.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-97c26d-R1_B23WHYVLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/569582cb532469a83da223add097b0/.command.out
Size: 52.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-97c26d-R1_B23WHYVLT4_1)
Attempt
Content

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 3659
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3659
=> 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:3659
  => 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 2 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: 
CRK--AC004253.2	HAVANA	gene	2211	8060	.	+	.	FI_gene_label "CRK^ENSG00000167193.8"  ; ID "CRK--AC004253.2^CRK^ENSG00000167193.8"  ; ccdsid "CCDS11002.1"  ; exon_id "ENSE00001199129.3"  ; exon_number 1 ; gene_id "CRK--AC004253.2^CRK^ENSG00000167193.8"  ; gene_name CRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000090317.4"  ; havana_transcript "OTTHUMT00000206679.2"  ; hgnc_id "HGNC:2362"  ; level 2 ; orig_coord_info "chr17,1455877,1456117,-"  ; protein_id "ENSP00000300574.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRK--AC004253.2^ENST00000300574.3"  ; transcript_name "CRK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CRK--AC004253.2	HAVANA	mRNA	2211	8060	.	+	.	FI_gene_label "CRK^ENSG00000167193.8"  ; ID "CRK--AC004253.2^ENST00000300574.3"  ; Parent "CRK--AC004253.2^CRK^ENSG00000167193.8"  ; ccdsid "CCDS11002.1"  ; exon_id "ENSE00001199129.3"  ; exon_number 1 ; gene_id "CRK--AC004253.2^CRK^ENSG00000167193.8"  ; gene_name CRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000090317.4"  ; havana_transcript "OTTHUMT00000206679.2"  ; hgnc_id "HGNC:2362"  ; level 2 ; orig_coord_info "chr17,1455877,1456117,-"  ; protein_id "ENSP00000300574.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRK--AC004253.2^ENST00000300574.3"  ; transcript_name "CRK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CRK--COPRS	HAVANA	gene	2211	8060	.	+	.	FI_gene_label "CRK^ENSG00000167193.8"  ; ID "CRK--COPRS^CRK^ENSG00000167193.8"  ; ccdsid "CCDS11002.1"  ; exon_id "ENSE00001199129.3"  ; exon_number 1 ; gene_id "CRK--COPRS^CRK^ENSG00000167193.8"  ; gene_name CRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000090317.4"  ; havana_transcript "OTTHUMT00000206679.2"  ; hgnc_id "HGNC:2362"  ; level 2 ; orig_coord_info "chr17,1455877,1456117,-"  ; protein_id "ENSP00000300574.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRK--COPRS^ENST00000300574.3"  ; transcript_name "CRK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CRK--COPRS	HAVANA	mRNA	2211	8060	.	+	.	FI_gene_label "CRK^ENSG00000167193.8"  ; ID "CRK--COPRS^ENST00000300574.3"  ; Parent "CRK--COPRS^CRK^ENSG00000167193.8"  ; ccdsid "CCDS11002.1"  ; exon_id "ENSE00001199129.3"  ; exon_number 1 ; gene_id "CRK--COPRS^CRK^ENSG00000167193.8"  ; gene_name CRK ; gene_type protein_coding ; havana_gene "OTTHUMG00000090317.4"  ; havana_transcript "OTTHUMT00000206679.2"  ; hgnc_id "HGNC:2362"  ; level 2 ; orig_coord_info "chr17,1455877,1456117,-"  ; protein_id "ENSP00000300574.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CRK--COPRS^ENST00000300574.3"  ; transcript_name "CRK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CRK--COPRS	HAVANA	gene	11112	15059	.	+	.	