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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/bd145872490c54b99b644f10c92d3f/.command.log
Size: 44.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_ciJ-T1-TRNA-1_B23WHTKLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8614fb18873f00b8cabbbbf87ab056/fi_workdir/659_ciJ-T1-TRNA-1_B23WHTKLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/bd145872490c54b99b644f10c92d3f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/bd145872490c54b99b644f10c92d3f/.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: 2730
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2730
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => CDS exon
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:2730
  => 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: 
CCDC6--RET	HAVANA	gene	1001	16128	.	+	.	FI_gene_label "CCDC6^ENSG00000108091.11"  ; ID "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; ccdsid "CCDS7257.1"  ; exon_id "ENSE00001950758.3"  ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3"  ; havana_transcript "OTTHUMT00000048176.3"  ; hgnc_id "HGNC:18782"  ; level 2 ; orig_coord_info "chr10,59906122,59906424,-"  ; protein_id "ENSP00000263102.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7"  ; transcript_name "CCDC6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET	HAVANA	mRNA	1001	16128	.	+	.	FI_gene_label "CCDC6^ENSG00000108091.11"  ; ID "CCDC6--RET^ENST00000263102.7"  ; Parent "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; ccdsid "CCDS7257.1"  ; exon_id "ENSE00001950758.3"  ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3"  ; havana_transcript "OTTHUMT00000048176.3"  ; hgnc_id "HGNC:18782"  ; level 2 ; orig_coord_info "chr10,59906122,59906424,-"  ; protein_id "ENSP00000263102.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7"  ; transcript_name "CCDC6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCDC6--RET	HAVANA	gene	19134	39754	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "CCDC6--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET	HAVANA	mRNA	19134	39754	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "CCDC6--RET^ENST00000340058.6"  ; Parent "CCDC6--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAJC1--AL513128.1	HAVANA	gene	1040	14616	.	+	.	FI_gene_label "DNAJC1^ENSG00000136770.11"  ; ID "DNAJC1--AL513128.1^DNAJC1^ENSG00000136770.11"  ; ccdsid "CCDS7136.1"  ; exon_id "ENSE00001940957.2"  ; exon_number 1 ; gene_id "DNAJC1--AL513128.1^DNAJC1^ENSG00000136770.11"  ; gene_name DNAJC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017800.6"  ; havana_transcript "OTTHUMT00000047149.2"  ; hgnc_id "HGNC:20090"  ; level 2 ; orig_coord_info "chr10,22003213,22003434,-"  ; protein_id "ENSP00000366179.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJC1--AL513128.1^ENST00000376980.8"  ; transcript_name "DNAJC1-202"  ; transcript_support_level 1 ; transcript_type protein_coding
