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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/38d22a1fcc4d603ebf2cf51bb7ca57/.command.log
Size: 49.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cRa-T1-TRNA-1_B23WHTKLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/36375048b913e3c514de89d502289b/fi_workdir/659_cRa-T1-TRNA-1_B23WHTKLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/38d22a1fcc4d603ebf2cf51bb7ca57/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/38d22a1fcc4d603ebf2cf51bb7ca57/.command.run
==> STAGING COMPLETE (3 inputs)

Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 6414
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 6414
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:6414
  => 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: 
AC092807.3--DDAH1	HAVANA	gene	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1	HAVANA	mRNA	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^ENST00000284031.13"  ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AFF1--C4orf36	HAVANA	gene	35401	41196	.	+	.	FI_gene_label "C4orf36^ENSG00000163633.12"  ; ID "AFF1--C4orf36^C4orf36^ENSG00000163633.12"  ; ccdsid "CCDS3615.1"  ; exon_id "ENSE00003815117.1"  ; exon_number 2 ; gene_id "AFF1--C4orf36^C4orf36^ENSG00000163633.12"  ; gene_name C4orf36 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130597.5"  ; havana_transcript "OTTHUMT00000253044.2"  ; hgnc_id "HGNC:28386"  ; level 2 ; orig_coord_info "chr4,86891456,86891520,-"  ; protein_id "ENSP00000295898.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AFF1--C4orf36^ENST00000295898.8"  ; transcript_name "C4orf36-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AFF1--C4orf36	HAVANA	mRNA	35401	41196	.	+	.	FI_gene_label "C4orf36^ENSG00000163633.12"  ; ID "AFF1--C4orf36^ENST00000295898.8"  ; Parent "AFF1--C4orf36^C4orf36^ENSG00000163633.12"  ; ccdsid "CCDS3615.1"  ; exon_id "ENSE00003815117.1"  ; exon_number 2 ; gene_id "AFF1--C4orf36^C4orf36^ENSG00000163633.12"  ; gene_name C4orf36 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130597.5"  ; havana_transcript "OTTHUMT00000253044.2"  ; hgnc_id "HGNC:28386"  ; level 2 ; orig_coord_info "chr4,86891456,86891520,-"  ; protein_id "ENSP00000295898.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AFF1--C4orf36^ENST00000295898.8"  ; transcript_name "C4orf36-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AFF1--C4orf36	HAVANA	gene	5860	32384	.	+	.	FI_gene_label "AFF1^ENSG00000172493.22"  ; ID "AFF1--C4orf36^AFF1^ENSG00000172493.22"  ; ccdsid "CCDS3616.1"  ; exon_id "ENSE00001150935.3"  ; exon_number 1 ; gene_id "AFF1--C4orf36^AFF1^ENSG00000172493.22"  ; gene_name AFF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130603.9"  ; havana_transcript "OTTHUMT00000253053.3"  ; hgnc_id "HGNC:7135"  ; level 2 ; orig_coord_info "chr4,87007408,87007424,+"  ; protein_id "ENSP00000305689.6"  ; tag basic appris_principal_4 CCDS ; transcript_id "AFF1--C4orf36^ENST00000307808.10"  ; transcript_name "AFF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AFF1--C4orf36	HAVANA	mRNA	5860	32384	.	+	.	FI_gene_label "AFF1^ENSG00000172493.22"  ; ID "AFF1--C4orf36^ENST00000307808.10"  ; Parent "AFF1--C4orf36^AFF1^ENSG00000172493.22"  ; ccdsid "CCDS3616.1"  ; exon_id "ENSE00001150935.3"  ; exon_number 1 ; gene_id "AFF1--C4orf36^AFF1^ENSG00000172493.22"  ; gene_name AFF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130603.9"  ; havana_transcript "OTTHUMT00000253053.3"  ; hgnc_id "HGNC:7135"  ; level 2 ; orig_coord_info "chr4,87007408,87007424,+"  ; protein_id "ENSP00000305689.6"  ; tag basic appris_principal_4 CCDS ; transcript_id "AFF1--C4orf36^ENST00000307808.10"  ; transcript_name "AFF1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
C2CD5--PTPRD	HAVANA	gene	1001	32969	.	+	.	FI_gene_label "C2CD5^ENSG00000111731.12"  ; ID "C2CD5--PTPRD^C2CD5^ENSG00000111731.12"  ; ccdsid "CCDS31758.1"  ; exon_id "ENSE00003632309.1"  ; exon_number 2 ; gene_id "C2CD5--PTPRD^C2CD5^ENSG00000111731.12"  ; gene_name C2CD5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169100.3"  ; havana_transcript "OTTHUMT00000402257.1"  ; hgnc_id "HGNC:29062"  ; level 2 ; orig_coord_info "chr12,22544061,22544150,-"  ; protein_id "ENSP00000334229.4"  ; tag basic appris_alternative_1 CCDS ; transcript_id "C2CD5--PTPRD^ENST00000333957.8"  ; transcript_name "C2CD5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