FI_gene_label "COPRS^ENSG00000172301.11"  ; ID "CRK--COPRS^COPRS^ENSG00000172301.11"  ; ccdsid "CCDS11268.1"  ; exon_id "ENSE00002720400.2"  ; exon_number 1 ; gene_id "CRK--COPRS^COPRS^ENSG00000172301.11"  ; gene_name COPRS ; gene_type protein_coding ; havana_gene "OTTHUMG00000132812.4"  ; havana_transcript "OTTHUMT00000256257.3"  ; hgnc_id "HGNC:28848"  ; level 2 ; orig_coord_info "chr17,31859101,31859199,-"  ; protein_id "ENSP00000304327.6"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CRK--COPRS^ENST00000302362.11"  ; transcript_name "COPRS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CRK--COPRS	HAVANA	mRNA	11112	15059	.	+	.	FI_gene_label "COPRS^ENSG00000172301.11"  ; ID "CRK--COPRS^ENST00000302362.11"  ; Parent "CRK--COPRS^COPRS^ENSG00000172301.11"  ; ccdsid "CCDS11268.1"  ; exon_id "ENSE00002720400.2"  ; exon_number 1 ; gene_id "CRK--COPRS^COPRS^ENSG00000172301.11"  ; gene_name COPRS ; gene_type protein_coding ; havana_gene "OTTHUMG00000132812.4"  ; havana_transcript "OTTHUMT00000256257.3"  ; hgnc_id "HGNC:28848"  ; level 2 ; orig_coord_info "chr17,31859101,31859199,-"  ; protein_id "ENSP00000304327.6"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "CRK--COPRS^ENST00000302362.11"  ; transcript_name "COPRS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
H4-16--CD163	HAVANA	gene	1001	4133	.	+	.	FI_gene_label "H4-16^ENSG00000197837.3"  ; ID "H4-16--CD163^H4-16^ENSG00000197837.3"  ; ccdsid "CCDS8665.1"  ; exon_id "ENSE00001428888.2"  ; exon_number 1 ; gene_id "H4-16--CD163^H4-16^ENSG00000197837.3"  ; gene_name "H4-16"  ; gene_type protein_coding ; havana_gene "OTTHUMG00000168735.1"  ; havana_transcript "OTTHUMT00000400839.1"  ; hgnc_id "HGNC:20510"  ; level 2 ; orig_coord_info "chr12,14770776,14771084,-"  ; protein_id "ENSP00000350767.3"  ; tag CCDS ; transcript_id "H4-16--CD163^ENST00000358064.3"  ; transcript_name "H4-16-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
H4-16--CD163	HAVANA	mRNA	1001	4133	.	+	.	FI_gene_label "H4-16^ENSG00000197837.3"  ; ID "H4-16--CD163^ENST00000358064.3"  ; Parent "H4-16--CD163^H4-16^ENSG00000197837.3"  ; ccdsid "CCDS8665.1"  ; exon_id "ENSE00001428888.2"  ; exon_number 1 ; gene_id "H4-16--CD163^H4-16^ENSG00000197837.3"  ; gene_name "H4-16"  ; gene_type protein_coding ; havana_gene "OTTHUMG00000168735.1"  ; havana_transcript "OTTHUMT00000400839.1"  ; hgnc_id "HGNC:20510"  ; level 2 ; orig_coord_info "chr12,14770776,14771084,-"  ; protein_id "ENSP00000350767.3"  ; tag CCDS ; transcript_id "H4-16--CD163^ENST00000358064.3"  ; transcript_name "H4-16-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
H4-16--CD163	HAVANA	gene	7134	25397	.	+	.	FI_gene_label "CD163^ENSG00000177575.13"  ; ID "H4-16--CD163^CD163^ENSG00000177575.13"  ; ccdsid "CCDS8578.1"  ; exon_id "ENSE00002286128.1"  ; exon_number 1 ; gene_id "H4-16--CD163^CD163^ENSG00000177575.13"  ; gene_name CD163 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168353.2"  ; havana_transcript "OTTHUMT00000399396.2"  ; hgnc_id "HGNC:1631"  ; level 2 ; orig_coord_info "chr12,7503645,7503690,-"  ; protein_id "ENSP00000352071.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "H4-16--CD163^ENST00000359156.8"  ; transcript_name "CD163-201"  ; transcript_support_level 1 ; transcript_type protein_coding