DNAJC1--AL513128.1	HAVANA	mRNA	1040	14616	.	+	.	FI_gene_label "DNAJC1^ENSG00000136770.11"  ; ID "DNAJC1--AL513128.1^ENST00000376980.8"  ; Parent "DNAJC1--AL513128.1^DNAJC1^ENSG00000136770.11"  ; ccdsid "CCDS7136.1"  ; exon_id "ENSE00001940957.2"  ; exon_number 1 ; gene_id "DNAJC1--AL513128.1^DNAJC1^ENSG00000136770.11"  ; gene_name DNAJC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017800.6"  ; havana_transcript "OTTHUMT00000047149.2"  ; hgnc_id "HGNC:20090"  ; level 2 ; orig_coord_info "chr10,22003213,22003434,-"  ; protein_id "ENSP00000366179.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJC1--AL513128.1^ENST00000376980.8"  ; transcript_name "DNAJC1-202"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAJC1--SPAG6	HAVANA	gene	17669	31805	.	+	.	FI_gene_label "SPAG6^ENSG00000077327.16"  ; ID "DNAJC1--SPAG6^SPAG6^ENSG00000077327.16"  ; ccdsid "CCDS7140.1"  ; exon_id "ENSE00001814494.1"  ; exon_number 1 ; gene_id "DNAJC1--SPAG6^SPAG6^ENSG00000077327.16"  ; gene_name SPAG6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017808.4"  ; havana_transcript "OTTHUMT00000047188.1"  ; hgnc_id "HGNC:11215"  ; level 2 ; orig_coord_info "chr10,22345612,22345636,+"  ; protein_id "ENSP00000323599.6"  ; tag basic CCDS ; transcript_id "DNAJC1--SPAG6^ENST00000313311.10"  ; transcript_name "SPAG6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DNAJC1--SPAG6	HAVANA	mRNA	17669	31805	.	+	.	FI_gene_label "SPAG6^ENSG00000077327.16"  ; ID "DNAJC1--SPAG6^ENST00000313311.10"  ; Parent "DNAJC1--SPAG6^SPAG6^ENSG00000077327.16"  ; ccdsid "CCDS7140.1"  ; exon_id "ENSE00001814494.1"  ; exon_number 1 ; gene_id "DNAJC1--SPAG6^SPAG6^ENSG00000077327.16"  ; gene_name SPAG6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017808.4"  ; havana_transcript "OTTHUMT00000047188.1"  ; hgnc_id "HGNC:11215"  ; level 2 ; orig_coord_info "chr10,22345612,22345636,+"  ; protein_id "ENSP00000323599.6"  ; tag basic CCDS ; transcript_id "DNAJC1--SPAG6^ENST00000313311.10"  ; transcript_name "SPAG6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAJC1--SPAG6	HAVANA	gene	1040	14616	.	+	.	FI_gene_label "DNAJC1^ENSG00000136770.11"  ; ID "DNAJC1--SPAG6^DNAJC1^ENSG00000136770.11"  ; ccdsid "CCDS7136.1"  ; exon_id "ENSE00001940957.2"  ; exon_number 1 ; gene_id "DNAJC1--SPAG6^DNAJC1^ENSG00000136770.11"  ; gene_name DNAJC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017800.6"  ; havana_transcript "OTTHUMT00000047149.2"  ; hgnc_id "HGNC:20090"  ; level 2 ; orig_coord_info "chr10,22003213,22003434,-"  ; protein_id "ENSP00000366179.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJC1--SPAG6^ENST00000376980.8"  ; transcript_name "DNAJC1-202"  ; transcript_support_level 1 ; transcript_type protein_coding
DNAJC1--SPAG6	HAVANA	mRNA	1040	14616	.	+	.	FI_gene_label "DNAJC1^ENSG00000136770.11"  ; ID "DNAJC1--SPAG6^ENST00000376980.8"  ; Parent "DNAJC1--SPAG6^DNAJC1^ENSG00000136770.11"  ; ccdsid "CCDS7136.1"  ; exon_id "ENSE00001940957.2"  ; exon_number 1 ; gene_id "DNAJC1--SPAG6^DNAJC1^ENSG00000136770.11"  ; gene_name DNAJC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017800.6"  ; havana_transcript "OTTHUMT00000047149.2"  ; hgnc_id "HGNC:20090"  ; level 2 ; orig_coord_info "chr10,22003213,22003434,-"  ; protein_id "ENSP00000366179.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJC1--SPAG6^ENST00000376980.8"  ; transcript_name "DNAJC1-202"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EIF2S3--KLHL15	HAVANA	gene	1011	14742	.	+	.	FI_gene_label "EIF2S3^ENSG00000130741.11"  ; ID "EIF2S3--KLHL15^EIF2S3^ENSG00000130741.11"  ; ccdsid "CCDS14210.1"  ; exon_id "ENSE00001895363.2"  ; exon_number 1 ; gene_id "EIF2S3--KLHL15^EIF2S3^ENSG00000130741.11"  ; gene_name EIF2S3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021262.3"  ; havana_transcript "OTTHUMT00000056079.2"  ; hgnc_id "HGNC:3267"  ; level 2 ; orig_coord_info "chrX,24054969,24055037,+"  ; protein_id "ENSP00000253039.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2S3--KLHL15^ENST00000253039.9"  ; transcript_name "EIF2S3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
