.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/ea762338ee7504ec50af7859f37321/.command.log
Size: 48.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/de56d1e20b34191d213e4954819b22/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/ea762338ee7504ec50af7859f37321/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/ea762338ee7504ec50af7859f37321/.command.run
==> STAGING COMPLETE (3 inputs)

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

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 3494
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3494
=> 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:3494
  => 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: 
AC233699.1--TBC1D3	HAVANA	gene	12976	22908	.	+	.	FI_gene_label "TBC1D3^ENSG00000274611.3"  ; ID "AC233699.1--TBC1D3^TBC1D3^ENSG00000274611.3"  ; ccdsid "CCDS45658.1"  ; exon_id "ENSE00003731868.1"  ; exon_number 2 ; gene_id "AC233699.1--TBC1D3^TBC1D3^ENSG00000274611.3"  ; gene_name TBC1D3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188487.1"  ; havana_transcript "OTTHUMT00000477408.1"  ; hgnc_id "HGNC:19031"  ; level 2 ; orig_coord_info "chr17,38190958,38191029,-"  ; protein_id "ENSP00000478683.1"  ; tag not_best_in_genome_evidence basic appris_principal_1 CCDS ; transcript_id "AC233699.1--TBC1D3^ENST00000620215.2"  ; transcript_name "TBC1D3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC233699.1--TBC1D3	HAVANA	mRNA	12976	22908	.	+	.	FI_gene_label "TBC1D3^ENSG00000274611.3"  ; ID "AC233699.1--TBC1D3^ENST00000620215.2"  ; Parent "AC233699.1--TBC1D3^TBC1D3^ENSG00000274611.3"  ; ccdsid "CCDS45658.1"  ; exon_id "ENSE00003731868.1"  ; exon_number 2 ; gene_id "AC233699.1--TBC1D3^TBC1D3^ENSG00000274611.3"  ; gene_name TBC1D3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000188487.1"  ; havana_transcript "OTTHUMT00000477408.1"  ; hgnc_id "HGNC:19031"  ; level 2 ; orig_coord_info "chr17,38190958,38191029,-"  ; protein_id "ENSP00000478683.1"  ; tag not_best_in_genome_evidence basic appris_principal_1 CCDS ; transcript_id "AC233699.1--TBC1D3^ENST00000620215.2"  ; transcript_name "TBC1D3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ADAP1--SNX8	HAVANA	gene	22096	38905	.	+	.	FI_gene_label "SNX8^ENSG00000106266.11"  ; ID "ADAP1--SNX8^SNX8^ENSG00000106266.11"  ; ccdsid "CCDS5331.1"  ; exon_id "ENSE00000831511.2"  ; exon_number 1 ; gene_id "ADAP1--SNX8^SNX8^ENSG00000106266.11"  ; gene_name SNX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151512.5"  ; havana_transcript "OTTHUMT00000322949.3"  ; hgnc_id "HGNC:14972"  ; level 2 ; orig_coord_info "chr7,2314328,2314421,-"  ; protein_id "ENSP00000222990.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAP1--SNX8^ENST00000222990.8"  ; transcript_name "SNX8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ADAP1--SNX8	HAVANA	mRNA	22096	38905	.	+	.	FI_gene_label "SNX8^ENSG00000106266.11"  ; ID "ADAP1--SNX8^ENST00000222990.8"  ; Parent "ADAP1--SNX8^SNX8^ENSG00000106266.11"  ; ccdsid "CCDS5331.1"  ; exon_id "ENSE00000831511.2"  ; exon_number 1 ; gene_id "ADAP1--SNX8^SNX8^ENSG00000106266.11"  ; gene_name SNX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151512.5"  ; havana_transcript "OTTHUMT00000322949.3"  ; hgnc_id "HGNC:14972"  ; level 2 ; orig_coord_info "chr7,2314328,2314421,-"  ; protein_id "ENSP00000222990.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAP1--SNX8^ENST00000222990.8"  ; transcript_name "SNX8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ADAP1--SNX8	HAVANA	gene	1728	16832	.	+	.	FI_gene_label "ADAP1^ENSG00000105963.15"  ; ID "ADAP1--SNX8^ADAP1^ENSG00000105963.15"  ; ccdsid "CCDS5318.1"  ; exon_id "ENSE00003850789.1"  ; exon_number 1 ; gene_id "ADAP1--SNX8^ADAP1^ENSG00000105963.15"  ; gene_name ADAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023380.16"  ; havana_transcript "OTTHUMT00000059701.3"  ; hgnc_id "HGNC:16486"  ; level 2 ; orig_coord_info "chr7,954396,954477,-"  ; protein_id "ENSP00000265846.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAP1--SNX8^ENST00000265846.10"  ; transcript_name "ADAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ADAP1--SNX8	HAVANA	mRNA	1728	16832	.	+	.	FI_gene_label "ADAP1^ENSG00000105963.15"  ; ID "ADAP1--SNX8^ENST00000265846.10"  ; Parent "ADAP1--SNX8^ADAP1^ENSG00000105963.15"  ; ccdsid "CCDS5318.1"  ; exon_id "ENSE00003850789.1"  ; exon_number 1 ; gene_id "ADAP1--SNX8^ADAP1^ENSG00000105963.15"  ; gene_name ADAP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023380.16"  ; havana_transcript "OTTHUMT00000059701.3"  ; hgnc_id "HGNC:16486"  ; level 2 ; orig_coord_info "chr7,954396,954477,-"  ; protein_id "ENSP00000265846.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAP1--SNX8^ENST00000265846.10"  ; transcript_name "ADAP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COL1A1--SLC45A4	HAVANA	gene	25435	34927	.	