr19,42242183,42242465,-"  ; protein_id "ENSP00000222330.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PAFAH1B3--GSK3A^ENST00000222330.8"  ; transcript_name "GSK3A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PAFAH1B3--GSK3A	HAVANA	mRNA	8325	18727	.	+	.	FI_gene_label "GSK3A^ENSG00000105723.13"  ; ID "PAFAH1B3--GSK3A^ENST00000222330.8"  ; Parent "PAFAH1B3--GSK3A^GSK3A^ENSG00000105723.13"  ; ccdsid "CCDS12599.1"  ; exon_id "ENSE00001053028.4"  ; exon_number 1 ; gene_id "PAFAH1B3--GSK3A^GSK3A^ENSG00000105723.13"  ; gene_name GSK3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000150722.3"  ; havana_transcript "OTTHUMT00000319782.3"  ; hgnc_id "HGNC:4616"  ; level 2 ; orig_coord_info "chr19,42242183,42242465,-"  ; protein_id "ENSP00000222330.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PAFAH1B3--GSK3A^ENST00000222330.8"  ; transcript_name "GSK3A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PAFAH1B3--GSK3A	HAVANA	gene	1923	5299	.	+	.	FI_gene_label "PAFAH1B3^ENSG00000079462.8"  ; ID "PAFAH1B3--GSK3A^PAFAH1B3^ENSG00000079462.8"  ; ccdsid "CCDS12602.1"  ; exon_id "ENSE00000897478.4"  ; exon_number 1 ; gene_id "PAFAH1B3--GSK3A^PAFAH1B3^ENSG00000079462.8"  ; gene_name PAFAH1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182795.2"  ; havana_transcript "OTTHUMT00000463726.1"  ; hgnc_id "HGNC:8576"  ; level 2 ; orig_coord_info "chr19,42302232,42302309,-"  ; protein_id "ENSP00000262890.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PAFAH1B3--GSK3A^ENST00000262890.8"  ; transcript_name "PAFAH1B3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PAFAH1B3--GSK3A	HAVANA	mRNA	1923	5299	.	+	.	FI_gene_label "PAFAH1B3^ENSG00000079462.8"  ; ID "PAFAH1B3--GSK3A^ENST00000262890.8"  ; Parent "PAFAH1B3--GSK3A^PAFAH1B3^ENSG00000079462.8"  ; ccdsid "CCDS12602.1"  ; exon_id "ENSE00000897478.4"  ; exon_number 1 ; gene_id "PAFAH1B3--GSK3A^PAFAH1B3^ENSG00000079462.8"  ; gene_name PAFAH1B3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182795.2"  ; havana_transcript "OTTHUMT00000463726.1"  ; hgnc_id "HGNC:8576"  ; level 2 ; orig_coord_info "chr19,42302232,42302309,-"  ; protein_id "ENSP00000262890.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PAFAH1B3--GSK3A^ENST00000262890.8"  ; transcript_name "PAFAH1B3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SAMD12--XKR6	HAVANA	gene	32877	35426	.	+	.	FI_gene_label "XKR6^ENSG00000171044.11"  ; ID "SAMD12--XKR6^XKR6^ENSG00000171044.11"  ; exon_id "ENSE00001492174.1"  ; exon_number 1 ; gene_id "SAMD12--XKR6^XKR6^ENSG00000171044.11"  ; gene_name XKR6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129351.6"  ; havana_transcript "OTTHUMT00000383960.2"  ; hgnc_id "HGNC:27806"  ; level 1 ; orig_coord_info "chr8,11200576,11201339,-"  ; protein_id "ENSP00000297303.4"  ; tag basic exp_conf ; transcript_id "SAMD12--XKR6^ENST00000297303.4"  ; transcript_name "XKR6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SAMD12--XKR6	HAVANA	mRNA	32877	35426	.	+	.	FI_gene_label "XKR6^ENSG00000171044.11"  ; ID "SAMD12--XKR6^ENST00000297303.4"  ; Parent "SAMD12--XKR6^XKR6^ENSG00000171044.11"  ; exon_id "ENSE00001492174.1"  ; exon_number 1 ; gene_id "SAMD12--XKR6^XKR6^ENSG00000171044.11"  ; gene_name XKR6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129351.6"  ; havana_transcript "OTTHUMT00000383960.2"  ; hgnc_id "HGNC:27806"  ; level 1 ; orig_coord_info "chr8,11200576,11201339,-"  ; protein_id "ENSP00000297303.4"  ; tag basic exp_conf ; transcript_id "SAMD12--XKR6^ENST00000297303.4"  ; transcript_name "XKR6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SAMD12--XKR6	HAVANA	gene	1150	12162	.	