H4-16--CD163	HAVANA	mRNA	7134	25397	.	+	.	FI_gene_label "CD163^ENSG00000177575.13"  ; ID "H4-16--CD163^ENST00000359156.8"  ; Parent "H4-16--CD163^CD163^ENSG00000177575.13"  ; ccdsid "CCDS8578.1"  ; exon_id "ENSE00002286128.1"  ; exon_number 1 ; gene_id "H4-16--CD163^CD163^ENSG00000177575.13"  ; gene_name CD163 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168353.2"  ; havana_transcript "OTTHUMT00000399396.2"  ; hgnc_id "HGNC:1631"  ; level 2 ; orig_coord_info "chr12,7503645,7503690,-"  ; protein_id "ENSP00000352071.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "H4-16--CD163^ENST00000359156.8"  ; transcript_name "CD163-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HS3ST3B1--LRRC75A	HAVANA	gene	1001	7369	.	+	.	FI_gene_label "HS3ST3B1^ENSG00000125430.9"  ; ID "HS3ST3B1--LRRC75A^HS3ST3B1^ENSG00000125430.9"  ; ccdsid "CCDS11167.1"  ; exon_id "ENSE00003842317.1"  ; exon_number 1 ; gene_id "HS3ST3B1--LRRC75A^HS3ST3B1^ENSG00000125430.9"  ; gene_name HS3ST3B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058810.4"  ; havana_transcript "OTTHUMT00000129998.2"  ; hgnc_id "HGNC:5198"  ; level 2 ; orig_coord_info "chr17,14301519,14302072,+"  ; protein_id "ENSP00000354213.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HS3ST3B1--LRRC75A^ENST00000360954.3"  ; transcript_name "HS3ST3B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HS3ST3B1--LRRC75A	HAVANA	mRNA	1001	7369	.	+	.	FI_gene_label "HS3ST3B1^ENSG00000125430.9"  ; ID "HS3ST3B1--LRRC75A^ENST00000360954.3"  ; Parent "HS3ST3B1--LRRC75A^HS3ST3B1^ENSG00000125430.9"  ; ccdsid "CCDS11167.1"  ; exon_id "ENSE00003842317.1"  ; exon_number 1 ; gene_id "HS3ST3B1--LRRC75A^HS3ST3B1^ENSG00000125430.9"  ; gene_name HS3ST3B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058810.4"  ; havana_transcript "OTTHUMT00000129998.2"  ; hgnc_id "HGNC:5198"  ; level 2 ; orig_coord_info "chr17,14301519,14302072,+"  ; protein_id "ENSP00000354213.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HS3ST3B1--LRRC75A^ENST00000360954.3"  ; transcript_name "HS3ST3B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HS3ST3B1--LRRC75A	HAVANA	gene	10410	17480	.	+	.	FI_gene_label "LRRC75A^ENSG00000181350.12"  ; ID "HS3ST3B1--LRRC75A^LRRC75A^ENSG00000181350.12"  ; ccdsid "CCDS11178.2"  ; exon_id "ENSE00001812457.1"  ; exon_number 1 ; gene_id "HS3ST3B1--LRRC75A^LRRC75A^ENSG00000181350.12"  ; gene_name LRRC75A ; gene_type protein_coding ; havana_gene "OTTHUMG00000058988.4"  ; havana_transcript "OTTHUMT00000130461.2"  ; hgnc_id "HGNC:32403"  ; level 1 ; orig_coord_info "chr17,16491745,16491990,-"  ; protein_id "ENSP00000386504.3"  ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "HS3ST3B1--LRRC75A^ENST00000409083.7"  ; transcript_name "LRRC75A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
HS3ST3B1--LRRC75A	HAVANA	mRNA	10410	17480	.	+	.	FI_gene_label "LRRC75A^ENSG00000181350.12"  ; ID "HS3ST3B1--LRRC75A^ENST00000409083.7"  ; Parent "HS3ST3B1--LRRC75A^LRRC75A^ENSG00000181350.12"  ; ccdsid "CCDS11178.2"  ; exon_id "ENSE00001812457.1"  ; exon_number 1 ; gene_id "HS3ST3B1--LRRC75A^LRRC75A^ENSG00000181350.12"  ; gene_name LRRC75A ; gene_type protein_coding ; havana_gene "OTTHUMG00000058988.4"  ; havana_transcript "OTTHUMT00000130461.2"  ; hgnc_id "HGNC:32403"  ; level 1 ; orig_coord_info "chr17,16491745,16491990,-"  ; protein_id "ENSP00000386504.3"  ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "HS3ST3B1--LRRC75A^ENST00000409083.7"  ; transcript_name "LRRC75A-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