+	.	FI_gene_label "SLC45A4^ENSG00000022567.10"  ; ID "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; ccdsid "CCDS34948.1"  ; exon_id "ENSE00001475008.1"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; gene_name SLC45A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164393.4"  ; havana_transcript "OTTHUMT00000378571.3"  ; hgnc_id "HGNC:29196"  ; level 2 ; orig_coord_info "chr8,141228179,141228266,-"  ; protein_id "ENSP00000024061.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000024061.7"  ; transcript_name "SLC45A4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COL1A1--SLC45A4	HAVANA	mRNA	25435	34927	.	+	.	FI_gene_label "SLC45A4^ENSG00000022567.10"  ; ID "COL1A1--SLC45A4^ENST00000024061.7"  ; Parent "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; ccdsid "CCDS34948.1"  ; exon_id "ENSE00001475008.1"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; gene_name SLC45A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164393.4"  ; havana_transcript "OTTHUMT00000378571.3"  ; hgnc_id "HGNC:29196"  ; level 2 ; orig_coord_info "chr8,141228179,141228266,-"  ; protein_id "ENSP00000024061.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000024061.7"  ; transcript_name "SLC45A4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COL1A1--SLC45A4	HAVANA	gene	1002	18313	.	+	.	FI_gene_label "COL1A1^ENSG00000108821.14"  ; ID "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; ccdsid "CCDS11561.1"  ; exon_id "ENSE00003500023.2"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; gene_name COL1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148674.9"  ; havana_transcript "OTTHUMT00000309036.3"  ; hgnc_id "HGNC:2197"  ; level 2 ; orig_coord_info "chr17,50201411,50201513,-"  ; protein_id "ENSP00000225964.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000225964.10"  ; transcript_name "COL1A1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COL1A1--SLC45A4	HAVANA	mRNA	1002	18313	.	+	.	FI_gene_label "COL1A1^ENSG00000108821.14"  ; ID "COL1A1--SLC45A4^ENST00000225964.10"  ; Parent "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; ccdsid "CCDS11561.1"  ; exon_id "ENSE00003500023.2"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; gene_name COL1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148674.9"  ; havana_transcript "OTTHUMT00000309036.3"  ; hgnc_id "HGNC:2197"  ; level 2 ; orig_coord_info "chr17,50201411,50201513,-"  ; protein_id "ENSP00000225964.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000225964.10"  ; transcript_name "COL1A1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COX19--SNX8	HAVANA	gene	22296	39105	.	+	.	FI_gene_label "SNX8^ENSG00000106266.11"  ; ID "COX19--SNX8^SNX8^ENSG00000106266.11"  ; ccdsid "CCDS5331.1"  ; exon_id "ENSE00000831511.2"  ; exon_number 1 ; gene_id "COX19--SNX8^SNX8^ENSG00000106266.11"  ; gene_name SNX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151512.5"  ; havana_transcript "OTTHUMT00000322949.3"  ; hgnc_id "HGNC:14972"  ; level 2 ; orig_coord_info "chr7,2314328,2314421,-"  ; protein_id "ENSP00000222990.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COX19--SNX8^ENST00000222990.8"  ; transcript_name "SNX8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COX19--SNX8	HAVANA	mRNA	22296	39105	.	+	.	FI_gene_label "SNX8^ENSG00000106266.11"  ; ID "COX19--SNX8^ENST00000222990.8"  ; Parent "COX19--SNX8^SNX8^ENSG00000106266.11"  ; ccdsid "CCDS5331.1"  ; exon_id "ENSE00000831511.2"  ; exon_number 1 ; gene_id "COX19--SNX8^SNX8^ENSG00000106266.11"  ; gene_name SNX8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151512.5"  ; havana_transcript "OTTHUMT00000322949.3"  ; hgnc_id "HGNC:14972"  ; level 2 ; orig_coord_info "chr7,2314328,2314421,-"  ; protein_id "ENSP00000222990.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COX19--SNX8^ENST00000222990.8"  ; transcript_name "SNX8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COX19--SNX8	HAVANA	gene	1001	8840	.	+	.	FI_gene_label "COX19^ENSG00000240230.6"  ; ID "COX19--SNX8^COX19^ENSG00000240230.6"  ; ccdsid "CCDS34582.1"  ; exon_id "ENSE00003485938.1"  ; exon_number 1 ; gene_id "COX19--SNX8^COX19^ENSG00000240230.6"  ; gene_name COX19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151476.2"  ; havana_transcript "OTTHUMT00000322812.2"  ; hgnc_id "HGNC:28074"  ; level 2 ; orig_coord_info "chr7,975428,975509,-"  ; protein_id "ENSP00000342015.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COX19--SNX8^ENST00000344111.4"  ; transcript_name "COX19-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COX19--SNX8	HAVANA	mRNA	1001	8840	.	+	.	