EIF2S3--KLHL15	HAVANA	mRNA	1011	14742	.	+	.	FI_gene_label "EIF2S3^ENSG00000130741.11"  ; ID "EIF2S3--KLHL15^ENST00000253039.9"  ; Parent "EIF2S3--KLHL15^EIF2S3^ENSG00000130741.11"  ; ccdsid "CCDS14210.1"  ; exon_id "ENSE00001895363.2"  ; exon_number 1 ; gene_id "EIF2S3--KLHL15^EIF2S3^ENSG00000130741.11"  ; gene_name EIF2S3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021262.3"  ; havana_transcript "OTTHUMT00000056079.2"  ; hgnc_id "HGNC:3267"  ; level 2 ; orig_coord_info "chrX,24054969,24055037,+"  ; protein_id "ENSP00000253039.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2S3--KLHL15^ENST00000253039.9"  ; transcript_name "EIF2S3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
EIF2S3--KLHL15	HAVANA	gene	17743	27014	.	+	.	FI_gene_label "KLHL15^ENSG00000174010.9"  ; ID "EIF2S3--KLHL15^KLHL15^ENSG00000174010.9"  ; ccdsid "CCDS35217.1"  ; exon_id "ENSE00001422972.2"  ; exon_number 3 ; gene_id "EIF2S3--KLHL15^KLHL15^ENSG00000174010.9"  ; gene_name KLHL15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021261.1"  ; havana_transcript "OTTHUMT00000056078.1"  ; hgnc_id "HGNC:29347"  ; level 2 ; orig_coord_info "chrX,24005989,24006693,-"  ; protein_id "ENSP00000332791.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2S3--KLHL15^ENST00000328046.8"  ; transcript_name "KLHL15-201"  ; transcript_support_level 2 ; transcript_type protein_coding
EIF2S3--KLHL15	HAVANA	mRNA	17743	27014	.	+	.	FI_gene_label "KLHL15^ENSG00000174010.9"  ; ID "EIF2S3--KLHL15^ENST00000328046.8"  ; Parent "EIF2S3--KLHL15^KLHL15^ENSG00000174010.9"  ; ccdsid "CCDS35217.1"  ; exon_id "ENSE00001422972.2"  ; exon_number 3 ; gene_id "EIF2S3--KLHL15^KLHL15^ENSG00000174010.9"  ; gene_name KLHL15 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021261.1"  ; havana_transcript "OTTHUMT00000056078.1"  ; hgnc_id "HGNC:29347"  ; level 2 ; orig_coord_info "chrX,24005989,24006693,-"  ; protein_id "ENSP00000332791.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EIF2S3--KLHL15^ENST00000328046.8"  ; transcript_name "KLHL15-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
EIF3H--SLC30A8	HAVANA	gene	1671	17177	.	+	.	FI_gene_label "EIF3H^ENSG00000147677.11"  ; ID "EIF3H--SLC30A8^EIF3H^ENSG00000147677.11"  ; exon_id "ENSE00002101437.1"  ; exon_number 2 ; gene_id "EIF3H--SLC30A8^EIF3H^ENSG00000147677.11"  ; gene_name EIF3H ; gene_type protein_coding ; havana_gene "OTTHUMG00000164919.3"  ; havana_transcript "OTTHUMT00000380913.1"  ; hgnc_id "HGNC:3273"  ; level 1 ; orig_coord_info "chr8,116755952,116755993,-"  ; protein_id "ENSP00000276682.4"  ; tag basic exp_conf ; transcript_id "EIF3H--SLC30A8^ENST00000276682.8"  ; transcript_name "EIF3H-201"  ; transcript_support_level 2 ; transcript_type protein_coding
