.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-387c73-R1_A23WJ53LT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/3bf34322c71933a510665b09a38a08/.command.out
Size: 44.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-387c73-R1_A23WJ53LT4_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: 1619
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1619
=> 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:1619
  => 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: 
FBXO25--AC240565.1	HAVANA	gene	2640	15007	.	+	.	FI_gene_label "FBXO25^ENSG00000147364.17"  ; ID "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17"  ; ccdsid "CCDS5954.1"  ; exon_id "ENSE00003460930.1"  ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17"  ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8"  ; havana_transcript "OTTHUMT00000206713.2"  ; hgnc_id "HGNC:13596"  ; level 2 ; orig_coord_info "chr8,431358,431444,+"  ; protein_id "ENSP00000276326.6"  ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9"  ; transcript_name "FBXO25-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FBXO25--AC240565.1	HAVANA	mRNA	2640	15007	.	+	.	FI_gene_label "FBXO25^ENSG00000147364.17"  ; ID "FBXO25--AC240565.1^ENST00000276326.9"  ; Parent "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17"  ; ccdsid "CCDS5954.1"  ; exon_id "ENSE00003460930.1"  ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17"  ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8"  ; havana_transcript "OTTHUMT00000206713.2"  ; hgnc_id "HGNC:13596"  ; level 2 ; orig_coord_info "chr8,431358,431444,+"  ; protein_id "ENSP00000276326.6"  ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9"  ; transcript_name "FBXO25-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FSIP1--AC013652.1	HAVANA	gene	1001	15962	.	+	.	FI_gene_label "FSIP1^ENSG00000150667.8"  ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; ccdsid "CCDS10050.1"  ; exon_id "ENSE00003574039.1"  ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3"  ; havana_transcript "OTTHUMT00000252118.4"  ; hgnc_id "HGNC:21674"  ; level 2 ; orig_coord_info "chr15,39776399,39776524,-"  ; protein_id "ENSP00000280236.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4"  ; transcript_name "FSIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1	HAVANA	mRNA	1001	15962	.	+	.	FI_gene_label "FSIP1^ENSG00000150667.8"  ; ID "FSIP1--AC013652.1^ENST00000350221.4"  ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; ccdsid "CCDS10050.1"  ; exon_id "ENSE00003574039.1"  ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3"  ; havana_transcript "OTTHUMT00000252118.4"  ; hgnc_id "HGNC:21674"  ; level 2 ; orig_coord_info "chr15,39776399,39776524,-"  ; protein_id "ENSP00000280236.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4"  ; transcript_name "FSIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IL27RA--RFX1	HAVANA	gene	14462	32858	.	+	.	FI_gene_label "RFX1^ENSG00000132005.9"  ; ID "IL27RA--RFX1^RFX1^ENSG00000132005.9"  ; ccdsid "CCDS12301.1"  ; exon_id "ENSE00003553019.1"  ; exon_number 2 ; gene_id "IL27RA--RFX1^RFX1^ENSG00000132005.9"  ; gene_name RFX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181979.4"  ; havana_transcript "OTTHUMT00000458510.2"  ; hgnc_id "HGNC:9982"  ; level 2 ; orig_coord_info "chr19,13993525,13993843,-"  ; protein_id "ENSP00000254325.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IL27RA--RFX1^ENST00000254325.9"  ; transcript_name "RFX1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IL27RA--RFX1	HAVANA	mRNA	14462	32858	.	+	.	