FI_gene_label "COX19^ENSG00000240230.6"  ; ID "COX19--SNX8^ENST00000344111.4"  ; Parent "COX19--SNX8^COX19^ENSG00000240230.6"  ; ccdsid "CCDS34582.1"  ; exon_id "ENSE00003485938.1"  ; exon_number 1 ; gene_id "COX19--SNX8^COX19^ENSG00000240230.6"  ; gene_name COX19 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151476.2"  ; havana_transcript "OTTHUMT00000322812.2"  ; hgnc_id "HGNC:28074"  ; level 2 ; orig_coord_info "chr7,975428,975509,-"  ; protein_id "ENSP00000342015.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COX19--SNX8^ENST00000344111.4"  ; transcript_name "COX19-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAAF5--AC009412.1	HAVANA	gene	1001	22349	.	+	.	FI_gene_label "DNAAF5^ENSG00000164818.16"  ; ID "DNAAF5--AC009412.1^DNAAF5^ENSG00000164818.16"  ; ccdsid "CCDS34580.1"  ; exon_id "ENSE00001492828.2"  ; exon_number 1 ; gene_id "DNAAF5--AC009412.1^DNAAF5^ENSG00000164818.16"  ; gene_name DNAAF5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151416.4"  ; havana_transcript "OTTHUMT00000322542.2"  ; hgnc_id "HGNC:26013"  ; level 2 ; orig_coord_info "chr7,726721,727315,+"  ; protein_id "ENSP00000297440.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAAF5--AC009412.1^ENST00000297440.11"  ; transcript_name "DNAAF5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DNAAF5--AC009412.1	HAVANA	mRNA	1001	22349	.	+	.	FI_gene_label "DNAAF5^ENSG00000164818.16"  ; ID "DNAAF5--AC009412.1^ENST00000297440.11"  ; Parent "DNAAF5--AC009412.1^DNAAF5^ENSG00000164818.16"  ; ccdsid "CCDS34580.1"  ; exon_id "ENSE00001492828.2"  ; exon_number 1 ; gene_id "DNAAF5--AC009412.1^DNAAF5^ENSG00000164818.16"  ; gene_name DNAAF5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151416.4"  ; havana_transcript "OTTHUMT00000322542.2"  ; hgnc_id "HGNC:26013"  ; level 2 ; orig_coord_info "chr7,726721,727315,+"  ; protein_id "ENSP00000297440.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAAF5--AC009412.1^ENST00000297440.11"  ; transcript_name "DNAAF5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAAF5--AC009412.1	HAVANA	gene	25350	26556	.	+	.	FI_gene_label "AC009412.1^ENSG00000286075.2"  ; ID "DNAAF5--AC009412.1^AC009412.1^ENSG00000286075.2"  ; exon_id "ENSE00002731125.1"  ; exon_number 1 ; gene_id "DNAAF5--AC009412.1^AC009412.1^ENSG00000286075.2"  ; gene_name "AC009412.1"  ; gene_type protein_coding ; havana_gene "OTTHUMG00000122091.6"  ; havana_transcript "OTTHUMT00000448409.2"  ; level 2 ; orig_coord_info "chr7,6348573,6348758,-"  ; protein_id "ENSP00000464009.1"  ; tag basic appris_principal_1 ; transcript_id "DNAAF5--AC009412.1^ENST00000578372.1"  ; transcript_name "AC009412.1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DNAAF5--AC009412.1	HAVANA	mRNA	25350	26556	.	+	.	FI_gene_label "AC009412.1^ENSG00000286075.2"  ; ID "DNAAF5--AC009412.1^ENST00000578372.1"  ; Parent "DNAAF5--AC009412.1^AC009412.1^ENSG00000286075.2"  ; exon_id "ENSE00002731125.1"  ; exon_number 1 ; gene_id "DNAAF5--AC009412.1^AC009412.1^ENSG00000286075.2"  ; gene_name "AC009412.1"  ; gene_type protein_coding ; havana_gene "OTTHUMG00000122091.6"  ; havana_transcript "OTTHUMT00000448409.2"  ; level 2 ; orig_coord_info "chr7,6348573,6348758,-"  ; protein_id "ENSP00000464009.1"  ; tag basic appris_principal_1 ; transcript_id "DNAAF5--AC009412.1^ENST00000578372.1"  ; transcript_name "AC009412.1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAAF5--FAM220A	HAVANA	gene	1001	22349	.	+	.	FI_gene_label "DNAAF5^ENSG00000164818.16"  ; ID "DNAAF5--FAM220A^DNAAF5^ENSG00000164818.16"  ; ccdsid "CCDS34580.1"  ; exon_id "ENSE00001492828.2"  ; exon_number 1 ; gene_id "DNAAF5--FAM220A^DNAAF5^ENSG00000164818.16"  ; gene_name DNAAF5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151416.4"  ; havana_transcript "OTTHUMT00000322542.2"  ; hgnc_id "HGNC:26013"  ; level 2 ; orig_coord_info "chr7,726721,727315,+"  ; protein_id "ENSP00000297440.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAAF5--FAM220A^ENST00000297440.11"  ; transcript_name "DNAAF5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DNAAF5--FAM220A	HAVANA	mRNA	1001	22349	.	+	.	FI_gene_label "DNAAF5^ENSG00000164818.16"  ; ID "DNAAF5--FAM220A^ENST00000297440.11"  ; Parent "DNAAF5--FAM220A^DNAAF5^ENSG00000164818.16"  ; ccdsid "CCDS34580.1"  ; exon_id "ENSE00001492828.2"  ; exon_number 1 ; gene_id "DNAAF5--FAM220A^DNAAF5^ENSG00000164818.16"  ; gene_name DNAAF5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151416.4"  ; havana_transcript "OTTHUMT00000322542.2"  ; hgnc_id "HGNC:26013"  ; level 2 ; orig_coord_info "chr7,726721,727315,+"  ; protein_id "ENSP00000297440.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAAF5--FAM220A^ENST00000297440.11"  ; transcript_name "DNAAF5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAAF5--FAM220A	HAVANA	gene	25364	30742	.	+	.	