C2CD5--PTPRD	HAVANA	mRNA	1001	32969	.	+	.	FI_gene_label "C2CD5^ENSG00000111731.12"  ; ID "C2CD5--PTPRD^ENST00000333957.8"  ; Parent "C2CD5--PTPRD^C2CD5^ENSG00000111731.12"  ; ccdsid "CCDS31758.1"  ; exon_id "ENSE00003632309.1"  ; exon_number 2 ; gene_id "C2CD5--PTPRD^C2CD5^ENSG00000111731.12"  ; gene_name C2CD5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000169100.3"  ; havana_transcript "OTTHUMT00000402257.1"  ; hgnc_id "HGNC:29062"  ; level 2 ; orig_coord_info "chr12,22544061,22544150,-"  ; protein_id "ENSP00000334229.4"  ; tag basic appris_alternative_1 CCDS ; transcript_id "C2CD5--PTPRD^ENST00000333957.8"  ; transcript_name "C2CD5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
C2CD5--PTPRD	ENSEMBL	gene	49006	93900	.	+	.	FI_gene_label "PTPRD^ENSG00000153707.17"  ; ID "C2CD5--PTPRD^PTPRD^ENSG00000153707.17"  ; ccdsid "CCDS55290.1"  ; exon_id "ENSE00001254389.3"  ; exon_number 1 ; gene_id "C2CD5--PTPRD^PTPRD^ENSG00000153707.17"  ; gene_name PTPRD ; gene_type protein_coding ; havana_gene "OTTHUMG00000021005.6"  ; hgnc_id "HGNC:9668"  ; level 3 ; orig_coord_info "chr9,8733780,8733843,-"  ; protein_id "ENSP00000347373.5"  ; tag basic CCDS ; transcript_id "C2CD5--PTPRD^ENST00000355233.9"  ; transcript_name "PTPRD-201"  ; transcript_support_level 1 ; transcript_type protein_coding
C2CD5--PTPRD	ENSEMBL	mRNA	49006	93900	.	+	.	FI_gene_label "PTPRD^ENSG00000153707.17"  ; ID "C2CD5--PTPRD^ENST00000355233.9"  ; Parent "C2CD5--PTPRD^PTPRD^ENSG00000153707.17"  ; ccdsid "CCDS55290.1"  ; exon_id "ENSE00001254389.3"  ; exon_number 1 ; gene_id "C2CD5--PTPRD^PTPRD^ENSG00000153707.17"  ; gene_name PTPRD ; gene_type protein_coding ; havana_gene "OTTHUMG00000021005.6"  ; hgnc_id "HGNC:9668"  ; level 3 ; orig_coord_info "chr9,8733780,8733843,-"  ; protein_id "ENSP00000347373.5"  ; tag basic CCDS ; transcript_id "C2CD5--PTPRD^ENST00000355233.9"  ; transcript_name "PTPRD-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GLI1--SCNN1A	HAVANA	gene	1001	11169	.	+	.	FI_gene_label "GLI1^ENSG00000111087.10"  ; ID "GLI1--SCNN1A^GLI1^ENSG00000111087.10"  ; ccdsid "CCDS8940.1"  ; exon_id "ENSE00002313701.1"  ; exon_number 2 ; gene_id "GLI1--SCNN1A^GLI1^ENSG00000111087.10"  ; gene_name GLI1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167332.3"  ; havana_transcript "OTTHUMT00000394197.2"  ; hgnc_id "HGNC:4317"  ; level 2 ; orig_coord_info "chr12,57463692,57463791,+"  ; protein_id "ENSP00000228682.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GLI1--SCNN1A^ENST00000228682.7"  ; transcript_name "GLI1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GLI1--SCNN1A	HAVANA	mRNA	1001	11169	.	+	.	FI_gene_label "GLI1^ENSG00000111087.10"  ; ID "GLI1--SCNN1A^ENST00000228682.7"  ; Parent "GLI1--SCNN1A^GLI1^ENSG00000111087.10"  ; ccdsid "CCDS8940.1"  ; exon_id "ENSE00002313701.1"  ; exon_number 2 ; gene_id "GLI1--SCNN1A^GLI1^ENSG00000111087.10"  ; gene_name GLI1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167332.3"  ; havana_transcript "OTTHUMT00000394197.2"  ; hgnc_id "HGNC:4317"  ; level 2 ; orig_coord_info "chr12,57463692,57463791,+"  ; protein_id "ENSP00000228682.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GLI1--SCNN1A^ENST00000228682.7"  ; transcript_name "GLI1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GLI1--SCNN1A	HAVANA	gene	16210	28159	.	+	.	FI_gene_label "SCNN1A^ENSG00000111319.13"  ; ID "GLI1--SCNN1A^SCNN1A^ENSG00000111319.13"  ; ccdsid "CCDS8543.1"  ; exon_id "ENSE00003515810.1"  ; exon_number 2 ; gene_id "GLI1--SCNN1A^SCNN1A^ENSG00000111319.13"  ; gene_name SCNN1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000168268.3"  ; havana_transcript "OTTHUMT00000399055.2"  ; hgnc_id "HGNC:10599"  ; level 2 ; orig_coord_info "chr12,6374368,6374783,-"  ; protein_id "ENSP00000228916.2"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "GLI1--SCNN1A^ENST00000228916.7"  ; transcript_name "SCNN1A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GLI1--SCNN1A	HAVANA	mRNA	16210	28159	.	+	.	