+	.	FI_gene_label "SAMD12^ENSG00000177570.15"  ; ID "SAMD12--XKR6^SAMD12^ENSG00000177570.15"  ; ccdsid "CCDS6325.1"  ; exon_id "ENSE00002146278.2"  ; exon_number 1 ; gene_id "SAMD12--XKR6^SAMD12^ENSG00000177570.15"  ; gene_name SAMD12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059817.6"  ; havana_transcript "OTTHUMT00000132989.3"  ; hgnc_id "HGNC:31750"  ; level 2 ; orig_coord_info "chr8,118621804,118621816,-"  ; protein_id "ENSP00000314173.4"  ; tag basic MANE_Select CCDS ; transcript_id "SAMD12--XKR6^ENST00000314727.9"  ; transcript_name "SAMD12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SAMD12--XKR6	HAVANA	mRNA	1150	12162	.	+	.	FI_gene_label "SAMD12^ENSG00000177570.15"  ; ID "SAMD12--XKR6^ENST00000314727.9"  ; Parent "SAMD12--XKR6^SAMD12^ENSG00000177570.15"  ; ccdsid "CCDS6325.1"  ; exon_id "ENSE00002146278.2"  ; exon_number 1 ; gene_id "SAMD12--XKR6^SAMD12^ENSG00000177570.15"  ; gene_name SAMD12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059817.6"  ; havana_transcript "OTTHUMT00000132989.3"  ; hgnc_id "HGNC:31750"  ; level 2 ; orig_coord_info "chr8,118621804,118621816,-"  ; protein_id "ENSP00000314173.4"  ; tag basic MANE_Select CCDS ; transcript_id "SAMD12--XKR6^ENST00000314727.9"  ; transcript_name "SAMD12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SSU72--FBXO42	HAVANA	gene	1001	11569	.	+	.	FI_gene_label "SSU72^ENSG00000160075.12"  ; ID "SSU72--FBXO42^SSU72^ENSG00000160075.12"  ; ccdsid "CCDS32.1"  ; exon_id "ENSE00001478524.4"  ; exon_number 1 ; gene_id "SSU72--FBXO42^SSU72^ENSG00000160075.12"  ; gene_name SSU72 ; gene_type protein_coding ; havana_gene "OTTHUMG00000000576.6"  ; havana_transcript "OTTHUMT00000001366.2"  ; hgnc_id "HGNC:25016"  ; level 2 ; orig_coord_info "chr1,1574478,1574557,-"  ; protein_id "ENSP00000291386.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSU72--FBXO42^ENST00000291386.4"  ; transcript_name "SSU72-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SSU72--FBXO42	HAVANA	mRNA	1001	11569	.	+	.	FI_gene_label "SSU72^ENSG00000160075.12"  ; ID "SSU72--FBXO42^ENST00000291386.4"  ; Parent "SSU72--FBXO42^SSU72^ENSG00000160075.12"  ; ccdsid "CCDS32.1"  ; exon_id "ENSE00001478524.4"  ; exon_number 1 ; gene_id "SSU72--FBXO42^SSU72^ENSG00000160075.12"  ; gene_name SSU72 ; gene_type protein_coding ; havana_gene "OTTHUMG00000000576.6"  ; havana_transcript "OTTHUMT00000001366.2"  ; hgnc_id "HGNC:25016"  ; level 2 ; orig_coord_info "chr1,1574478,1574557,-"  ; protein_id "ENSP00000291386.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSU72--FBXO42^ENST00000291386.4"  ; transcript_name "SSU72-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SSU72--FBXO42	HAVANA	gene	14570	30724	.	+	.	FI_gene_label "FBXO42^ENSG00000037637.11"  ; ID "SSU72--FBXO42^FBXO42^ENSG00000037637.11"  ; ccdsid "CCDS30613.1"  ; exon_id "ENSE00001467565.1"  ; exon_number 2 ; gene_id "SSU72--FBXO42^FBXO42^ENSG00000037637.11"  ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3"  ; havana_transcript "OTTHUMT00000006285.2"  ; hgnc_id "HGNC:29249"  ; level 2 ; orig_coord_info "chr1,16315169,16315418,-"  ; protein_id "ENSP00000364742.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSU72--FBXO42^ENST00000375592.8"  ; transcript_name "FBXO42-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SSU72--FBXO42	HAVANA	mRNA	14570	30724	.	+	.	