EIF3H--SLC30A8	HAVANA	mRNA	1671	17177	.	+	.	FI_gene_label "EIF3H^ENSG00000147677.11"  ; ID "EIF3H--SLC30A8^ENST00000276682.8"  ; Parent "EIF3H--SLC30A8^EIF3H^ENSG00000147677.11"  ; exon_id "ENSE00002101437.1"  ; exon_number 2 ; gene_id "EIF3H--SLC30A8^EIF3H^ENSG00000147677.11"  ; gene_name EIF3H ; gene_type protein_coding ; havana_gene "OTTHUMG00000164919.3"  ; havana_transcript "OTTHUMT00000380913.1"  ; hgnc_id "HGNC:3273"  ; level 1 ; orig_coord_info "chr8,116755952,116755993,-"  ; protein_id "ENSP00000276682.4"  ; tag basic exp_conf ; transcript_id "EIF3H--SLC30A8^ENST00000276682.8"  ; transcript_name "EIF3H-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
EIF3H--SLC30A8	ENSEMBL	gene	23559	40144	.	+	.	FI_gene_label "SLC30A8^ENSG00000164756.12"  ; ID "EIF3H--SLC30A8^SLC30A8^ENSG00000164756.12"  ; ccdsid "CCDS55272.1"  ; exon_id "ENSE00003598822.1"  ; exon_number 5 ; gene_id "EIF3H--SLC30A8^SLC30A8^ENSG00000164756.12"  ; gene_name SLC30A8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164962.3"  ; hgnc_id "HGNC:20303"  ; level 3 ; orig_coord_info "chr8,117147030,117147153,+"  ; protein_id "ENSP00000407505.2"  ; tag basic CCDS ; transcript_id "EIF3H--SLC30A8^ENST00000427715.2"  ; transcript_name "SLC30A8-201"  ; transcript_support_level 2 ; transcript_type protein_coding
EIF3H--SLC30A8	ENSEMBL	mRNA	23559	40144	.	+	.	FI_gene_label "SLC30A8^ENSG00000164756.12"  ; ID "EIF3H--SLC30A8^ENST00000427715.2"  ; Parent "EIF3H--SLC30A8^SLC30A8^ENSG00000164756.12"  ; ccdsid "CCDS55272.1"  ; exon_id "ENSE00003598822.1"  ; exon_number 5 ; gene_id "EIF3H--SLC30A8^SLC30A8^ENSG00000164756.12"  ; gene_name SLC30A8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164962.3"  ; hgnc_id "HGNC:20303"  ; level 3 ; orig_coord_info "chr8,117147030,117147153,+"  ; protein_id "ENSP00000407505.2"  ; tag basic CCDS ; transcript_id "EIF3H--SLC30A8^ENST00000427715.2"  ; transcript_name "SLC30A8-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
MIPEP--CYCSP33	HAVANA	gene	1001	23048	.	+	.	FI_gene_label "MIPEP^ENSG00000027001.10"  ; ID "MIPEP--CYCSP33^MIPEP^ENSG00000027001.10"  ; ccdsid "CCDS9303.1"  ; exon_id "ENSE00001491306.4"  ; exon_number 1 ; gene_id "MIPEP--CYCSP33^MIPEP^ENSG00000027001.10"  ; gene_name MIPEP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016573.3"  ; havana_transcript "OTTHUMT00000044169.2"  ; hgnc_id "HGNC:7104"  ; level 2 ; orig_coord_info "chr13,23889132,23889320,-"  ; protein_id "ENSP00000371607.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MIPEP--CYCSP33^ENST00000382172.4"  ; transcript_name "MIPEP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MIPEP--CYCSP33	HAVANA	mRNA	1001	23048	.	+	.	FI_gene_label "MIPEP^ENSG00000027001.10"  ; ID "MIPEP--CYCSP33^ENST00000382172.4"  ; Parent "MIPEP--CYCSP33^MIPEP^ENSG00000027001.10"  ; ccdsid "CCDS9303.1"  ; exon_id "ENSE00001491306.4"  ; exon_number 1 ; gene_id "MIPEP--CYCSP33^MIPEP^ENSG00000027001.10"  ; gene_name MIPEP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016573.3"  ; havana_transcript "OTTHUMT00000044169.2"  ; hgnc_id "HGNC:7104"  ; level 2 ; orig_coord_info "chr13,23889132,23889320,-"  ; protein_id "ENSP00000371607.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MIPEP--CYCSP33^ENST00000382172.4"  ; transcript_name "MIPEP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MIPEP--TPTE2P6	HAVANA	gene	1001	23048	.	+	.	