FI_gene_label "RFX1^ENSG00000132005.9"  ; ID "IL27RA--RFX1^ENST00000254325.9"  ; Parent "IL27RA--RFX1^RFX1^ENSG00000132005.9"  ; ccdsid "CCDS12301.1"  ; exon_id "ENSE00003553019.1"  ; exon_number 2 ; gene_id "IL27RA--RFX1^RFX1^ENSG00000132005.9"  ; gene_name RFX1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181979.4"  ; havana_transcript "OTTHUMT00000458510.2"  ; hgnc_id "HGNC:9982"  ; level 2 ; orig_coord_info "chr19,13993525,13993843,-"  ; protein_id "ENSP00000254325.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IL27RA--RFX1^ENST00000254325.9"  ; transcript_name "RFX1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IL27RA--RFX1	HAVANA	gene	1001	10742	.	+	.	FI_gene_label "IL27RA^ENSG00000104998.4"  ; ID "IL27RA--RFX1^IL27RA^ENSG00000104998.4"  ; ccdsid "CCDS12303.1"  ; exon_id "ENSE00001126468.3"  ; exon_number 1 ; gene_id "IL27RA--RFX1^IL27RA^ENSG00000104998.4"  ; gene_name IL27RA ; gene_type protein_coding ; havana_gene "OTTHUMG00000181990.3"  ; havana_transcript "OTTHUMT00000458539.3"  ; hgnc_id "HGNC:17290"  ; level 2 ; orig_coord_info "chr19,14031873,14031972,+"  ; protein_id "ENSP00000263379.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IL27RA--RFX1^ENST00000263379.4"  ; transcript_name "IL27RA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IL27RA--RFX1	HAVANA	mRNA	1001	10742	.	+	.	FI_gene_label "IL27RA^ENSG00000104998.4"  ; ID "IL27RA--RFX1^ENST00000263379.4"  ; Parent "IL27RA--RFX1^IL27RA^ENSG00000104998.4"  ; ccdsid "CCDS12303.1"  ; exon_id "ENSE00001126468.3"  ; exon_number 1 ; gene_id "IL27RA--RFX1^IL27RA^ENSG00000104998.4"  ; gene_name IL27RA ; gene_type protein_coding ; havana_gene "OTTHUMG00000181990.3"  ; havana_transcript "OTTHUMT00000458539.3"  ; hgnc_id "HGNC:17290"  ; level 2 ; orig_coord_info "chr19,14031873,14031972,+"  ; protein_id "ENSP00000263379.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IL27RA--RFX1^ENST00000263379.4"  ; transcript_name "IL27RA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IL27RA--RLN3	HAVANA	gene	1001	10742	.	+	.	FI_gene_label "IL27RA^ENSG00000104998.4"  ; ID "IL27RA--RLN3^IL27RA^ENSG00000104998.4"  ; ccdsid "CCDS12303.1"  ; exon_id "ENSE00001126468.3"  ; exon_number 1 ; gene_id "IL27RA--RLN3^IL27RA^ENSG00000104998.4"  ; gene_name IL27RA ; gene_type protein_coding ; havana_gene "OTTHUMG00000181990.3"  ; havana_transcript "OTTHUMT00000458539.3"  ; hgnc_id "HGNC:17290"  ; level 2 ; orig_coord_info "chr19,14031873,14031972,+"  ; protein_id "ENSP00000263379.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IL27RA--RLN3^ENST00000263379.4"  ; transcript_name "IL27RA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IL27RA--RLN3	HAVANA	mRNA	1001	10742	.	+	.	FI_gene_label "IL27RA^ENSG00000104998.4"  ; ID "IL27RA--RLN3^ENST00000263379.4"  ; Parent "IL27RA--RLN3^IL27RA^ENSG00000104998.4"  ; ccdsid "CCDS12303.1"  ; exon_id "ENSE00001126468.3"  ; exon_number 1 ; gene_id "IL27RA--RLN3^IL27RA^ENSG00000104998.4"  ; gene_name IL27RA ; gene_type protein_coding ; havana_gene "OTTHUMG00000181990.3"  ; havana_transcript "OTTHUMT00000458539.3"  ; hgnc_id "HGNC:17290"  ; level 2 ; orig_coord_info "chr19,14031873,14031972,+"  ; protein_id "ENSP00000263379.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IL27RA--RLN3^ENST00000263379.4"  ; transcript_name "IL27RA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
IL27RA--RLN3	HAVANA	gene	13743	16296	.	+	.	FI_gene_label "RLN3^ENSG00000171136.7"  ; ID "IL27RA--RLN3^RLN3^ENSG00000171136.7"  ; ccdsid "CCDS12302.1"  ; exon_id "ENSE00001687869.2"  ; exon_number 1 ; gene_id "IL27RA--RLN3^RLN3^ENSG00000171136.7"  ; gene_name RLN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181986.2"  ; havana_transcript "OTTHUMT00000458529.2"  ; hgnc_id "HGNC:17135"  ; level 2 ; orig_coord_info "chr19,14028205,14028394,+"  ; protein_id "ENSP00000397415.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IL27RA--RLN3^ENST00000431365.3"  ; transcript_name "RLN3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IL27RA--RLN3	HAVANA	mRNA	13743	16296	.	