FI_gene_label "FAM220A^ENSG00000178397.13"  ; ID "DNAAF5--FAM220A^FAM220A^ENSG00000178397.13"  ; ccdsid "CCDS34599.1"  ; exon_id "ENSE00001404127.4"  ; exon_number 2 ; gene_id "DNAAF5--FAM220A^FAM220A^ENSG00000178397.13"  ; gene_name FAM220A ; gene_type protein_coding ; havana_gene "OTTHUMG00000193524.2"  ; havana_transcript "OTTHUMT00000242853.3"  ; hgnc_id "HGNC:22422"  ; level 2 ; orig_coord_info "chr7,6330378,6331154,-"  ; protein_id "ENSP00000317289.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAAF5--FAM220A^ENST00000313324.9"  ; transcript_name "FAM220A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DNAAF5--FAM220A	HAVANA	mRNA	25364	30742	.	+	.	FI_gene_label "FAM220A^ENSG00000178397.13"  ; ID "DNAAF5--FAM220A^ENST00000313324.9"  ; Parent "DNAAF5--FAM220A^FAM220A^ENSG00000178397.13"  ; ccdsid "CCDS34599.1"  ; exon_id "ENSE00001404127.4"  ; exon_number 2 ; gene_id "DNAAF5--FAM220A^FAM220A^ENSG00000178397.13"  ; gene_name FAM220A ; gene_type protein_coding ; havana_gene "OTTHUMG00000193524.2"  ; havana_transcript "OTTHUMT00000242853.3"  ; hgnc_id "HGNC:22422"  ; level 2 ; orig_coord_info "chr7,6330378,6331154,-"  ; protein_id "ENSP00000317289.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAAF5--FAM220A^ENST00000313324.9"  ; transcript_name "FAM220A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GOLGA6L10--GOLGA2P6	HAVANA	gene	1001	9781	.	+	.	FI_gene_label "GOLGA6L10^ENSG00000278662.5"  ; ID "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5"  ; ccdsid "CCDS45325.2"  ; exon_id "ENSE00002255247.2"  ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5"  ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4"  ; havana_transcript "OTTHUMT00000419277.4"  ; hgnc_id "HGNC:37228"  ; level 2 ; orig_coord_info "chr15,82349292,82349375,-"  ; protein_id "ENSP00000479362.1"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000610657.2"  ; transcript_name "GOLGA6L10-207"  ; transcript_support_level 2 ; transcript_type protein_coding
GOLGA6L10--GOLGA2P6	HAVANA	mRNA	1001	9781	.	+	.	FI_gene_label "GOLGA6L10^ENSG00000278662.5"  ; ID "GOLGA6L10--GOLGA2P6^ENST00000610657.2"  ; Parent "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5"  ; ccdsid "CCDS45325.2"  ; exon_id "ENSE00002255247.2"  ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5"  ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4"  ; havana_transcript "OTTHUMT00000419277.4"  ; hgnc_id "HGNC:37228"  ; level 2 ; orig_coord_info "chr15,82349292,82349375,-"  ; protein_id "ENSP00000479362.1"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000610657.2"  ; transcript_name "GOLGA6L10-207"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
INTS1--GLCCI1	HAVANA	gene	34419	50771	.	+	.	FI_gene_label "GLCCI1^ENSG00000106415.13"  ; ID "INTS1--GLCCI1^GLCCI1^ENSG00000106415.13"  ; ccdsid "CCDS34601.1"  ; exon_id "ENSE00001901274.2"  ; exon_number 1 ; gene_id "INTS1--GLCCI1^GLCCI1^ENSG00000106415.13"  ; gene_name GLCCI1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151984.5"  ; havana_transcript "OTTHUMT00000324672.2"  ; hgnc_id "HGNC:18713"  ; level 2 ; orig_coord_info "chr7,7969351,7969807,+"  ; protein_id "ENSP00000223145.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "INTS1--GLCCI1^ENST00000223145.10"  ; transcript_name "GLCCI1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
INTS1--GLCCI1	HAVANA	mRNA	34419	50771	.	+	.	FI_gene_label "GLCCI1^ENSG00000106415.13"  ; ID "INTS1--GLCCI1^ENST00000223145.10"  ; Parent "INTS1--GLCCI1^GLCCI1^ENSG00000106415.13"  ; ccdsid "CCDS34601.1"  ; exon_id "ENSE00001901274.2"  ; exon_number 1 ; gene_id "INTS1--GLCCI1^GLCCI1^ENSG00000106415.13"  ; gene_name GLCCI1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151984.5"  ; havana_transcript "OTTHUMT00000324672.2"  ; hgnc_id "HGNC:18713"  ; level 2 ; orig_coord_info "chr7,7969351,7969807,+"  ; protein_id "ENSP00000223145.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "INTS1--GLCCI1^ENST00000223145.10"  ; transcript_name "GLCCI1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
INTS1--GLCCI1	HAVANA	gene	1001	31418	.	+	.	FI_gene_label "INTS1^ENSG00000164880.16"  ; ID "INTS1--GLCCI1^INTS1^ENSG00000164880.16"  ; ccdsid "CCDS47526.1"  ; exon_id "ENSE00003571544.1"  ; exon_number 2 ; gene_id "INTS1--GLCCI1^INTS1^ENSG00000164880.16"  ; gene_name INTS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151449.5"  ; havana_transcript "OTTHUMT00000323683.2"  ; hgnc_id "HGNC:24555"  ; level 2 ; orig_coord_info "chr7,1503903,1503960,-"  ; protein_id "ENSP00000385722.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "INTS1--GLCCI1^ENST00000404767.8"  ; transcript_name "INTS1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