FI_gene_label "MIPEP^ENSG00000027001.10"  ; ID "MIPEP--TPTE2P6^MIPEP^ENSG00000027001.10"  ; ccdsid "CCDS9303.1"  ; exon_id "ENSE00001491306.4"  ; exon_number 1 ; gene_id "MIPEP--TPTE2P6^MIPEP^ENSG00000027001.10"  ; gene_name MIPEP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016573.3"  ; havana_transcript "OTTHUMT00000044169.2"  ; hgnc_id "HGNC:7104"  ; level 2 ; orig_coord_info "chr13,23889132,23889320,-"  ; protein_id "ENSP00000371607.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MIPEP--TPTE2P6^ENST00000382172.4"  ; transcript_name "MIPEP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MIPEP--TPTE2P6	HAVANA	mRNA	1001	23048	.	+	.	FI_gene_label "MIPEP^ENSG00000027001.10"  ; ID "MIPEP--TPTE2P6^ENST00000382172.4"  ; Parent "MIPEP--TPTE2P6^MIPEP^ENSG00000027001.10"  ; ccdsid "CCDS9303.1"  ; exon_id "ENSE00001491306.4"  ; exon_number 1 ; gene_id "MIPEP--TPTE2P6^MIPEP^ENSG00000027001.10"  ; gene_name MIPEP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016573.3"  ; havana_transcript "OTTHUMT00000044169.2"  ; hgnc_id "HGNC:7104"  ; level 2 ; orig_coord_info "chr13,23889132,23889320,-"  ; protein_id "ENSP00000371607.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MIPEP--TPTE2P6^ENST00000382172.4"  ; transcript_name "MIPEP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RAI1--MYO15A	HAVANA	gene	1001	17921	.	+	.	FI_gene_label "RAI1^ENSG00000108557.19"  ; ID "RAI1--MYO15A^RAI1^ENSG00000108557.19"  ; ccdsid "CCDS11188.1"  ; exon_id "ENSE00001291642.2"  ; exon_number 3 ; gene_id "RAI1--MYO15A^RAI1^ENSG00000108557.19"  ; gene_name RAI1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059314.4"  ; havana_transcript "OTTHUMT00000131775.2"  ; hgnc_id "HGNC:9834"  ; level 2 ; orig_coord_info "chr17,17792949,17798513,+"  ; protein_id "ENSP00000323074.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAI1--MYO15A^ENST00000353383.6"  ; transcript_name "RAI1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RAI1--MYO15A	HAVANA	mRNA	1001	17921	.	+	.	FI_gene_label "RAI1^ENSG00000108557.19"  ; ID "RAI1--MYO15A^ENST00000353383.6"  ; Parent "RAI1--MYO15A^RAI1^ENSG00000108557.19"  ; ccdsid "CCDS11188.1"  ; exon_id "ENSE00001291642.2"  ; exon_number 3 ; gene_id "RAI1--MYO15A^RAI1^ENSG00000108557.19"  ; gene_name RAI1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059314.4"  ; havana_transcript "OTTHUMT00000131775.2"  ; hgnc_id "HGNC:9834"  ; level 2 ; orig_coord_info "chr17,17792949,17798513,+"  ; protein_id "ENSP00000323074.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RAI1--MYO15A^ENST00000353383.6"  ; transcript_name "RAI1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RAI1--MYO15A	HAVANA	gene	51481	71206	.	+	.	FI_gene_label "MYO15A^ENSG00000091536.19"  ; ID "RAI1--MYO15A^MYO15A^ENSG00000091536.19"  ; exon_id "ENSE00003795816.1"  ; exon_number 3 ; gene_id "RAI1--MYO15A^MYO15A^ENSG00000091536.19"  ; gene_name MYO15A ; gene_type protein_coding ; havana_gene "OTTHUMG00000059390.14"  ; havana_transcript "OTTHUMT00000446125.1"  ; hgnc_id "HGNC:7594"  ; level 1 ; orig_coord_info "chr17,18154740,18154755,+"  ; protein_id "ENSP00000408800.3"  ; tag basic exp_conf ; transcript_id "RAI1--MYO15A^ENST00000418233.7"  ; transcript_name "MYO15A-202"  ; transcript_support_level 2 ; transcript_type protein_coding