FI_gene_label "FBXO42^ENSG00000037637.11"  ; ID "SSU72--FBXO42^ENST00000375592.8"  ; Parent "SSU72--FBXO42^FBXO42^ENSG00000037637.11"  ; ccdsid "CCDS30613.1"  ; exon_id "ENSE00001467565.1"  ; exon_number 2 ; gene_id "SSU72--FBXO42^FBXO42^ENSG00000037637.11"  ; gene_name FBXO42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000002218.3"  ; havana_transcript "OTTHUMT00000006285.2"  ; hgnc_id "HGNC:29249"  ; level 2 ; orig_coord_info "chr1,16315169,16315418,-"  ; protein_id "ENSP00000364742.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SSU72--FBXO42^ENST00000375592.8"  ; transcript_name "FBXO42-201"  ; 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: 
TEX2--AC105021.1	HAVANA	gene	1034	24053	.	+	.	FI_gene_label "TEX2^ENSG00000136478.8"  ; ID "TEX2--AC105021.1^TEX2^ENSG00000136478.8"  ; ccdsid "CCDS11658.1"  ; exon_id "ENSE00001324420.1"  ; exon_number 2 ; gene_id "TEX2--AC105021.1^TEX2^ENSG00000136478.8"  ; gene_name TEX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178881.2"  ; havana_transcript "OTTHUMT00000443743.1"  ; hgnc_id "HGNC:30884"  ; level 2 ; orig_coord_info "chr17,64212574,64214217,-"  ; protein_id "ENSP00000258991.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "TEX2--AC105021.1^ENST00000258991.7"  ; transcript_name "TEX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TEX2--AC105021.1	HAVANA	mRNA	1034	24053	.	+	.	FI_gene_label "TEX2^ENSG00000136478.8"  ; ID "TEX2--AC105021.1^ENST00000258991.7"  ; Parent "TEX2--AC105021.1^TEX2^ENSG00000136478.8"  ; ccdsid "CCDS11658.1"  ; exon_id "ENSE00001324420.1"  ; exon_number 2 ; gene_id "TEX2--AC105021.1^TEX2^ENSG00000136478.8"  ; gene_name TEX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178881.2"  ; havana_transcript "OTTHUMT00000443743.1"  ; hgnc_id "HGNC:30884"  ; level 2 ; orig_coord_info "chr17,64212574,64214217,-"  ; protein_id "ENSP00000258991.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "TEX2--AC105021.1^ENST00000258991.7"  ; transcript_name "TEX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TEX2--TMEM100	HAVANA	gene	1034	24053	.	+	.	FI_gene_label "TEX2^ENSG00000136478.8"  ; ID "TEX2--TMEM100^TEX2^ENSG00000136478.8"  ; ccdsid "CCDS11658.1"  ; exon_id "ENSE00001324420.1"  ; exon_number 2 ; gene_id "TEX2--TMEM100^TEX2^ENSG00000136478.8"  ; gene_name TEX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178881.2"  ; havana_transcript "OTTHUMT00000443743.1"  ; hgnc_id "HGNC:30884"  ; level 2 ; orig_coord_info "chr17,64212574,64214217,-"  ; protein_id "ENSP00000258991.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "TEX2--TMEM100^ENST00000258991.7"  ; transcript_name "TEX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TEX2--TMEM100	HAVANA	mRNA	1034	24053	.	+	.	FI_gene_label "TEX2^ENSG00000136478.8"  ; ID "TEX2--TMEM100^ENST00000258991.7"  ; Parent "TEX2--TMEM100^TEX2^ENSG00000136478.8"  ; ccdsid "CCDS11658.1"  ; exon_id "ENSE00001324420.1"  ; exon_number 2 ; gene_id "TEX2--TMEM100^TEX2^ENSG00000136478.8"  ; gene_name TEX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178881.2"  ; havana_transcript "OTTHUMT00000443743.1"  ; hgnc_id "HGNC:30884"  ; level 2 ; orig_coord_info "chr17,64212574,64214217,-"  ; protein_id "ENSP00000258991.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "TEX2--TMEM100^ENST00000258991.7"  ; transcript_name "TEX2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TEX2--TMEM100	HAVANA	gene	29847	33084	.	+	.	