+	.	FI_gene_label "RLN3^ENSG00000171136.7"  ; ID "IL27RA--RLN3^ENST00000431365.3"  ; Parent "IL27RA--RLN3^RLN3^ENSG00000171136.7"  ; ccdsid "CCDS12302.1"  ; exon_id "ENSE00001687869.2"  ; exon_number 1 ; gene_id "IL27RA--RLN3^RLN3^ENSG00000171136.7"  ; gene_name RLN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181986.2"  ; havana_transcript "OTTHUMT00000458529.2"  ; hgnc_id "HGNC:17135"  ; level 2 ; orig_coord_info "chr19,14028205,14028394,+"  ; protein_id "ENSP00000397415.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "IL27RA--RLN3^ENST00000431365.3"  ; transcript_name "RLN3-201"  ; 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: 
PMS2P6--CCDC146	HAVANA	gene	9058	29425	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PMS2P6--CCDC146	HAVANA	mRNA	9058	29425	.	+	.	FI_gene_label "CCDC146^ENSG00000135205.15"  ; ID "PMS2P6--CCDC146^ENST00000285871.5"  ; Parent "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; ccdsid "CCDS34671.1"  ; exon_id "ENSE00003536120.1"  ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15"  ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3"  ; havana_transcript "OTTHUMT00000341449.2"  ; hgnc_id "HGNC:29296"  ; level 2 ; orig_coord_info "chr7,77167669,77167824,+"  ; protein_id "ENSP00000285871.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5"  ; transcript_name "CCDC146-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRSS27--TPSB2	HAVANA	gene	1328	8540	.	+	.	FI_gene_label "PRSS27^ENSG00000172382.10"  ; ID "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; ccdsid "CCDS10476.1"  ; exon_id "ENSE00001215985.4"  ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3"  ; havana_transcript "OTTHUMT00000250908.2"  ; hgnc_id "HGNC:15475"  ; level 2 ; orig_coord_info "chr16,2720115,2720160,-"  ; protein_id "ENSP00000306390.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8"  ; transcript_name "PRSS27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2	HAVANA	mRNA	1328	8540	.	+	.	FI_gene_label "PRSS27^ENSG00000172382.10"  ; ID "PRSS27--TPSB2^ENST00000302641.8"  ; Parent "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; ccdsid "CCDS10476.1"  ; exon_id "ENSE00001215985.4"  ; exon_number 1 ; gene_id "PRSS27--TPSB2^PRSS27^ENSG00000172382.10"  ; gene_name PRSS27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000128929.3"  ; havana_transcript "OTTHUMT00000250908.2"  ; hgnc_id "HGNC:15475"  ; level 2 ; orig_coord_info "chr16,2720115,2720160,-"  ; protein_id "ENSP00000306390.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PRSS27--TPSB2^ENST00000302641.8"  ; transcript_name "PRSS27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PRSS27--TPSB2	HAVANA	gene	11544	13392	.	+	.	FI_gene_label "TPSB2^ENSG00000197253.13"  ; ID "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; exon_id "ENSE00003747406.1"  ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4"  ; havana_transcript "OTTHUMT00000342363.2"  ; hgnc_id "HGNC:14120"  ; level 2 ; orig_coord_info "chr16,1229891,1229951,-"  ; protein_id "ENSP00000482743.1"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5"  ; transcript_name "TPSB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PRSS27--TPSB2	HAVANA	mRNA	11544	13392	.	+	.	FI_gene_label "TPSB2^ENSG00000197253.13"  ; ID "PRSS27--TPSB2^ENST00000606293.5"  ; Parent "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; exon_id "ENSE00003747406.1"  ; exon_number 2 ; gene_id "PRSS27--TPSB2^TPSB2^ENSG00000197253.13"  ; gene_name TPSB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155926.4"  ; havana_transcript "OTTHUMT00000342363.2"  ; hgnc_id "HGNC:14120"  ; level 2 ; orig_coord_info "chr16,1229891,1229951,-"  ; protein_id "ENSP00000482743.1"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "PRSS27--TPSB2^ENST00000606293.5"  ; transcript_name "TPSB2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SNX29--AC096639.1	HAVANA	gene	23819	27354	.	