INTS1--GLCCI1	HAVANA	mRNA	1001	31418	.	+	.	FI_gene_label "INTS1^ENSG00000164880.16"  ; ID "INTS1--GLCCI1^ENST00000404767.8"  ; Parent "INTS1--GLCCI1^INTS1^ENSG00000164880.16"  ; ccdsid "CCDS47526.1"  ; exon_id "ENSE00003571544.1"  ; exon_number 2 ; gene_id "INTS1--GLCCI1^INTS1^ENSG00000164880.16"  ; gene_name INTS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151449.5"  ; havana_transcript "OTTHUMT00000323683.2"  ; hgnc_id "HGNC:24555"  ; level 2 ; orig_coord_info "chr7,1503903,1503960,-"  ; protein_id "ENSP00000385722.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "INTS1--GLCCI1^ENST00000404767.8"  ; transcript_name "INTS1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MAD1L1--CHST12	HAVANA	gene	43033	60572	.	+	.	FI_gene_label "CHST12^ENSG00000136213.10"  ; ID "MAD1L1--CHST12^CHST12^ENSG00000136213.10"  ; ccdsid "CCDS5333.1"  ; exon_id "ENSE00000923850.10"  ; exon_number 2 ; gene_id "MAD1L1--CHST12^CHST12^ENSG00000136213.10"  ; gene_name CHST12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023849.9"  ; havana_transcript "OTTHUMT00000060170.4"  ; hgnc_id "HGNC:17423"  ; level 2 ; orig_coord_info "chr7,2432640,2433881,+"  ; protein_id "ENSP00000258711.6"  ; tag basic appris_principal_1 CCDS ; transcript_id "MAD1L1--CHST12^ENST00000258711.7"  ; transcript_name "CHST12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAD1L1--CHST12	HAVANA	mRNA	43033	60572	.	+	.	FI_gene_label "CHST12^ENSG00000136213.10"  ; ID "MAD1L1--CHST12^ENST00000258711.7"  ; Parent "MAD1L1--CHST12^CHST12^ENSG00000136213.10"  ; ccdsid "CCDS5333.1"  ; exon_id "ENSE00000923850.10"  ; exon_number 2 ; gene_id "MAD1L1--CHST12^CHST12^ENSG00000136213.10"  ; gene_name CHST12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023849.9"  ; havana_transcript "OTTHUMT00000060170.4"  ; hgnc_id "HGNC:17423"  ; level 2 ; orig_coord_info "chr7,2432640,2433881,+"  ; protein_id "ENSP00000258711.6"  ; tag basic appris_principal_1 CCDS ; transcript_id "MAD1L1--CHST12^ENST00000258711.7"  ; transcript_name "CHST12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAD1L1--CHST12	HAVANA	gene	1299	40030	.	+	.	FI_gene_label "MAD1L1^ENSG00000002822.16"  ; ID "MAD1L1--CHST12^MAD1L1^ENSG00000002822.16"  ; ccdsid "CCDS43539.1"  ; exon_id "ENSE00002228326.1"  ; exon_number 3 ; gene_id "MAD1L1--CHST12^MAD1L1^ENSG00000002822.16"  ; gene_name MAD1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151493.7"  ; hgnc_id "HGNC:6762"  ; level 2 ; orig_coord_info "chr7,2229984,2230133,-"  ; protein_id "ENSP00000265854.7"  ; tag alternative_5_UTR CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAD1L1--CHST12^ENST00000265854.12"  ; transcript_name "MAD1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAD1L1--CHST12	HAVANA	mRNA	1299	40030	.	+	.	FI_gene_label "MAD1L1^ENSG00000002822.16"  ; ID "MAD1L1--CHST12^ENST00000265854.12"  ; Parent "MAD1L1--CHST12^MAD1L1^ENSG00000002822.16"  ; ccdsid "CCDS43539.1"  ; exon_id "ENSE00002228326.1"  ; exon_number 3 ; gene_id "MAD1L1--CHST12^MAD1L1^ENSG00000002822.16"  ; gene_name MAD1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151493.7"  ; hgnc_id "HGNC:6762"  ; level 2 ; orig_coord_info "chr7,2229984,2230133,-"  ; protein_id "ENSP00000265854.7"  ; tag alternative_5_UTR CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAD1L1--CHST12^ENST00000265854.12"  ; transcript_name "MAD1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAD1L1--OR7E39P	HAVANA	gene	1299	40030	.	+	.	FI_gene_label "MAD1L1^ENSG00000002822.16"  ; ID "MAD1L1--OR7E39P^MAD1L1^ENSG00000002822.16"  ; ccdsid "CCDS43539.1"  ; exon_id "ENSE00002228326.1"  ; exon_number 3 ; gene_id "MAD1L1--OR7E39P^MAD1L1^ENSG00000002822.16"  ; gene_name MAD1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151493.7"  ; hgnc_id "HGNC:6762"  ; level 2 ; orig_coord_info "chr7,2229984,2230133,-"  ; protein_id "ENSP00000265854.7"  ; tag alternative_5_UTR CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAD1L1--OR7E39P^ENST00000265854.12"  ; transcript_name "MAD1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAD1L1--OR7E39P	HAVANA	mRNA	1299	40030	.	+	.	FI_gene_label "MAD1L1^ENSG00000002822.16"  ; ID "MAD1L1--OR7E39P^ENST00000265854.12"  ; Parent "MAD1L1--OR7E39P^MAD1L1^ENSG00000002822.16"  ; ccdsid "CCDS43539.1"  ; exon_id "ENSE00002228326.1"  ; exon_number 3 ; gene_id "MAD1L1--OR7E39P^MAD1L1^ENSG00000002822.16"  ; gene_name MAD1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151493.7"  ; hgnc_id "HGNC:6762"  ; level 2 ; orig_coord_info "chr7,2229984,2230133,-"  ; protein_id "ENSP00000265854.7"  ; tag alternative_5_UTR CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "MAD1L1--OR7E39P^ENST00000265854.12"  ; transcript_name "MAD1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PHF14--TNRC18	HAVANA	gene	63380	67693	.	+	.	FI_gene_label "TNRC18^ENSG00000182095.14"  ; ID "PHF14--TNRC18^TNRC18^ENSG00000182095.14"  ; exon_id "ENSE00001625690.1"  ; exon_number 1 ; gene_id "PHF14--TNRC18^TNRC18^ENSG00000182095.14"  ; gene_name TNRC18 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151831.8"  ; havana_transcript "OTTHUMT00000325408.2"  ; hgnc_id "HGNC:11962"  ; level 2 ; orig_coord_info "chr7,5320532,5320607,-"  ; protein_id "ENSP00000329902.3"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "PHF14--TNRC18^ENST00000328270.3"  ; transcript_name "TNRC18-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PHF14--TNRC18	HAVANA	mRNA	63380	67693	.	