RAI1--MYO15A	HAVANA	mRNA	51481	71206	.	+	.	FI_gene_label "MYO15A^ENSG00000091536.19"  ; ID "RAI1--MYO15A^ENST00000418233.7"  ; Parent "RAI1--MYO15A^MYO15A^ENSG00000091536.19"  ; exon_id "ENSE00003795816.1"  ; exon_number 3 ; gene_id "RAI1--MYO15A^MYO15A^ENSG00000091536.19"  ; gene_name MYO15A ; gene_type protein_coding ; havana_gene "OTTHUMG00000059390.14"  ; havana_transcript "OTTHUMT00000446125.1"  ; hgnc_id "HGNC:7594"  ; level 1 ; orig_coord_info "chr17,18154740,18154755,+"  ; protein_id "ENSP00000408800.3"  ; tag basic exp_conf ; transcript_id "RAI1--MYO15A^ENST00000418233.7"  ; transcript_name "MYO15A-202"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
STOM--AL359644.1	HAVANA	gene	1055	10169	.	+	.	FI_gene_label "STOM^ENSG00000148175.13"  ; ID "STOM--AL359644.1^STOM^ENSG00000148175.13"  ; ccdsid "CCDS6830.1"  ; exon_id "ENSE00001950406.2"  ; exon_number 1 ; gene_id "STOM--AL359644.1^STOM^ENSG00000148175.13"  ; gene_name STOM ; gene_type protein_coding ; havana_gene "OTTHUMG00000020590.3"  ; havana_transcript "OTTHUMT00000053889.2"  ; hgnc_id "HGNC:3383"  ; level 2 ; orig_coord_info "chr9,121370127,121370187,-"  ; protein_id "ENSP00000286713.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STOM--AL359644.1^ENST00000286713.7"  ; transcript_name "STOM-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STOM--AL359644.1	HAVANA	mRNA	1055	10169	.	+	.	FI_gene_label "STOM^ENSG00000148175.13"  ; ID "STOM--AL359644.1^ENST00000286713.7"  ; Parent "STOM--AL359644.1^STOM^ENSG00000148175.13"  ; ccdsid "CCDS6830.1"  ; exon_id "ENSE00001950406.2"  ; exon_number 1 ; gene_id "STOM--AL359644.1^STOM^ENSG00000148175.13"  ; gene_name STOM ; gene_type protein_coding ; havana_gene "OTTHUMG00000020590.3"  ; havana_transcript "OTTHUMT00000053889.2"  ; hgnc_id "HGNC:3383"  ; level 2 ; orig_coord_info "chr9,121370127,121370187,-"  ; protein_id "ENSP00000286713.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STOM--AL359644.1^ENST00000286713.7"  ; transcript_name "STOM-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^ENST00000225576.7"  ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^ENST00000619038.5"  ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
VPS8--AC099560.1	HAVANA	gene	1001	61785	.	+	.	FI_gene_label "VPS8^ENSG00000156931.16"  ; ID "VPS8--AC099560.1^VPS8^ENSG00000156931.16"  ; exon_id "ENSE00001491382.1"  ; exon_number 2 ; gene_id "VPS8--AC099560.1^VPS8^ENSG00000156931.16"  ; gene_name VPS8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156707.10"  ; hgnc_id "HGNC:29122"  ; level 2 ; orig_coord_info "chr3,184824633,184824785,+"  ; protein_id "ENSP00000287546.4"  ; tag basic appris_alternative_1 ; transcript_id "VPS8--AC099560.1^ENST00000287546.8"  ; transcript_name "VPS8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
VPS8--AC099560.1	HAVANA	mRNA	1001	61785	.	+	.	FI_gene_label "VPS8^ENSG00000156931.16"  ; ID "VPS8--AC099560.1^ENST00000287546.8"  ; Parent "VPS8--AC099560.1^VPS8^ENSG00000156931.16"  ; exon_id "ENSE00001491382.1"  ; exon_number 2 ; gene_id "VPS8--AC099560.1^VPS8^ENSG00000156931.16"  ; gene_name VPS8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156707.10"  ; hgnc_id "HGNC:29122"  ; level 2 ; orig_coord_info "chr3,184824633,184824785,+"  ; protein_id "ENSP00000287546.4"  ; tag basic appris_alternative_1 ; transcript_id "VPS8--AC099560.1^ENST00000287546.8"  ; transcript_name "VPS8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DNAJC1--AL513128.1	HAVANA	gene	17617	19085	.	