+	.	FI_gene_label "SNX29^ENSG00000048471.14"  ; ID "SNX29--AC096639.1^SNX29^ENSG00000048471.14"  ; exon_id "ENSE00002616399.1"  ; exon_number 1 ; gene_id "SNX29--AC096639.1^SNX29^ENSG00000048471.14"  ; gene_name SNX29 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129827.4"  ; havana_transcript "OTTHUMT00000422625.1"  ; hgnc_id "HGNC:30542"  ; level 2 ; orig_coord_info "chr16,12356253,12356279,+"  ; protein_id "ENSP00000455327.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "SNX29--AC096639.1^ENST00000562510.1"  ; transcript_name "SNX29-201"  ; transcript_support_level 3 ; transcript_type protein_coding
SNX29--AC096639.1	HAVANA	mRNA	23819	27354	.	+	.	FI_gene_label "SNX29^ENSG00000048471.14"  ; ID "SNX29--AC096639.1^ENST00000562510.1"  ; Parent "SNX29--AC096639.1^SNX29^ENSG00000048471.14"  ; exon_id "ENSE00002616399.1"  ; exon_number 1 ; gene_id "SNX29--AC096639.1^SNX29^ENSG00000048471.14"  ; gene_name SNX29 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129827.4"  ; havana_transcript "OTTHUMT00000422625.1"  ; hgnc_id "HGNC:30542"  ; level 2 ; orig_coord_info "chr16,12356253,12356279,+"  ; protein_id "ENSP00000455327.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "SNX29--AC096639.1^ENST00000562510.1"  ; transcript_name "SNX29-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STON1--GTF2A1L	HAVANA	gene	15060	24138	.	+	.	FI_gene_label "GTF2A1L^ENSG00000242441.8"  ; ID "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; ccdsid "CCDS46281.1"  ; exon_id "ENSE00001939761.2"  ; exon_number 1 ; gene_id "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17"  ; havana_transcript "OTTHUMT00000323852.5"  ; hgnc_id "HGNC:30727"  ; level 2 ; orig_coord_info "chr2,48617875,48617895,+"  ; protein_id "ENSP00000384597.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000403751.8"  ; transcript_name "GTF2A1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STON1--GTF2A1L	HAVANA	mRNA	15060	24138	.	+	.	FI_gene_label "GTF2A1L^ENSG00000242441.8"  ; ID "STON1--GTF2A1L^ENST00000403751.8"  ; Parent "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; ccdsid "CCDS46281.1"  ; exon_id "ENSE00001939761.2"  ; exon_number 1 ; gene_id "STON1--GTF2A1L^GTF2A1L^ENSG00000242441.8"  ; gene_name GTF2A1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000152038.17"  ; havana_transcript "OTTHUMT00000323852.5"  ; hgnc_id "HGNC:30727"  ; level 2 ; orig_coord_info "chr2,48617875,48617895,+"  ; protein_id "ENSP00000384597.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000403751.8"  ; transcript_name "GTF2A1L-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STON1--GTF2A1L	HAVANA	gene	1772	12001	.	+	.	FI_gene_label "STON1^ENSG00000243244.7"  ; ID "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; ccdsid "CCDS1841.1"  ; exon_id "ENSE00003530448.1"  ; exon_number 2 ; gene_id "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; gene_name STON1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129169.7"  ; havana_transcript "OTTHUMT00000325006.1"  ; hgnc_id "HGNC:17003"  ; level 2 ; orig_coord_info "chr2,48580634,48582563,+"  ; protein_id "ENSP00000385273.1"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000404752.6"  ; transcript_name "STON1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STON1--GTF2A1L	HAVANA	mRNA	1772	12001	.	+	.	FI_gene_label "STON1^ENSG00000243244.7"  ; ID "STON1--GTF2A1L^ENST00000404752.6"  ; Parent "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; ccdsid "CCDS1841.1"  ; exon_id "ENSE00003530448.1"  ; exon_number 2 ; gene_id "STON1--GTF2A1L^STON1^ENSG00000243244.7"  ; gene_name STON1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129169.7"  ; havana_transcript "OTTHUMT00000325006.1"  ; hgnc_id "HGNC:17003"  ; level 2 ; orig_coord_info "chr2,48580634,48582563,+"  ; protein_id "ENSP00000385273.1"  ; tag alternative_5_UTR basic MANE_Select appris_principal_1 CCDS ; transcript_id "STON1--GTF2A1L^ENST00000404752.6"  ; transcript_name "STON1-201"  ; 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: 