+	.	FI_gene_label "TNRC18^ENSG00000182095.14"  ; ID "PHF14--TNRC18^ENST00000328270.3"  ; Parent "PHF14--TNRC18^TNRC18^ENSG00000182095.14"  ; exon_id "ENSE00001625690.1"  ; exon_number 1 ; gene_id "PHF14--TNRC18^TNRC18^ENSG00000182095.14"  ; gene_name TNRC18 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151831.8"  ; havana_transcript "OTTHUMT00000325408.2"  ; hgnc_id "HGNC:11962"  ; level 2 ; orig_coord_info "chr7,5320532,5320607,-"  ; protein_id "ENSP00000329902.3"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "PHF14--TNRC18^ENST00000328270.3"  ; transcript_name "TNRC18-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PHF14--TNRC18	HAVANA	gene	1537	22235	.	+	.	FI_gene_label "PHF14^ENSG00000106443.17"  ; ID "PHF14--TNRC18^PHF14^ENSG00000106443.17"  ; ccdsid "CCDS47542.1"  ; exon_id "ENSE00003465315.1"  ; exon_number 1 ; gene_id "PHF14--TNRC18^PHF14^ENSG00000106443.17"  ; gene_name PHF14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150463.5"  ; havana_transcript "OTTHUMT00000318212.1"  ; hgnc_id "HGNC:22203"  ; level 2 ; orig_coord_info "chr7,10974324,10974324,+"  ; protein_id "ENSP00000385795.3"  ; tag basic CCDS ; transcript_id "PHF14--TNRC18^ENST00000403050.7"  ; transcript_name "PHF14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PHF14--TNRC18	HAVANA	mRNA	1537	22235	.	+	.	FI_gene_label "PHF14^ENSG00000106443.17"  ; ID "PHF14--TNRC18^ENST00000403050.7"  ; Parent "PHF14--TNRC18^PHF14^ENSG00000106443.17"  ; ccdsid "CCDS47542.1"  ; exon_id "ENSE00003465315.1"  ; exon_number 1 ; gene_id "PHF14--TNRC18^PHF14^ENSG00000106443.17"  ; gene_name PHF14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150463.5"  ; havana_transcript "OTTHUMT00000318212.1"  ; hgnc_id "HGNC:22203"  ; level 2 ; orig_coord_info "chr7,10974324,10974324,+"  ; protein_id "ENSP00000385795.3"  ; tag basic CCDS ; transcript_id "PHF14--TNRC18^ENST00000403050.7"  ; transcript_name "PHF14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SUN1--GRIFIN	HAVANA	gene	1001	28018	.	+	.	FI_gene_label "SUN1^ENSG00000164828.18"  ; ID "SUN1--GRIFIN^SUN1^ENSG00000164828.18"  ; ccdsid "CCDS43533.1"  ; exon_id "ENSE00003682941.1"  ; exon_number 2 ; gene_id "SUN1--GRIFIN^SUN1^ENSG00000164828.18"  ; gene_name SUN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151426.10"  ; havana_transcript "OTTHUMT00000322567.3"  ; hgnc_id "HGNC:18587"  ; level 2 ; orig_coord_info "chr7,838871,838986,+"  ; protein_id "ENSP00000374225.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "SUN1--GRIFIN^ENST00000389574.7"  ; transcript_name "SUN1-202"  ; transcript_support_level 2 ; transcript_type protein_coding
SUN1--GRIFIN	HAVANA	mRNA	1001	28018	.	+	.	FI_gene_label "SUN1^ENSG00000164828.18"  ; ID "SUN1--GRIFIN^ENST00000389574.7"  ; Parent "SUN1--GRIFIN^SUN1^ENSG00000164828.18"  ; ccdsid "CCDS43533.1"  ; exon_id "ENSE00003682941.1"  ; exon_number 2 ; gene_id "SUN1--GRIFIN^SUN1^ENSG00000164828.18"  ; gene_name SUN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151426.10"  ; havana_transcript "OTTHUMT00000322567.3"  ; hgnc_id "HGNC:18587"  ; level 2 ; orig_coord_info "chr7,838871,838986,+"  ; protein_id "ENSP00000374225.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "SUN1--GRIFIN^ENST00000389574.7"  ; transcript_name "SUN1-202"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
SUN1--GRIFIN	HAVANA	gene	39640	41179	.	+	.	FI_gene_label "GRIFIN^ENSG00000275572.1"  ; ID "SUN1--GRIFIN^GRIFIN^ENSG00000275572.1"  ; exon_id "ENSE00003730550.1"  ; exon_number 1 ; gene_id "SUN1--GRIFIN^GRIFIN^ENSG00000275572.1"  ; gene_name GRIFIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000152042.4"  ; havana_transcript "OTTHUMT00000336933.3"  ; hgnc_id "HGNC:4577"  ; level 2 ; orig_coord_info "chr7,2476372,2476383,-"  ; protein_id "ENSP00000481185.1"  ; tag dotter_confirmed not_organism_supported basic appris_principal_1 ; transcript_id "SUN1--GRIFIN^ENST00000614228.1"  ; transcript_name "GRIFIN-202"  ; transcript_support_level 5 ; transcript_type protein_coding