FI_gene_label "SCNN1A^ENSG00000111319.13"  ; ID "GLI1--SCNN1A^ENST00000228916.7"  ; Parent "GLI1--SCNN1A^SCNN1A^ENSG00000111319.13"  ; ccdsid "CCDS8543.1"  ; exon_id "ENSE00003515810.1"  ; exon_number 2 ; gene_id "GLI1--SCNN1A^SCNN1A^ENSG00000111319.13"  ; gene_name SCNN1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000168268.3"  ; havana_transcript "OTTHUMT00000399055.2"  ; hgnc_id "HGNC:10599"  ; level 2 ; orig_coord_info "chr12,6374368,6374783,-"  ; protein_id "ENSP00000228916.2"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "GLI1--SCNN1A^ENST00000228916.7"  ; transcript_name "SCNN1A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GOLGA4--FLNB	HAVANA	gene	41754	94703	.	+	.	FI_gene_label "FLNB^ENSG00000136068.15"  ; ID "GOLGA4--FLNB^FLNB^ENSG00000136068.15"  ; ccdsid "CCDS2885.1"  ; exon_id "ENSE00000000021.2"  ; exon_number 1 ; gene_id "GOLGA4--FLNB^FLNB^ENSG00000136068.15"  ; gene_name FLNB ; gene_type protein_coding ; havana_gene "OTTHUMG00000159158.1"  ; havana_transcript "OTTHUMT00000353569.1"  ; hgnc_id "HGNC:3755"  ; level 2 ; orig_coord_info "chr3,58008565,58008856,+"  ; protein_id "ENSP00000295956.5"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "GOLGA4--FLNB^ENST00000295956.9"  ; transcript_name "FLNB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GOLGA4--FLNB	HAVANA	mRNA	41754	94703	.	+	.	FI_gene_label "FLNB^ENSG00000136068.15"  ; ID "GOLGA4--FLNB^ENST00000295956.9"  ; Parent "GOLGA4--FLNB^FLNB^ENSG00000136068.15"  ; ccdsid "CCDS2885.1"  ; exon_id "ENSE00000000021.2"  ; exon_number 1 ; gene_id "GOLGA4--FLNB^FLNB^ENSG00000136068.15"  ; gene_name FLNB ; gene_type protein_coding ; havana_gene "OTTHUMG00000159158.1"  ; havana_transcript "OTTHUMT00000353569.1"  ; hgnc_id "HGNC:3755"  ; level 2 ; orig_coord_info "chr3,58008565,58008856,+"  ; protein_id "ENSP00000295956.5"  ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "GOLGA4--FLNB^ENST00000295956.9"  ; transcript_name "FLNB-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GOLGA4--FLNB	HAVANA	gene	1076	38725	.	+	.	FI_gene_label "GOLGA4^ENSG00000144674.16"  ; ID "GOLGA4--FLNB^GOLGA4^ENSG00000144674.16"  ; ccdsid "CCDS54564.1"  ; exon_id "ENSE00001776192.1"  ; exon_number 1 ; gene_id "GOLGA4--FLNB^GOLGA4^ENSG00000144674.16"  ; gene_name GOLGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130799.7"  ; havana_transcript "OTTHUMT00000342257.2"  ; hgnc_id "HGNC:4427"  ; level 2 ; orig_coord_info "chr3,37243551,37243622,+"  ; protein_id "ENSP00000349305.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "GOLGA4--FLNB^ENST00000356847.8"  ; transcript_name "GOLGA4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GOLGA4--FLNB	HAVANA	mRNA	1076	38725	.	+	.	FI_gene_label "GOLGA4^ENSG00000144674.16"  ; ID "GOLGA4--FLNB^ENST00000356847.8"  ; Parent "GOLGA4--FLNB^GOLGA4^ENSG00000144674.16"  ; ccdsid "CCDS54564.1"  ; exon_id "ENSE00001776192.1"  ; exon_number 1 ; gene_id "GOLGA4--FLNB^GOLGA4^ENSG00000144674.16"  ; gene_name GOLGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130799.7"  ; havana_transcript "OTTHUMT00000342257.2"  ; hgnc_id "HGNC:4427"  ; level 2 ; orig_coord_info "chr3,37243551,37243622,+"  ; protein_id "ENSP00000349305.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "GOLGA4--FLNB^ENST00000356847.8"  ; transcript_name "GOLGA4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GOLGA4--PPIAP16	HAVANA	gene	1076	38725	.	+	.	FI_gene_label "GOLGA4^ENSG00000144674.16"  ; ID "GOLGA4--PPIAP16^GOLGA4^ENSG00000144674.16"  ; ccdsid "CCDS54564.1"  ; exon_id "ENSE00001776192.1"  ; exon_number 1 ; gene_id "GOLGA4--PPIAP16^GOLGA4^ENSG00000144674.16"  ; gene_name GOLGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130799.7"  ; havana_transcript "OTTHUMT00000342257.2"  ; hgnc_id "HGNC:4427"  ; level 2 ; orig_coord_info "chr3,37243551,37243622,+"  ; protein_id "ENSP00000349305.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "GOLGA4--PPIAP16^ENST00000356847.8"  ; transcript_name "GOLGA4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GOLGA4--PPIAP16	HAVANA	mRNA	1076	38725	.	+	.	