FI_gene_label "TMEM100^ENSG00000166292.12"  ; ID "TEX2--TMEM100^TMEM100^ENSG00000166292.12"  ; ccdsid "CCDS11587.1"  ; exon_id "ENSE00002683681.1"  ; exon_number 2 ; gene_id "TEX2--TMEM100^TMEM100^ENSG00000166292.12"  ; gene_name TMEM100 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177858.5"  ; havana_transcript "OTTHUMT00000439265.2"  ; hgnc_id "HGNC:25607"  ; level 2 ; orig_coord_info "chr17,55720669,55721070,-"  ; protein_id "ENSP00000395328.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TEX2--TMEM100^ENST00000424486.3"  ; transcript_name "TMEM100-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TEX2--TMEM100	HAVANA	mRNA	29847	33084	.	+	.	FI_gene_label "TMEM100^ENSG00000166292.12"  ; ID "TEX2--TMEM100^ENST00000424486.3"  ; Parent "TEX2--TMEM100^TMEM100^ENSG00000166292.12"  ; ccdsid "CCDS11587.1"  ; exon_id "ENSE00002683681.1"  ; exon_number 2 ; gene_id "TEX2--TMEM100^TMEM100^ENSG00000166292.12"  ; gene_name TMEM100 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177858.5"  ; havana_transcript "OTTHUMT00000439265.2"  ; hgnc_id "HGNC:25607"  ; level 2 ; orig_coord_info "chr17,55720669,55721070,-"  ; protein_id "ENSP00000395328.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TEX2--TMEM100^ENST00000424486.3"  ; transcript_name "TMEM100-201"  ; 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: 
TPTE--AL356585.3	HAVANA	gene	1023	23850	.	+	.	FI_gene_label "TPTE^ENSG00000274391.5"  ; ID "TPTE--AL356585.3^TPTE^ENSG00000274391.5"  ; ccdsid "CCDS74773.1"  ; exon_id "ENSE00003735534.1"  ; exon_number 4 ; gene_id "TPTE--AL356585.3^TPTE^ENSG00000274391.5"  ; gene_name TPTE ; gene_type protein_coding ; havana_gene "OTTHUMG00000074127.15"  ; havana_transcript "OTTHUMT00000157414.2"  ; hgnc_id "HGNC:12023"  ; level 2 ; orig_coord_info "chr21,10538724,10538734,+"  ; protein_id "ENSP00000482488.1"  ; tag basic appris_alternative_2 CCDS ; transcript_id "TPTE--AL356585.3^ENST00000427445.6"  ; transcript_name "TPTE-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TPTE--AL356585.3	HAVANA	mRNA	1023	23850	.	+	.	FI_gene_label "TPTE^ENSG00000274391.5"  ; ID "TPTE--AL356585.3^ENST00000427445.6"  ; Parent "TPTE--AL356585.3^TPTE^ENSG00000274391.5"  ; ccdsid "CCDS74773.1"  ; exon_id "ENSE00003735534.1"  ; exon_number 4 ; gene_id "TPTE--AL356585.3^TPTE^ENSG00000274391.5"  ; gene_name TPTE ; gene_type protein_coding ; havana_gene "OTTHUMG00000074127.15"  ; havana_transcript "OTTHUMT00000157414.2"  ; hgnc_id "HGNC:12023"  ; level 2 ; orig_coord_info "chr21,10538724,10538734,+"  ; protein_id "ENSP00000482488.1"  ; tag basic appris_alternative_2 CCDS ; transcript_id "TPTE--AL356585.3^ENST00000427445.6"  ; transcript_name "TPTE-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: 
AC008443.2--BAGE2	HAVANA	gene	1001	2549	.	+	.	FI_gene_label "AC008443.2^ENSG00000248103.1"  ; ID "AC008443.2--BAGE2^AC008443.2^ENSG00000248103.1"  ; exon_id "ENSE00002038514.1"  ; exon_number 1 ; gene_id "AC008443.2--BAGE2^AC008443.2^ENSG00000248103.1"  ; gene_name "AC008443.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163377.1"  ; havana_transcript "OTTHUMT00000372940.1"  ; level 1 ; orig_coord_info "chr5,181281375,181281612,+"  ; tag basic exp_conf ; transcript_id "AC008443.2--BAGE2^ENST00000412295.2"  ; transcript_name "AC008443.2-201"  ; transcript_support_level 4 ; transcript_type lncRNA