+	.	FI_gene_label "AL513128.1^ENSG00000233451.1"  ; ID "DNAJC1--AL513128.1^AL513128.1^ENSG00000233451.1"  ; exon_id "ENSE00001691485.1"  ; exon_number 1 ; gene_id "DNAJC1--AL513128.1^AL513128.1^ENSG00000233451.1"  ; gene_name "AL513128.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017809.1"  ; havana_transcript "OTTHUMT00000047192.1"  ; level 2 ; orig_coord_info "chr10,22361172,22361421,+"  ; tag basic ; transcript_id "DNAJC1--AL513128.1^ENST00000422675.1"  ; transcript_name "AL513128.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
DNAJC1--AL513128.1	HAVANA	RNA	17617	19085	.	+	.	FI_gene_label "AL513128.1^ENSG00000233451.1"  ; ID "DNAJC1--AL513128.1^ENST00000422675.1"  ; Parent "DNAJC1--AL513128.1^AL513128.1^ENSG00000233451.1"  ; exon_id "ENSE00001691485.1"  ; exon_number 1 ; gene_id "DNAJC1--AL513128.1^AL513128.1^ENSG00000233451.1"  ; gene_name "AL513128.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000017809.1"  ; havana_transcript "OTTHUMT00000047192.1"  ; level 2 ; orig_coord_info "chr10,22361172,22361421,+"  ; tag basic ; transcript_id "DNAJC1--AL513128.1^ENST00000422675.1"  ; transcript_name "AL513128.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
MIPEP--CYCSP33	HAVANA	gene	26049	26375	.	+	.	FI_gene_label "CYCSP33^ENSG00000233545.1"  ; ID "MIPEP--CYCSP33^CYCSP33^ENSG00000233545.1"  ; exon_id "ENSE00001758554.1"  ; exon_number 1 ; gene_id "MIPEP--CYCSP33^CYCSP33^ENSG00000233545.1"  ; gene_name CYCSP33 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000016581.3"  ; havana_transcript "OTTHUMT00000044188.3"  ; hgnc_id "HGNC:24407"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr13,24400703,24401029,+"  ; tag pseudo_consens basic ; transcript_id "MIPEP--CYCSP33^ENST00000414485.1"  ; transcript_name "CYCSP33-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
MIPEP--CYCSP33	HAVANA	RNA	26049	26375	.	+	.	FI_gene_label "CYCSP33^ENSG00000233545.1"  ; ID "MIPEP--CYCSP33^ENST00000414485.1"  ; Parent "MIPEP--CYCSP33^CYCSP33^ENSG00000233545.1"  ; exon_id "ENSE00001758554.1"  ; exon_number 1 ; gene_id "MIPEP--CYCSP33^CYCSP33^ENSG00000233545.1"  ; gene_name CYCSP33 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000016581.3"  ; havana_transcript "OTTHUMT00000044188.3"  ; hgnc_id "HGNC:24407"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr13,24400703,24401029,+"  ; tag pseudo_consens basic ; transcript_id "MIPEP--CYCSP33^ENST00000414485.1"  ; transcript_name "CYCSP33-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
MIPEP--TPTE2P6	HAVANA	gene	30340	36208	.	+	.	FI_gene_label "TPTE2P6^ENSG00000205822.10"  ; ID "MIPEP--TPTE2P6^TPTE2P6^ENSG00000205822.10"  ; exon_id "ENSE00001643591.1"  ; exon_number 1 ; gene_id "MIPEP--TPTE2P6^TPTE2P6^ENSG00000205822.10"  ; gene_name TPTE2P6 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000016586.1"  ; havana_transcript "OTTHUMT00000044194.1"  ; hgnc_id "HGNC:42644"  ; level 2 ; orig_coord_info "chr13,24586004,24586794,+"  ; tag basic ; transcript_id "MIPEP--TPTE2P6^ENST00000440905.5"  ; transcript_name "TPTE2P6-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