FI_gene_label "GOLGA4^ENSG00000144674.16"  ; ID "GOLGA4--PPIAP16^ENST00000356847.8"  ; Parent "GOLGA4--PPIAP16^GOLGA4^ENSG00000144674.16"  ; ccdsid "CCDS54564.1"  ; exon_id "ENSE00001776192.1"  ; exon_number 1 ; gene_id "GOLGA4--PPIAP16^GOLGA4^ENSG00000144674.16"  ; gene_name GOLGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130799.7"  ; havana_transcript "OTTHUMT00000342257.2"  ; hgnc_id "HGNC:4427"  ; level 2 ; orig_coord_info "chr3,37243551,37243622,+"  ; protein_id "ENSP00000349305.4"  ; tag basic appris_principal_4 CCDS ; transcript_id "GOLGA4--PPIAP16^ENST00000356847.8"  ; transcript_name "GOLGA4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NLRP2--ADAMTS13	HAVANA	gene	3577	21684	.	+	.	FI_gene_label "NLRP2^ENSG00000022556.16"  ; ID "NLRP2--ADAMTS13^NLRP2^ENSG00000022556.16"  ; ccdsid "CCDS86807.1"  ; exon_id "ENSE00003505640.1"  ; exon_number 2 ; gene_id "NLRP2--ADAMTS13^NLRP2^ENSG00000022556.16"  ; gene_name NLRP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167763.7"  ; havana_transcript "OTTHUMT00000396158.1"  ; hgnc_id "HGNC:22948"  ; level 2 ; orig_coord_info "chr19,54970016,54970295,+"  ; protein_id "ENSP00000263437.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NLRP2--ADAMTS13^ENST00000263437.10"  ; transcript_name "NLRP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
NLRP2--ADAMTS13	HAVANA	mRNA	3577	21684	.	+	.	FI_gene_label "NLRP2^ENSG00000022556.16"  ; ID "NLRP2--ADAMTS13^ENST00000263437.10"  ; Parent "NLRP2--ADAMTS13^NLRP2^ENSG00000022556.16"  ; ccdsid "CCDS86807.1"  ; exon_id "ENSE00003505640.1"  ; exon_number 2 ; gene_id "NLRP2--ADAMTS13^NLRP2^ENSG00000022556.16"  ; gene_name NLRP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167763.7"  ; havana_transcript "OTTHUMT00000396158.1"  ; hgnc_id "HGNC:22948"  ; level 2 ; orig_coord_info "chr19,54970016,54970295,+"  ; protein_id "ENSP00000263437.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NLRP2--ADAMTS13^ENST00000263437.10"  ; transcript_name "NLRP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NLRP2--ADAMTS13	HAVANA	gene	26346	51698	.	+	.	FI_gene_label "ADAMTS13^ENSG00000160323.19"  ; ID "NLRP2--ADAMTS13^ADAMTS13^ENSG00000160323.19"  ; ccdsid "CCDS6972.1"  ; exon_id "ENSE00003904238.1"  ; exon_number 1 ; gene_id "NLRP2--ADAMTS13^ADAMTS13^ENSG00000160323.19"  ; gene_name ADAMTS13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020876.4"  ; havana_transcript "OTTHUMT00000054921.1"  ; hgnc_id "HGNC:1366"  ; level 2 ; orig_coord_info "chr9,133422444,133422548,+"  ; protein_id "ENSP00000347927.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NLRP2--ADAMTS13^ENST00000355699.7"  ; transcript_name "ADAMTS13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NLRP2--ADAMTS13	HAVANA	mRNA	26346	51698	.	+	.	FI_gene_label "ADAMTS13^ENSG00000160323.19"  ; ID "NLRP2--ADAMTS13^ENST00000355699.7"  ; Parent "NLRP2--ADAMTS13^ADAMTS13^ENSG00000160323.19"  ; ccdsid "CCDS6972.1"  ; exon_id "ENSE00003904238.1"  ; exon_number 1 ; gene_id "NLRP2--ADAMTS13^ADAMTS13^ENSG00000160323.19"  ; gene_name ADAMTS13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020876.4"  ; havana_transcript "OTTHUMT00000054921.1"  ; hgnc_id "HGNC:1366"  ; level 2 ; orig_coord_info "chr9,133422444,133422548,+"  ; protein_id "ENSP00000347927.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NLRP2--ADAMTS13^ENST00000355699.7"  ; transcript_name "ADAMTS13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPHP3--ACAD11	HAVANA	gene	34363	56719	.	+	.	FI_gene_label "ACAD11^ENSG00000240303.8"  ; ID "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; ccdsid "CCDS3074.1"  ; exon_id "ENSE00001878063.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; gene_name ACAD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159780.6"  ; havana_transcript "OTTHUMT00000357279.4"  ; hgnc_id "HGNC:30211"  ; level 2 ; orig_coord_info "chr3,132659603,132659751,-"  ; protein_id "ENSP00000264990.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000264990.11"  ; transcript_name "ACAD11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPHP3--ACAD11	HAVANA	mRNA	34363	56719	.	+	.	FI_gene_label "ACAD11^ENSG00000240303.8"  ; ID "NPHP3--ACAD11^ENST00000264990.11"  ; Parent "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; ccdsid "CCDS3074.1"  ; exon_id "ENSE00001878063.