AC008443.2--BAGE2	HAVANA	RNA	1001	2549	.	+	.	FI_gene_label "AC008443.2^ENSG00000248103.1"  ; ID "AC008443.2--BAGE2^ENST00000412295.2"  ; Parent "AC008443.2--BAGE2^AC008443.2^ENSG00000248103.1"  ; exon_id "ENSE00002038514.1"  ; exon_number 1 ; gene_id "AC008443.2--BAGE2^AC008443.2^ENSG00000248103.1"  ; gene_name "AC008443.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000163377.1"  ; havana_transcript "OTTHUMT00000372940.1"  ; level 1 ; orig_coord_info "chr5,181281375,181281612,+"  ; tag basic exp_conf ; transcript_id "AC008443.2--BAGE2^ENST00000412295.2"  ; transcript_name "AC008443.2-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
AC008443.2--BAGE2	HAVANA	gene	5605	17808	.	+	.	FI_gene_label "BAGE2^ENSG00000187172.15"  ; ID "AC008443.2--BAGE2^BAGE2^ENSG00000187172.15"  ; exon_id "ENSE00001647801.1"  ; exon_number 1 ; gene_id "AC008443.2--BAGE2^BAGE2^ENSG00000187172.15"  ; gene_name BAGE2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074128.5"  ; havana_transcript "OTTHUMT00000157417.3"  ; hgnc_id "HGNC:15723"  ; level 2 ; orig_coord_info "chr21,10413532,10413754,+"  ; tag mRNA_end_NF ; transcript_id "AC008443.2--BAGE2^ENST00000470054.5"  ; transcript_name "BAGE2-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
AC008443.2--BAGE2	HAVANA	RNA	5605	17808	.	+	.	FI_gene_label "BAGE2^ENSG00000187172.15"  ; ID "AC008443.2--BAGE2^ENST00000470054.5"  ; Parent "AC008443.2--BAGE2^BAGE2^ENSG00000187172.15"  ; exon_id "ENSE00001647801.1"  ; exon_number 1 ; gene_id "AC008443.2--BAGE2^BAGE2^ENSG00000187172.15"  ; gene_name BAGE2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074128.5"  ; havana_transcript "OTTHUMT00000157417.3"  ; hgnc_id "HGNC:15723"  ; level 2 ; orig_coord_info "chr21,10413532,10413754,+"  ; tag mRNA_end_NF ; transcript_id "AC008443.2--BAGE2^ENST00000470054.5"  ; transcript_name "BAGE2-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
CU104787.1--KMT2C	HAVANA	gene	1001	2288	.	+	.	FI_gene_label "CU104787.1^ENSG00000279973.2"  ; ID "CU104787.1--KMT2C^CU104787.1^ENSG00000279973.2"  ; exon_id "ENSE00003758096.2"  ; exon_number 1 ; gene_id "CU104787.1--KMT2C^CU104787.1^ENSG00000279973.2"  ; gene_name "CU104787.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000192006.1"  ; havana_transcript "OTTHUMT00000491988.1"  ; level 2 ; orig_coord_info "chr22,11066418,11066515,+"  ; tag basic ; transcript_id "CU104787.1--KMT2C^ENST00000624155.2"  ; transcript_name "CU104787.1-201"  ; transcript_support_level 1 ; transcript_type lncRNA
CU104787.1--KMT2C	HAVANA	RNA	1001	2288	.	+	.	FI_gene_label "CU104787.1^ENSG00000279973.2"  ; ID "CU104787.1--KMT2C^ENST00000624155.2"  ; Parent "CU104787.1--KMT2C^CU104787.1^ENSG00000279973.2"  ; exon_id "ENSE00003758096.2"  ; exon_number 1 ; gene_id "CU104787.1--KMT2C^CU104787.1^ENSG00000279973.2"  ; gene_name "CU104787.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000192006.1"  ; havana_transcript "OTTHUMT00000491988.1"  ; level 2 ; orig_coord_info "chr22,11066418,11066515,+"  ; tag basic ; transcript_id "CU104787.1--KMT2C^ENST00000624155.2"  ; transcript_name "CU104787.1-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
FBXO42--OSTCP2	HAVANA	gene	20156	20599	.	+	.	FI_gene_label "OSTCP2^ENSG00000225294.1"  ; ID "FBXO42--OSTCP2^OSTCP2^ENSG00000225294.1"  ; exon_id "ENSE00001720295.1"  ; exon_number 1 ; gene_id "FBXO42--OSTCP2^OSTCP2^ENSG00000225294.1"  ; gene_name OSTCP2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000004276.1"  ; havana_transcript "OTTHUMT00000012345.1"  ; hgnc_id "HGNC:42864"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr1,26985897,26986340,-"  ; tag pseudo_consens basic ; transcript_id "FBXO42--OSTCP2^ENST00000437956.1"  ; transcript_name "OSTCP2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