MIPEP--TPTE2P6	HAVANA	RNA	30340	36208	.	+	.	FI_gene_label "TPTE2P6^ENSG00000205822.10"  ; ID "MIPEP--TPTE2P6^ENST00000440905.5"  ; Parent "MIPEP--TPTE2P6^TPTE2P6^ENSG00000205822.10"  ; exon_id "ENSE00001643591.1"  ; exon_number 1 ; gene_id "MIPEP--TPTE2P6^TPTE2P6^ENSG00000205822.10"  ; gene_name TPTE2P6 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000016586.1"  ; havana_transcript "OTTHUMT00000044194.1"  ; hgnc_id "HGNC:42644"  ; level 2 ; orig_coord_info "chr13,24586004,24586794,+"  ; tag basic ; transcript_id "MIPEP--TPTE2P6^ENST00000440905.5"  ; transcript_name "TPTE2P6-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
STOM--AL359644.1	HAVANA	gene	15496	19062	.	+	.	FI_gene_label "AL359644.1^ENSG00000227355.3"  ; ID "STOM--AL359644.1^AL359644.1^ENSG00000227355.3"  ; exon_id "ENSE00001666539.1"  ; exon_number 1 ; gene_id "STOM--AL359644.1^AL359644.1^ENSG00000227355.3"  ; gene_name "AL359644.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000020591.3"  ; havana_transcript "OTTHUMT00000053891.1"  ; level 2 ; orig_coord_info "chr9,121375241,121375325,+"  ; transcript_id "STOM--AL359644.1^ENST00000440807.1"  ; transcript_name "AL359644.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
STOM--AL359644.1	HAVANA	RNA	15496	19062	.	+	.	FI_gene_label "AL359644.1^ENSG00000227355.3"  ; ID "STOM--AL359644.1^ENST00000440807.1"  ; Parent "STOM--AL359644.1^AL359644.1^ENSG00000227355.3"  ; exon_id "ENSE00001666539.1"  ; exon_number 1 ; gene_id "STOM--AL359644.1^AL359644.1^ENSG00000227355.3"  ; gene_name "AL359644.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000020591.3"  ; havana_transcript "OTTHUMT00000053891.1"  ; level 2 ; orig_coord_info "chr9,121375241,121375325,+"  ; transcript_id "STOM--AL359644.1^ENST00000440807.1"  ; transcript_name "AL359644.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
VPS8--AC099560.1	HAVANA	gene	65843	70925	.	+	.	FI_gene_label "AC099560.1^ENSG00000231873.2"  ; ID "VPS8--AC099560.1^AC099560.1^ENSG00000231873.2"  ; exon_id "ENSE00001712642.1"  ; exon_number 1 ; gene_id "VPS8--AC099560.1^AC099560.1^ENSG00000231873.2"  ; gene_name "AC099560.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000156011.2"  ; havana_transcript "OTTHUMT00000342724.1"  ; level 1 ; orig_coord_info "chr3,40766207,40766352,+"  ; tag basic exp_conf ; transcript_id "VPS8--AC099560.1^ENST00000412811.1"  ; transcript_name "AC099560.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
VPS8--AC099560.1	HAVANA	RNA	65843	70925	.	+	.	FI_gene_label "AC099560.1^ENSG00000231873.2"  ; ID "VPS8--AC099560.1^ENST00000412811.1"  ; Parent "VPS8--AC099560.1^AC099560.1^ENSG00000231873.2"  ; exon_id "ENSE00001712642.1"  ; exon_number 1 ; gene_id "VPS8--AC099560.1^AC099560.1^ENSG00000231873.2"  ; gene_name "AC099560.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000156011.2"  ; havana_transcript "OTTHUMT00000342724.1"  ; level 1 ; orig_coord_info "chr3,40766207,40766352,+"  ; tag basic exp_conf ; transcript_id "VPS8--AC099560.1^ENST00000412811.1"  ; transcript_name "AC099560.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
206 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 ------------------------------
355 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 17 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