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^ACAD11^ENSG00000240303.8"  ; gene_name ACAD11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159780.6"  ; havana_transcript "OTTHUMT00000357279.4"  ; hgnc_id "HGNC:30211"  ; level 2 ; orig_coord_info "chr3,132659603,132659751,-"  ; protein_id "ENSP00000264990.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000264990.11"  ; transcript_name "ACAD11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NPHP3--ACAD11	HAVANA	gene	1006	31089	.	+	.	FI_gene_label "NPHP3^ENSG00000113971.20"  ; ID "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; ccdsid "CCDS3078.1"  ; exon_id "ENSE00001810363.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; gene_name NPHP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159713.4"  ; havana_transcript "OTTHUMT00000357020.3"  ; hgnc_id "HGNC:7907"  ; level 2 ; orig_coord_info "chr3,132721963,132722355,-"  ; protein_id "ENSP00000338766.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000337331.10"  ; transcript_name "NPHP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NPHP3--ACAD11	HAVANA	mRNA	1006	31089	.	+	.	FI_gene_label "NPHP3^ENSG00000113971.20"  ; ID "NPHP3--ACAD11^ENST00000337331.10"  ; Parent "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; ccdsid "CCDS3078.1"  ; exon_id "ENSE00001810363.2"  ; exon_number 1 ; gene_id "NPHP3--ACAD11^NPHP3^ENSG00000113971.20"  ; gene_name NPHP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159713.4"  ; havana_transcript "OTTHUMT00000357020.3"  ; hgnc_id "HGNC:7907"  ; level 2 ; orig_coord_info "chr3,132721963,132722355,-"  ; protein_id "ENSP00000338766.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NPHP3--ACAD11^ENST00000337331.10"  ; transcript_name "NPHP3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PARN--AC061997.1	HAVANA	gene	2363	42399	.	+	.	FI_gene_label "PARN^ENSG00000140694.17"  ; ID "PARN--AC061997.1^PARN^ENSG00000140694.17"  ; ccdsid "CCDS45420.1"  ; exon_id "ENSE00003684352.1"  ; exon_number 4 ; gene_id "PARN--AC061997.1^PARN^ENSG00000140694.17"  ; gene_name PARN ; gene_type protein_coding ; havana_gene "OTTHUMG00000173199.14"  ; havana_transcript "OTTHUMT00000422385.2"  ; hgnc_id "HGNC:8609"  ; level 2 ; orig_coord_info "chr16,14627269,14627330,-"  ; protein_id "ENSP00000345456.7"  ; tag basic CCDS ; transcript_id "PARN--AC061997.1^ENST00000341484.11"  ; transcript_name "PARN-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PARN--AC061997.1	HAVANA	mRNA	2363	42399	.	+	.	FI_gene_label "PARN^ENSG00000140694.17"  ; ID "PARN--AC061997.1^ENST00000341484.11"  ; Parent "PARN--AC061997.1^PARN^ENSG00000140694.17"  ; ccdsid "CCDS45420.1"  ; exon_id "ENSE00003684352.1"  ; exon_number 4 ; gene_id "PARN--AC061997.1^PARN^ENSG00000140694.17"  ; gene_name PARN ; gene_type protein_coding ; havana_gene "OTTHUMG00000173199.14"  ; havana_transcript "OTTHUMT00000422385.2"  ; hgnc_id "HGNC:8609"  ; level 2 ; orig_coord_info "chr16,14627269,14627330,-"  ; protein_id "ENSP00000345456.7"  ; tag basic CCDS ; transcript_id "PARN--AC061997.1^ENST00000341484.11"  ; transcript_name "PARN-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
PARN--AC104042.1	HAVANA	gene	2363	42399	.	+	.	FI_gene_label "PARN^ENSG00000140694.17"  ; ID "PARN--AC104042.1^PARN^ENSG00000140694.17"  ; ccdsid "CCDS45420.1"  ; exon_id "ENSE00003684352.1"  ; exon_number 4 ; gene_id "PARN--AC104042.1^PARN^ENSG00000140694.17"  ; gene_name PARN ; gene_type protein_coding ; havana_gene "OTTHUMG00000173199.14"  ; havana_transcript "OTTHUMT00000422385.2"  ; hgnc_id "HGNC:8609"  ; level 2 ; orig_coord_info "chr16,14627269,14627330,-"  ; protein_id "ENSP00000345456.7"  ; tag basic CCDS ; transcript_id "PARN--AC104042.1^ENST00000341484.11"  ; transcript_name "PARN-201"  ; transcript_support_level 2 ; transcript_type protein_coding
PARN--AC104042.1	HAVANA	mRNA	2363	42399	.	+	.	FI_gene_label "PARN^ENSG00000140694.17"  ; ID "PARN--AC104042.1^ENST00000341484.11"  ; Parent "PARN--AC104042.1^PARN^ENSG00000140694.17"  ; ccdsid "CCDS45420.1"  ; exon_id "ENSE00003684352.1"  ; exon_number 4 ; gene_id "PARN--AC104042.1^PARN^ENSG00000140694.17"  ; gene_name PARN ; gene_type protein_coding ; havana_gene "OTTHUMG00000173199.14"  ; havana_transcript "OTTHUMT00000422385.2"  ; hgnc_id "HGNC:8609"  ; level 2 ; orig_coord_info "chr16,14627269,14627330,-"  ; protein_id "ENSP00000345456.7"  ; tag basic CCDS ; transcript_id "PARN--AC104042.1^ENST00000341484.11"  ; transcript_name "PARN-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