FBXO42--OSTCP2	HAVANA	RNA	20156	20599	.	+	.	FI_gene_label "OSTCP2^ENSG00000225294.1"  ; ID "FBXO42--OSTCP2^ENST00000437956.1"  ; Parent "FBXO42--OSTCP2^OSTCP2^ENSG00000225294.1"  ; exon_id "ENSE00001720295.1"  ; exon_number 1 ; gene_id "FBXO42--OSTCP2^OSTCP2^ENSG00000225294.1"  ; gene_name OSTCP2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000004276.1"  ; havana_transcript "OTTHUMT00000012345.1"  ; hgnc_id "HGNC:42864"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr1,26985897,26986340,-"  ; tag pseudo_consens basic ; transcript_id "FBXO42--OSTCP2^ENST00000437956.1"  ; transcript_name "OSTCP2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TEX2--AC105021.1	HAVANA	gene	27540	29841	.	+	.	FI_gene_label "AC105021.1^ENSG00000236319.2"  ; ID "TEX2--AC105021.1^AC105021.1^ENSG00000236319.2"  ; exon_id "ENSE00001598631.1"  ; exon_number 1 ; gene_id "TEX2--AC105021.1^AC105021.1^ENSG00000236319.2"  ; gene_name "AC105021.1"  ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000177856.1"  ; havana_transcript "OTTHUMT00000439262.1"  ; level 2 ; orig_coord_info "chr17,55560957,55561091,-"  ; tag basic ; transcript_id "TEX2--AC105021.1^ENST00000455347.1"  ; transcript_name "AC105021.1-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
TEX2--AC105021.1	HAVANA	RNA	27540	29841	.	+	.	FI_gene_label "AC105021.1^ENSG00000236319.2"  ; ID "TEX2--AC105021.1^ENST00000455347.1"  ; Parent "TEX2--AC105021.1^AC105021.1^ENSG00000236319.2"  ; exon_id "ENSE00001598631.1"  ; exon_number 1 ; gene_id "TEX2--AC105021.1^AC105021.1^ENSG00000236319.2"  ; gene_name "AC105021.1"  ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000177856.1"  ; havana_transcript "OTTHUMT00000439262.1"  ; level 2 ; orig_coord_info "chr17,55560957,55561091,-"  ; tag basic ; transcript_id "TEX2--AC105021.1^ENST00000455347.1"  ; transcript_name "AC105021.1-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
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: 
TPTE--AL356585.3	HAVANA	gene	27275	34055	.	+	.	FI_gene_label "AL356585.3^ENSG00000279231.1"  ; ID "TPTE--AL356585.3^AL356585.3^ENSG00000279231.1"  ; exon_id "ENSE00003757265.1"  ; exon_number 1 ; gene_id "TPTE--AL356585.3^AL356585.3^ENSG00000279231.1"  ; gene_name "AL356585.3"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000189384.1"  ; havana_transcript "OTTHUMT00000479525.1"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr13,18331933,18332052,+"  ; tag basic ; transcript_id "TPTE--AL356585.3^ENST00000625196.1"  ; transcript_name "AL356585.3-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
TPTE--AL356585.3	HAVANA	RNA	27275	34055	.	+	.	FI_gene_label "AL356585.3^ENSG00000279231.1"  ; ID "TPTE--AL356585.3^ENST00000625196.1"  ; Parent "TPTE--AL356585.3^AL356585.3^ENSG00000279231.1"  ; exon_id "ENSE00003757265.1"  ; exon_number 1 ; gene_id "TPTE--AL356585.3^AL356585.3^ENSG00000279231.1"  ; gene_name "AL356585.3"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000189384.1"  ; havana_transcript "OTTHUMT00000479525.1"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr13,18331933,18332052,+"  ; tag basic ; transcript_id "TPTE--AL356585.3^ENST00000625196.1"  ; transcript_name "AL356585.3-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
259 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 ------------------------------
475 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 19 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

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


GFF3 file parsed