SUN1--GRIFIN	HAVANA	mRNA	39640	41179	.	+	.	FI_gene_label "GRIFIN^ENSG00000275572.1"  ; ID "SUN1--GRIFIN^ENST00000614228.1"  ; Parent "SUN1--GRIFIN^GRIFIN^ENSG00000275572.1"  ; exon_id "ENSE00003730550.1"  ; exon_number 1 ; gene_id "SUN1--GRIFIN^GRIFIN^ENSG00000275572.1"  ; gene_name GRIFIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000152042.4"  ; havana_transcript "OTTHUMT00000336933.3"  ; hgnc_id "HGNC:4577"  ; level 2 ; orig_coord_info "chr7,2476372,2476383,-"  ; protein_id "ENSP00000481185.1"  ; tag dotter_confirmed not_organism_supported basic appris_principal_1 ; transcript_id "SUN1--GRIFIN^ENST00000614228.1"  ; transcript_name "GRIFIN-202"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SUN1--LFNG	HAVANA	gene	42665	49021	.	+	.	FI_gene_label "LFNG^ENSG00000106003.13"  ; ID "SUN1--LFNG^LFNG^ENSG00000106003.13"  ; ccdsid "CCDS34587.1"  ; exon_id "ENSE00001329541.4"  ; exon_number 1 ; gene_id "SUN1--LFNG^LFNG^ENSG00000106003.13"  ; gene_name LFNG ; gene_type protein_coding ; havana_gene "OTTHUMG00000152043.2"  ; havana_transcript "OTTHUMT00000325021.2"  ; hgnc_id "HGNC:6560"  ; level 2 ; orig_coord_info "chr7,2519862,2520293,+"  ; protein_id "ENSP00000222725.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SUN1--LFNG^ENST00000222725.10"  ; transcript_name "LFNG-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SUN1--LFNG	HAVANA	mRNA	42665	49021	.	+	.	FI_gene_label "LFNG^ENSG00000106003.13"  ; ID "SUN1--LFNG^ENST00000222725.10"  ; Parent "SUN1--LFNG^LFNG^ENSG00000106003.13"  ; ccdsid "CCDS34587.1"  ; exon_id "ENSE00001329541.4"  ; exon_number 1 ; gene_id "SUN1--LFNG^LFNG^ENSG00000106003.13"  ; gene_name LFNG ; gene_type protein_coding ; havana_gene "OTTHUMG00000152043.2"  ; havana_transcript "OTTHUMT00000325021.2"  ; hgnc_id "HGNC:6560"  ; level 2 ; orig_coord_info "chr7,2519862,2520293,+"  ; protein_id "ENSP00000222725.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SUN1--LFNG^ENST00000222725.10"  ; transcript_name "LFNG-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SUN1--LFNG	HAVANA	gene	1001	28018	.	+	.	FI_gene_label "SUN1^ENSG00000164828.18"  ; ID "SUN1--LFNG^SUN1^ENSG00000164828.18"  ; ccdsid "CCDS43533.1"  ; exon_id "ENSE00003682941.1"  ; exon_number 2 ; gene_id "SUN1--LFNG^SUN1^ENSG00000164828.18"  ; gene_name SUN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151426.10"  ; havana_transcript "OTTHUMT00000322567.3"  ; hgnc_id "HGNC:18587"  ; level 2 ; orig_coord_info "chr7,838871,838986,+"  ; protein_id "ENSP00000374225.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "SUN1--LFNG^ENST00000389574.7"  ; transcript_name "SUN1-202"  ; transcript_support_level 2 ; transcript_type protein_coding
SUN1--LFNG	HAVANA	mRNA	1001	28018	.	+	.	FI_gene_label "SUN1^ENSG00000164828.18"  ; ID "SUN1--LFNG^ENST00000389574.7"  ; Parent "SUN1--LFNG^SUN1^ENSG00000164828.18"  ; ccdsid "CCDS43533.1"  ; exon_id "ENSE00003682941.1"  ; exon_number 2 ; gene_id "SUN1--LFNG^SUN1^ENSG00000164828.18"  ; gene_name SUN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151426.10"  ; havana_transcript "OTTHUMT00000322567.3"  ; hgnc_id "HGNC:18587"  ; level 2 ; orig_coord_info "chr7,838871,838986,+"  ; protein_id "ENSP00000374225.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "SUN1--LFNG^ENST00000389574.7"  ; transcript_name "SUN1-202"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
TNRC18--MAD1L1	HAVANA	gene	41924	80655	.	+	.	FI_gene_label "MAD1L1^ENSG00000002822.16"  ; ID "TNRC18--MAD1L1^MAD1L1^ENSG00000002822.16"  ; ccdsid "CCDS43539.1"  ; exon_id "ENSE00002228326.1"  ; exon_number 3 ; gene_id "TNRC18--MAD1L1^MAD1L1^ENSG00000002822.16"  ; gene_name MAD1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151493.7"  ; hgnc_id "HGNC:6762"  ; level 2 ; orig_coord_info "chr7,2229984,2230133,-"  ; protein_id "ENSP00000265854.7"  ; tag alternative_5_UTR CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNRC18--MAD1L1^ENST00000265854.12"  ; transcript_name "MAD1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TNRC18--MAD1L1	HAVANA	mRNA	41924	80655	.	+	.	FI_gene_label "MAD1L1^ENSG00000002822.16"  ; ID "TNRC18--MAD1L1^ENST00000265854.12"  ; Parent "TNRC18--MAD1L1^MAD1L1^ENSG00000002822.16"  ; ccdsid "CCDS43539.1"  ; exon_id "ENSE00002228326.1"  ; exon_number 3 ; gene_id "TNRC18--MAD1L1^MAD1L1^ENSG00000002822.16"  ; gene_name MAD1L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151493.7"  ; hgnc_id "HGNC:6762"  ; level 2 ; orig_coord_info "chr7,2229984,2230133,-"  ; protein_id "ENSP00000265854.7"  ; tag alternative_5_UTR CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNRC18--MAD1L1^ENST00000265854.12"  ; transcript_name "MAD1L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TNRC18--MAD1L1	HAVANA	gene	30125	34438	.	+	.	FI_gene_label "TNRC18^ENSG00000182095.14"  ; ID "TNRC18--MAD1L1^TNRC18^ENSG00000182095.14"  ; exon_id "ENSE00001625690.1"  ; exon_number 1 ; gene_id "TNRC18--MAD1L1^TNRC18^ENSG00000182095.14"  ; gene_name TNRC18 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151831.8"  ; havana_transcript "OTTHUMT00000325408.2"  ; hgnc_id "HGNC:11962"  ; level 2 ; orig_coord_info "chr7,5320532,5320607,-"  ; protein_id "ENSP00000329902.3"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "TNRC18--MAD1L1^ENST00000328270.3"  ; transcript_name "TNRC18-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TNRC18--MAD1L1	HAVANA	mRNA	30125	34438	.	+	.	FI_gene_label "TNRC18^ENSG00000182095.14"  ; ID "TNRC18--MAD1L1^ENST00000328270.3"  ; Parent "TNRC18--MAD1L1^TNRC18^ENSG00000182095.14"  ; exon_id "ENSE00001625690.1"  ; exon_number 1 ; gene_id "TNRC18--MAD1L1^TNRC18^ENSG00000182095.14"  ; gene_name TNRC18 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151831.8"  ; havana_transcript "OTTHUMT00000325408.2"  ; hgnc_id "HGNC:11962"  ; level 2 ; orig_coord_info "chr7,5320532,5320607,-"  ; protein_id "ENSP00000329902.3"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "TNRC18--MAD1L1^ENST00000328270.3"  ; transcript_name "TNRC18-201"  ; transcript_support_level 5 ; 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: 