SH3BGRL2--BX890604.1	HAVANA	gene	1001	8603	.	+	.	FI_gene_label "SH3BGRL2^ENSG00000198478.8"  ; ID "SH3BGRL2--BX890604.1^SH3BGRL2^ENSG00000198478.8"  ; ccdsid "CCDS4991.1"  ; exon_id "ENSE00001451030.4"  ; exon_number 1 ; gene_id "SH3BGRL2--BX890604.1^SH3BGRL2^ENSG00000198478.8"  ; gene_name SH3BGRL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015081.3"  ; havana_transcript "OTTHUMT00000041309.3"  ; hgnc_id "HGNC:15567"  ; level 2 ; orig_coord_info "chr6,79631462,79631506,+"  ; protein_id "ENSP00000358853.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SH3BGRL2--BX890604.1^ENST00000369838.6"  ; transcript_name "SH3BGRL2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SH3BGRL2--BX890604.1	HAVANA	mRNA	1001	8603	.	+	.	FI_gene_label "SH3BGRL2^ENSG00000198478.8"  ; ID "SH3BGRL2--BX890604.1^ENST00000369838.6"  ; Parent "SH3BGRL2--BX890604.1^SH3BGRL2^ENSG00000198478.8"  ; ccdsid "CCDS4991.1"  ; exon_id "ENSE00001451030.4"  ; exon_number 1 ; gene_id "SH3BGRL2--BX890604.1^SH3BGRL2^ENSG00000198478.8"  ; gene_name SH3BGRL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015081.3"  ; havana_transcript "OTTHUMT00000041309.3"  ; hgnc_id "HGNC:15567"  ; level 2 ; orig_coord_info "chr6,79631462,79631506,+"  ; protein_id "ENSP00000358853.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SH3BGRL2--BX890604.1^ENST00000369838.6"  ; transcript_name "SH3BGRL2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--FAM157A^ENST00000326270.13"  ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--LINC01347	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--LINC01347^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--LINC01347^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--LINC01347^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--LINC01347	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--LINC01347^ENST00000326270.13"  ; Parent "TLK2--LINC01347^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--LINC01347^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--LINC01347^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: 
UBE2N--MRPL42	HAVANA	gene	1001	9541	.	+	.	FI_gene_label "UBE2N^ENSG00000177889.10"  ; ID "UBE2N--MRPL42^UBE2N^ENSG00000177889.10"  ; ccdsid "CCDS31875.1"  ; exon_id "ENSE00001277525.4"  ; exon_number 1 ; gene_id "UBE2N--MRPL42^UBE2N^ENSG00000177889.10"  ; gene_name UBE2N ; gene_type protein_coding ; havana_gene "OTTHUMG00000170156.5"  ; havana_transcript "OTTHUMT00000407710.3"  ; hgnc_id "HGNC:12492"  ; level 2 ; orig_coord_info "chr12,93441855,93441884,-"  ; protein_id "ENSP00000316176.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "UBE2N--MRPL42^ENST00000318066.7"  ; transcript_name "UBE2N-201"  ; transcript_support_level 1 ; transcript_type protein_coding
UBE2N--MRPL42	HAVANA	mRNA	1001	9541	.	+	.	FI_gene_label "UBE2N^ENSG00000177889.10"  ; ID "UBE2N--MRPL42^ENST00000318066.7"  ; Parent "UBE2N--MRPL42^UBE2N^ENSG00000177889.10"  ; ccdsid "CCDS31875.1"  ; exon_id "ENSE00001277525.4"  ; exon_number 1 ; gene_id "UBE2N--MRPL42^UBE2N^ENSG00000177889.10"  ; gene_name UBE2N ; gene_type protein_coding ; havana_gene "OTTHUMG00000170156.5"  ; havana_transcript "OTTHUMT00000407710.3"  ; hgnc_id "HGNC:12492"  ; level 2 ; orig_coord_info "chr12,93441855,93441884,-"  ; protein_id "ENSP00000316176.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "UBE2N--MRPL42^ENST00000318066.7"  ; transcript_name "UBE2N-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
UBE2N--MRPL42	HAVANA	gene	12557	21905	.	+	.	FI_gene_label "MRPL42^ENSG00000198015.14"  ; ID "UBE2N--MRPL42^MRPL42^ENSG00000198015.14"  ; exon_id "ENSE00003552476.1"  ; exon_number 2 ; gene_id "UBE2N--MRPL42^MRPL42^ENSG00000198015.14"  ; gene_name MRPL42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170157.4"  ; havana_transcript "OTTHUMT00000407720.1"  ; hgnc_id "HGNC:14493"  ; level 2 ; orig_coord_info "chr12,93469286,93469355,+"  ; protein_id "ENSP00000351506.3"  ; transcript_id "UBE2N--MRPL42^ENST00000358678.7"  ; transcript_name "MRPL42-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