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: 
ZNF519--ANKRD20A11P	HAVANA	gene	1062	20406	.	+	.	FI_gene_label "ZNF519^ENSG00000175322.12"  ; ID "ZNF519--ANKRD20A11P^ZNF519^ENSG00000175322.12"  ; exon_id "ENSE00003687993.1"  ; exon_number 1 ; gene_id "ZNF519--ANKRD20A11P^ZNF519^ENSG00000175322.12"  ; gene_name ZNF519 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182055.2"  ; havana_transcript "OTTHUMT00000459031.1"  ; hgnc_id "HGNC:30574"  ; level 2 ; orig_coord_info "chr18,14132275,14132277,-"  ; protein_id "ENSP00000468250.1"  ; transcript_id "ZNF519--ANKRD20A11P^ENST00000587419.5"  ; transcript_name "ZNF519-202"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
ZNF519--ANKRD20A11P	HAVANA	mRNA	1062	20406	.	+	.	FI_gene_label "ZNF519^ENSG00000175322.12"  ; ID "ZNF519--ANKRD20A11P^ENST00000587419.5"  ; Parent "ZNF519--ANKRD20A11P^ZNF519^ENSG00000175322.12"  ; exon_id "ENSE00003687993.1"  ; exon_number 1 ; gene_id "ZNF519--ANKRD20A11P^ZNF519^ENSG00000175322.12"  ; gene_name ZNF519 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182055.2"  ; havana_transcript "OTTHUMT00000459031.1"  ; hgnc_id "HGNC:30574"  ; level 2 ; orig_coord_info "chr18,14132275,14132277,-"  ; protein_id "ENSP00000468250.1"  ; transcript_id "ZNF519--ANKRD20A11P^ENST00000587419.5"  ; transcript_name "ZNF519-202"  ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
FBXO25--AC240565.1	HAVANA	gene	26102	34357	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "FBXO25--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 "FBXO25--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
FBXO25--AC240565.1	HAVANA	RNA	26102	34357	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "FBXO25--AC240565.1^ENST00000624936.2"  ; Parent "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "FBXO25--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 "FBXO25--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
FSIP1--AC013652.1	HAVANA	gene	21835	37275	.	+	.	FI_gene_label "AC013652.1^ENSG00000259345.7"  ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; exon_id "ENSE00002558629.1"  ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; gene_name "AC013652.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4"  ; havana_transcript "OTTHUMT00000418683.1"  ; level 2 ; orig_coord_info "chr15,39427098,39427195,-"  ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1"  ; transcript_name "AC013652.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1	HAVANA	RNA	21835	37275	.	+	.	FI_gene_label "AC013652.1^ENSG00000259345.7"  ; ID "FSIP1--AC013652.1^ENST00000558209.1"  ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; exon_id "ENSE00002558629.1"  ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; gene_name "AC013652.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4"  ; havana_transcript "OTTHUMT00000418683.1"  ; level 2 ; orig_coord_info "chr15,39427098,39427195,-"  ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1"  ; transcript_name "AC013652.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