HS3ST3B1--ZNF287	HAVANA	gene	1001	7369	.	+	.	FI_gene_label "HS3ST3B1^ENSG00000125430.9"  ; ID "HS3ST3B1--ZNF287^HS3ST3B1^ENSG00000125430.9"  ; ccdsid "CCDS11167.1"  ; exon_id "ENSE00003842317.1"  ; exon_number 1 ; gene_id "HS3ST3B1--ZNF287^HS3ST3B1^ENSG00000125430.9"  ; gene_name HS3ST3B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058810.4"  ; havana_transcript "OTTHUMT00000129998.2"  ; hgnc_id "HGNC:5198"  ; level 2 ; orig_coord_info "chr17,14301519,14302072,+"  ; protein_id "ENSP00000354213.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HS3ST3B1--ZNF287^ENST00000360954.3"  ; transcript_name "HS3ST3B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HS3ST3B1--ZNF287	HAVANA	mRNA	1001	7369	.	+	.	FI_gene_label "HS3ST3B1^ENSG00000125430.9"  ; ID "HS3ST3B1--ZNF287^ENST00000360954.3"  ; Parent "HS3ST3B1--ZNF287^HS3ST3B1^ENSG00000125430.9"  ; ccdsid "CCDS11167.1"  ; exon_id "ENSE00003842317.1"  ; exon_number 1 ; gene_id "HS3ST3B1--ZNF287^HS3ST3B1^ENSG00000125430.9"  ; gene_name HS3ST3B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058810.4"  ; havana_transcript "OTTHUMT00000129998.2"  ; hgnc_id "HGNC:5198"  ; level 2 ; orig_coord_info "chr17,14301519,14302072,+"  ; protein_id "ENSP00000354213.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HS3ST3B1--ZNF287^ENST00000360954.3"  ; transcript_name "HS3ST3B1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HS3ST3B1--ZNF287	HAVANA	gene	10405	17769	.	+	.	FI_gene_label "ZNF287^ENSG00000141040.15"  ; ID "HS3ST3B1--ZNF287^ZNF287^ENSG00000141040.15"  ; ccdsid "CCDS11179.2"  ; exon_id "ENSE00000946324.1"  ; exon_number 2 ; gene_id "HS3ST3B1--ZNF287^ZNF287^ENSG00000141040.15"  ; gene_name ZNF287 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058993.6"  ; havana_transcript "OTTHUMT00000130504.1"  ; hgnc_id "HGNC:13502"  ; level 2 ; orig_coord_info "chr17,16567329,16567731,-"  ; protein_id "ENSP00000379168.1"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "HS3ST3B1--ZNF287^ENST00000395824.5"  ; transcript_name "ZNF287-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HS3ST3B1--ZNF287	HAVANA	mRNA	10405	17769	.	+	.	FI_gene_label "ZNF287^ENSG00000141040.15"  ; ID "HS3ST3B1--ZNF287^ENST00000395824.5"  ; Parent "HS3ST3B1--ZNF287^ZNF287^ENSG00000141040.15"  ; ccdsid "CCDS11179.2"  ; exon_id "ENSE00000946324.1"  ; exon_number 2 ; gene_id "HS3ST3B1--ZNF287^ZNF287^ENSG00000141040.15"  ; gene_name ZNF287 ; gene_type protein_coding ; havana_gene "OTTHUMG00000058993.6"  ; havana_transcript "OTTHUMT00000130504.1"  ; hgnc_id "HGNC:13502"  ; level 2 ; orig_coord_info "chr17,16567329,16567731,-"  ; protein_id "ENSP00000379168.1"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "HS3ST3B1--ZNF287^ENST00000395824.5"  ; transcript_name "ZNF287-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP2--ERBB4	HAVANA	gene	1001	28320	.	+	.	