UBE2N--MRPL42	HAVANA	mRNA	12557	21905	.	+	.	FI_gene_label "MRPL42^ENSG00000198015.14"  ; ID "UBE2N--MRPL42^ENST00000358678.7"  ; Parent "UBE2N--MRPL42^MRPL42^ENSG00000198015.14"  ; exon_id "ENSE00003552476.1"  ; exon_number 2 ; gene_id "UBE2N--MRPL42^MRPL42^ENSG00000198015.14"  ; gene_name MRPL42 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170157.4"  ; havana_transcript "OTTHUMT00000407720.1"  ; hgnc_id "HGNC:14493"  ; level 2 ; orig_coord_info "chr12,93469286,93469355,+"  ; protein_id "ENSP00000351506.3"  ; transcript_id "UBE2N--MRPL42^ENST00000358678.7"  ; transcript_name "MRPL42-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
AC092807.3--DDAH1	HAVANA	gene	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1	HAVANA	RNA	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^ENST00000467530.5"  ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
GOLGA4--PPIAP16	HAVANA	gene	41732	42218	.	+	.	FI_gene_label "PPIAP16^ENSG00000213509.4"  ; ID "GOLGA4--PPIAP16^PPIAP16^ENSG00000213509.4"  ; exon_id "ENSE00001887226.1"  ; exon_number 1 ; gene_id "GOLGA4--PPIAP16^PPIAP16^ENSG00000213509.4"  ; gene_name PPIAP16 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000158640.1"  ; havana_transcript "OTTHUMT00000351603.1"  ; hgnc_id "HGNC:9269"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr3,57941818,57942304,+"  ; tag pseudo_consens basic ; transcript_id "GOLGA4--PPIAP16^ENST00000462517.1"  ; transcript_name "PPIAP16-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
GOLGA4--PPIAP16	HAVANA	RNA	41732	42218	.	+	.	FI_gene_label "PPIAP16^ENSG00000213509.4"  ; ID "GOLGA4--PPIAP16^ENST00000462517.1"  ; Parent "GOLGA4--PPIAP16^PPIAP16^ENSG00000213509.4"  ; exon_id "ENSE00001887226.1"  ; exon_number 1 ; gene_id "GOLGA4--PPIAP16^PPIAP16^ENSG00000213509.4"  ; gene_name PPIAP16 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000158640.1"  ; havana_transcript "OTTHUMT00000351603.1"  ; hgnc_id "HGNC:9269"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr3,57941818,57942304,+"  ; tag pseudo_consens basic ; transcript_id "GOLGA4--PPIAP16^ENST00000462517.1"  ; transcript_name "PPIAP16-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
PARN--AC061997.1	ENSEMBL	gene	46305	46400	.	+	.	FI_gene_label "AC061997.1^ENSG00000251838.1"  ; ID "PARN--AC061997.1^AC061997.1^ENSG00000251838.1"  ; exon_id "ENSE00002088306.1"  ; exon_number 1 ; gene_id "PARN--AC061997.1^AC061997.1^ENSG00000251838.1"  ; gene_name "AC061997.1"  ; gene_type snoRNA ; level 3 ; orig_coord_info "chr11,37702125,37702220,-"  ; tag basic ; transcript_id "PARN--AC061997.1^ENST00000516029.1"  ; transcript_name "AC061997.1-201"  ; transcript_support_level NA ; transcript_type snoRNA
PARN--AC061997.1	ENSEMBL	RNA	46305	46400	.	+	.	FI_gene_label "AC061997.1^ENSG00000251838.1"  ; ID "PARN--AC061997.1^ENST00000516029.1"  ; Parent "PARN--AC061997.1^AC061997.1^ENSG00000251838.1"  ; exon_id "ENSE00002088306.1"  ; exon_number 1 ; gene_id "PARN--AC061997.1^AC061997.1^ENSG00000251838.1"  ; gene_name "AC061997.1"  ; gene_type snoRNA ; level 3 ; orig_coord_info "chr11,37702125,37702220,-"  ; tag basic ; transcript_id "PARN--AC061997.1^ENST00000516029.1"  ; transcript_name "AC061997.1-201"  ; transcript_support_level NA ; transcript_type snoRNA
L1 and L2 created: 
PARN--AC104042.1	HAVANA	gene	46305	47855	.	+	.	FI_gene_label "AC104042.1^ENSG00000254498.1"  ; ID "PARN--AC104042.1^AC104042.1^ENSG00000254498.1"  ; exon_id "ENSE00002168998.1"  ; exon_number 1 ; gene_id "PARN--AC104042.1^AC104042.1^ENSG00000254498.1"  ; gene_name "AC104042.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166332.1"  ; havana_transcript "OTTHUMT00000389187.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr11,36696317,36697090,+"  ; tag pseudo_consens basic ; transcript_id "PARN--AC104042.1^ENST00000524806.1"  ; transcript_name "AC104042.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