AC233699.1--TBC1D3	HAVANA	gene	1001	9975	.	+	.	FI_gene_label "AC233699.1^ENSG00000261499.2"  ; ID "AC233699.1--TBC1D3^AC233699.1^ENSG00000261499.2"  ; exon_id "ENSE00002600750.2"  ; exon_number 1 ; gene_id "AC233699.1--TBC1D3^AC233699.1^ENSG00000261499.2"  ; gene_name "AC233699.1"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188425.1"  ; havana_transcript "OTTHUMT00000477176.1"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr17,36274191,36274283,+"  ; tag basic ; transcript_id "AC233699.1--TBC1D3^ENST00000569955.2"  ; transcript_name "AC233699.1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC233699.1--TBC1D3	HAVANA	RNA	1001	9975	.	+	.	FI_gene_label "AC233699.1^ENSG00000261499.2"  ; ID "AC233699.1--TBC1D3^ENST00000569955.2"  ; Parent "AC233699.1--TBC1D3^AC233699.1^ENSG00000261499.2"  ; exon_id "ENSE00002600750.2"  ; exon_number 1 ; gene_id "AC233699.1--TBC1D3^AC233699.1^ENSG00000261499.2"  ; gene_name "AC233699.1"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188425.1"  ; havana_transcript "OTTHUMT00000477176.1"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr17,36274191,36274283,+"  ; tag basic ; transcript_id "AC233699.1--TBC1D3^ENST00000569955.2"  ; transcript_name "AC233699.1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
GOLGA6L10--GOLGA2P6	HAVANA	gene	12782	20364	.	+	.	FI_gene_label "GOLGA2P6^ENSG00000241621.1"  ; ID "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1"  ; exon_id "ENSE00001603136.1"  ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1"  ; gene_name GOLGA2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000017890.1"  ; havana_transcript "OTTHUMT00000047421.1"  ; hgnc_id "HGNC:44948"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chr10,30374327,30374386,-"  ; tag pseudo_consens basic ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000340929.4"  ; transcript_name "GOLGA2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
GOLGA6L10--GOLGA2P6	HAVANA	RNA	12782	20364	.	+	.	FI_gene_label "GOLGA2P6^ENSG00000241621.1"  ; ID "GOLGA6L10--GOLGA2P6^ENST00000340929.4"  ; Parent "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1"  ; exon_id "ENSE00001603136.1"  ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1"  ; gene_name GOLGA2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000017890.1"  ; havana_transcript "OTTHUMT00000047421.1"  ; hgnc_id "HGNC:44948"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chr10,30374327,30374386,-"  ; tag pseudo_consens basic ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000340929.4"  ; transcript_name "GOLGA2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
MAD1L1--OR7E39P	HAVANA	gene	43033	43407	.	+	.	FI_gene_label "OR7E39P^ENSG00000273252.1"  ; ID "MAD1L1--OR7E39P^OR7E39P^ENSG00000273252.1"  ; exon_id "ENSE00003705839.1"  ; exon_number 1 ; gene_id "MAD1L1--OR7E39P^OR7E39P^ENSG00000273252.1"  ; gene_name OR7E39P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000185867.1"  ; havana_transcript "OTTHUMT00000471564.1"  ; hgnc_id "HGNC:8412"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,6835420,6835794,-"  ; tag basic ; transcript_id "MAD1L1--OR7E39P^ENST00000609433.1"  ; transcript_name "OR7E39P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
MAD1L1--OR7E39P	HAVANA	RNA	43033	43407	.	+	.	FI_gene_label "OR7E39P^ENSG00000273252.1"  ; ID "MAD1L1--OR7E39P^ENST00000609433.1"  ; Parent "MAD1L1--OR7E39P^OR7E39P^ENSG00000273252.1"  ; exon_id "ENSE00003705839.1"  ; exon_number 1 ; gene_id "MAD1L1--OR7E39P^OR7E39P^ENSG00000273252.1"  ; gene_name OR7E39P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000185867.1"  ; havana_transcript "OTTHUMT00000471564.1"  ; hgnc_id "HGNC:8412"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr7,6835420,6835794,-"  ; tag basic ; transcript_id "MAD1L1--OR7E39P^ENST00000609433.1"  ; transcript_name "OR7E39P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
310 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 ------------------------------
383 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 21 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