FI_gene_label "MAP2^ENSG00000078018.20"  ; ID "MAP2--ERBB4^MAP2^ENSG00000078018.20"  ; ccdsid "CCDS33369.1"  ; exon_id "ENSE00000934702.2"  ; exon_number 5 ; gene_id "MAP2--ERBB4^MAP2^ENSG00000078018.20"  ; gene_name MAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132962.7"  ; havana_transcript "OTTHUMT00000258126.1"  ; hgnc_id "HGNC:6839"  ; level 2 ; orig_coord_info "chr2,209653171,209653432,+"  ; protein_id "ENSP00000199940.6"  ; tag basic CCDS ; transcript_id "MAP2--ERBB4^ENST00000199940.10"  ; transcript_name "MAP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MAP2--ERBB4	HAVANA	mRNA	1001	28320	.	+	.	FI_gene_label "MAP2^ENSG00000078018.20"  ; ID "MAP2--ERBB4^ENST00000199940.10"  ; Parent "MAP2--ERBB4^MAP2^ENSG00000078018.20"  ; ccdsid "CCDS33369.1"  ; exon_id "ENSE00000934702.2"  ; exon_number 5 ; gene_id "MAP2--ERBB4^MAP2^ENSG00000078018.20"  ; gene_name MAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132962.7"  ; havana_transcript "OTTHUMT00000258126.1"  ; hgnc_id "HGNC:6839"  ; level 2 ; orig_coord_info "chr2,209653171,209653432,+"  ; protein_id "ENSP00000199940.6"  ; tag basic CCDS ; transcript_id "MAP2--ERBB4^ENST00000199940.10"  ; transcript_name "MAP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MAP2--ERBB4	HAVANA	gene	35233	58465	.	+	.	FI_gene_label "ERBB4^ENSG00000178568.15"  ; ID "MAP2--ERBB4^ERBB4^ENSG00000178568.15"  ; exon_id "ENSE00001775290.1"  ; exon_number 1 ; gene_id "MAP2--ERBB4^ERBB4^ENSG00000178568.15"  ; gene_name ERBB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133012.6"  ; havana_transcript "OTTHUMT00000336978.3"  ; hgnc_id "HGNC:3432"  ; level 2 ; orig_coord_info "chr2,212538449,212538529,-"  ; protein_id "ENSP00000260943.6"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "MAP2--ERBB4^ENST00000260943.10"  ; transcript_name "ERBB4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
MAP2--ERBB4	HAVANA	mRNA	35233	58465	.	+	.	FI_gene_label "ERBB4^ENSG00000178568.15"  ; ID "MAP2--ERBB4^ENST00000260943.10"  ; Parent "MAP2--ERBB4^ERBB4^ENSG00000178568.15"  ; exon_id "ENSE00001775290.1"  ; exon_number 1 ; gene_id "MAP2--ERBB4^ERBB4^ENSG00000178568.15"  ; gene_name ERBB4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133012.6"  ; havana_transcript "OTTHUMT00000336978.3"  ; hgnc_id "HGNC:3432"  ; level 2 ; orig_coord_info "chr2,212538449,212538529,-"  ; protein_id "ENSP00000260943.6"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "MAP2--ERBB4^ENST00000260943.10"  ; transcript_name "ERBB4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MPRIP--ASIC2	HAVANA	gene	54157	67638	.	+	.	FI_gene_label "ASIC2^ENSG00000108684.15"  ; ID "MPRIP--ASIC2^ASIC2^ENSG00000108684.15"  ; ccdsid "CCDS11276.1"  ; exon_id "ENSE00001248823.4"  ; exon_number 1 ; gene_id "MPRIP--ASIC2^ASIC2^ENSG00000108684.15"  ; gene_name ASIC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132885.4"  ; havana_transcript "OTTHUMT00000256378.1"  ; hgnc_id "HGNC:99"  ; level 2 ; orig_coord_info "chr17,33291408,33292115,-"  ; protein_id "ENSP00000225823.2"  ; tag basic MANE_Select CCDS ; transcript_id "MPRIP--ASIC2^ENST00000225823.7"  ; transcript_name "ASIC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MPRIP--ASIC2	HAVANA	mRNA	54157	67638	.	+	.	