PMS2P6--CCDC146	HAVANA	gene	1001	5876	.	+	.	FI_gene_label "PMS2P6^ENSG00000174384.9"  ; ID "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; exon_id "ENSE00002441642.1"  ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2"  ; havana_transcript "OTTHUMT00000347345.2"  ; hgnc_id "HGNC:33514"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,73093657,73093796,+"  ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5"  ; transcript_name "PMS2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
PMS2P6--CCDC146	HAVANA	RNA	1001	5876	.	+	.	FI_gene_label "PMS2P6^ENSG00000174384.9"  ; ID "PMS2P6--CCDC146^ENST00000333674.5"  ; Parent "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; exon_id "ENSE00002441642.1"  ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9"  ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2"  ; havana_transcript "OTTHUMT00000347345.2"  ; hgnc_id "HGNC:33514"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,73093657,73093796,+"  ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5"  ; transcript_name "PMS2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
SNX29--AC096639.1	HAVANA	gene	41266	42612	.	+	.	FI_gene_label "AC096639.1^ENSG00000228255.1"  ; ID "SNX29--AC096639.1^AC096639.1^ENSG00000228255.1"  ; exon_id "ENSE00001709024.1"  ; exon_number 1 ; gene_id "SNX29--AC096639.1^AC096639.1^ENSG00000228255.1"  ; gene_name "AC096639.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000041157.1"  ; havana_transcript "OTTHUMT00000098644.1"  ; level 2 ; orig_coord_info "chr1,213731416,213731558,+"  ; tag basic ; transcript_id "SNX29--AC096639.1^ENST00000456240.1"  ; transcript_name "AC096639.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
SNX29--AC096639.1	HAVANA	RNA	41266	42612	.	+	.	FI_gene_label "AC096639.1^ENSG00000228255.1"  ; ID "SNX29--AC096639.1^ENST00000456240.1"  ; Parent "SNX29--AC096639.1^AC096639.1^ENSG00000228255.1"  ; exon_id "ENSE00001709024.1"  ; exon_number 1 ; gene_id "SNX29--AC096639.1^AC096639.1^ENSG00000228255.1"  ; gene_name "AC096639.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000041157.1"  ; havana_transcript "OTTHUMT00000098644.1"  ; level 2 ; orig_coord_info "chr1,213731416,213731558,+"  ; tag basic ; transcript_id "SNX29--AC096639.1^ENST00000456240.1"  ; transcript_name "AC096639.1-201"  ; transcript_support_level 5 ; 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: 
ZNF519--ANKRD20A11P	HAVANA	gene	29338	43392	.	+	.	FI_gene_label "ANKRD20A11P^ENSG00000215559.8"  ; ID "ZNF519--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; exon_id "ENSE00002284794.1"  ; exon_number 1 ; gene_id "ZNF519--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; gene_name ANKRD20A11P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074237.2"  ; havana_transcript "OTTHUMT00000157750.1"  ; hgnc_id "HGNC:42024"  ; level 2 ; orig_coord_info "chr21,13979702,13980437,-"  ; tag basic ; transcript_id "ZNF519--ANKRD20A11P^ENST00000344693.5"  ; transcript_name "ANKRD20A11P-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
ZNF519--ANKRD20A11P	HAVANA	RNA	29338	43392	.	+	.	FI_gene_label "ANKRD20A11P^ENSG00000215559.8"  ; ID "ZNF519--ANKRD20A11P^ENST00000344693.5"  ; Parent "ZNF519--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; exon_id "ENSE00002284794.1"  ; exon_number 1 ; gene_id "ZNF519--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; gene_name ANKRD20A11P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074237.2"  ; havana_transcript "OTTHUMT00000157750.1"  ; hgnc_id "HGNC:42024"  ; level 2 ; orig_coord_info "chr21,13979702,13980437,-"  ; tag basic ; transcript_id "ZNF519--ANKRD20A11P^ENST00000344693.5"  ; transcript_name "ANKRD20A11P-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
164 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 ------------------------------
257 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 18 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