PARN--AC104042.1	HAVANA	RNA	46305	47855	.	+	.	FI_gene_label "AC104042.1^ENSG00000254498.1"  ; ID "PARN--AC104042.1^ENST00000524806.1"  ; Parent "PARN--AC104042.1^AC104042.1^ENSG00000254498.1"  ; exon_id "ENSE00002168998.1"  ; exon_number 1 ; gene_id "PARN--AC104042.1^AC104042.1^ENSG00000254498.1"  ; gene_name "AC104042.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166332.1"  ; havana_transcript "OTTHUMT00000389187.1"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr11,36696317,36697090,+"  ; tag pseudo_consens basic ; transcript_id "PARN--AC104042.1^ENST00000524806.1"  ; transcript_name "AC104042.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
SH3BGRL2--BX890604.1	HAVANA	gene	11604	14721	.	+	.	FI_gene_label "BX890604.1^ENSG00000285756.2"  ; ID "SH3BGRL2--BX890604.1^BX890604.1^ENSG00000285756.2"  ; exon_id "ENSE00001797454.1"  ; exon_number 1 ; gene_id "SH3BGRL2--BX890604.1^BX890604.1^ENSG00000285756.2"  ; gene_name "BX890604.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000067412.22"  ; havana_transcript "OTTHUMT00000144380.2"  ; level 2 ; orig_coord_info "chrX,3937652,3937855,-"  ; tag not_best_in_genome_evidence ; transcript_id "SH3BGRL2--BX890604.1^ENST00000381105.2"  ; transcript_name "BX890604.1-218"  ; transcript_support_level 5 ; transcript_type lncRNA
SH3BGRL2--BX890604.1	HAVANA	RNA	11604	14721	.	+	.	FI_gene_label "BX890604.1^ENSG00000285756.2"  ; ID "SH3BGRL2--BX890604.1^ENST00000381105.2"  ; Parent "SH3BGRL2--BX890604.1^BX890604.1^ENSG00000285756.2"  ; exon_id "ENSE00001797454.1"  ; exon_number 1 ; gene_id "SH3BGRL2--BX890604.1^BX890604.1^ENSG00000285756.2"  ; gene_name "BX890604.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000067412.22"  ; havana_transcript "OTTHUMT00000144380.2"  ; level 2 ; orig_coord_info "chrX,3937652,3937855,-"  ; tag not_best_in_genome_evidence ; transcript_id "SH3BGRL2--BX890604.1^ENST00000381105.2"  ; transcript_name "BX890604.1-218"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2--FAM157A	HAVANA	gene	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A	HAVANA	RNA	40046	44186	.	+	.	FI_gene_label "FAM157A^ENSG00000236438.7"  ; ID "TLK2--FAM157A^ENST00000437428.3"  ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; exon_id "ENSE00002579345.3"  ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7"  ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3"  ; havana_transcript "OTTHUMT00000488453.1"  ; hgnc_id "HGNC:34079"  ; level 2 ; orig_coord_info "chr3,198153287,198153409,+"  ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3"  ; transcript_name "FAM157A-201"  ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created: 
TLK2--LINC01347	HAVANA	gene	41405	47393	.	+	.	FI_gene_label "LINC01347^ENSG00000214837.8"  ; ID "TLK2--LINC01347^LINC01347^ENSG00000214837.8"  ; exon_id "ENSE00002389344.1"  ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8"  ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5"  ; havana_transcript "OTTHUMT00000481524.1"  ; hgnc_id "HGNC:50566"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr1,243097190,243097299,-"  ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2"  ; transcript_name "LINC01347-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TLK2--LINC01347	HAVANA	RNA	41405	47393	.	+	.	FI_gene_label "LINC01347^ENSG00000214837.8"  ; ID "TLK2--LINC01347^ENST00000417964.2"  ; Parent "TLK2--LINC01347^LINC01347^ENSG00000214837.8"  ; exon_id "ENSE00002389344.1"  ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8"  ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5"  ; havana_transcript "OTTHUMT00000481524.1"  ; hgnc_id "HGNC:50566"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr1,243097190,243097299,-"  ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2"  ; transcript_name "LINC01347-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
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
347 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 1 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 ------------------------------
759 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------

------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------

------------------------ Check12: all level1 locations -------------------------
We fixed 22 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

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


GFF3 file parsed