FI_gene_label "ASIC2^ENSG00000108684.15"  ; ID "MPRIP--ASIC2^ENST00000225823.7"  ; Parent "MPRIP--ASIC2^ASIC2^ENSG00000108684.15"  ; ccdsid "CCDS11276.1"  ; exon_id "ENSE00001248823.4"  ; exon_number 1 ; gene_id "MPRIP--ASIC2^ASIC2^ENSG00000108684.15"  ; gene_name ASIC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132885.4"  ; havana_transcript "OTTHUMT00000256378.1"  ; hgnc_id "HGNC:99"  ; level 2 ; orig_coord_info "chr17,33291408,33292115,-"  ; protein_id "ENSP00000225823.2"  ; tag basic MANE_Select CCDS ; transcript_id "MPRIP--ASIC2^ENST00000225823.7"  ; transcript_name "ASIC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MPRIP--ASIC2	HAVANA	gene	20478	37980	.	+	.	FI_gene_label "MPRIP^ENSG00000133030.22"  ; ID "MPRIP--ASIC2^MPRIP^ENSG00000133030.22"  ; exon_id "ENSE00001699698.1"  ; exon_number 1 ; gene_id "MPRIP--ASIC2^MPRIP^ENSG00000133030.22"  ; gene_name MPRIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000059276.11"  ; havana_transcript "OTTHUMT00000131588.4"  ; hgnc_id "HGNC:30321"  ; level 2 ; orig_coord_info "chr17,17158497,17159002,+"  ; protein_id "ENSP00000317786.6"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "MPRIP--ASIC2^ENST00000313485.10"  ; transcript_name "MPRIP-201"  ; transcript_support_level 5 ; transcript_type protein_coding
MPRIP--ASIC2	HAVANA	mRNA	20478	37980	.	+	.	FI_gene_label "MPRIP^ENSG00000133030.22"  ; ID "MPRIP--ASIC2^ENST00000313485.10"  ; Parent "MPRIP--ASIC2^MPRIP^ENSG00000133030.22"  ; exon_id "ENSE00001699698.1"  ; exon_number 1 ; gene_id "MPRIP--ASIC2^MPRIP^ENSG00000133030.22"  ; gene_name MPRIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000059276.11"  ; havana_transcript "OTTHUMT00000131588.4"  ; hgnc_id "HGNC:30321"  ; level 2 ; orig_coord_info "chr17,17158497,17159002,+"  ; protein_id "ENSP00000317786.6"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "MPRIP--ASIC2^ENST00000313485.10"  ; transcript_name "MPRIP-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MPRIP--POLDIP2	HAVANA	gene	20478	37980	.	+	.	FI_gene_label "MPRIP^ENSG00000133030.22"  ; ID "MPRIP--POLDIP2^MPRIP^ENSG00000133030.22"  ; exon_id "ENSE00001699698.1"  ; exon_number 1 ; gene_id "MPRIP--POLDIP2^MPRIP^ENSG00000133030.22"  ; gene_name MPRIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000059276.11"  ; havana_transcript "OTTHUMT00000131588.4"  ; hgnc_id "HGNC:30321"  ; level 2 ; orig_coord_info "chr17,17158497,17159002,+"  ; protein_id "ENSP00000317786.6"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "MPRIP--POLDIP2^ENST00000313485.10"  ; transcript_name "MPRIP-201"  ; transcript_support_level 5 ; transcript_type protein_coding
MPRIP--POLDIP2	HAVANA	mRNA	20478	37980	.	+	.	FI_gene_label "MPRIP^ENSG00000133030.22"  ; ID "MPRIP--POLDIP2^ENST00000313485.10"  ; Parent "MPRIP--POLDIP2^MPRIP^ENSG00000133030.22"  ; exon_id "ENSE00001699698.1"  ; exon_number 1 ; gene_id "MPRIP--POLDIP2^MPRIP^ENSG00000133030.22"  ; gene_name MPRIP ; gene_type protein_coding ; havana_gene "OTTHUMG00000059276.11"  ; havana_transcript "OTTHUMT00000131588.4"  ; hgnc_id "HGNC:30321"  ; level 2 ; orig_coord_info "chr17,17158497,17159002,+"  ; protein_id "ENSP00000317786.6"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "MPRIP--POLDIP2^ENST00000313485.10"  ; transcript_name "MPRIP-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MPRIP--POLDIP2	HAVANA	gene	50435	60323	.	+	.	FI_gene_label "POLDIP2^ENSG00000004142.12"  ; ID "MPRIP--POLDIP2^POLDIP2^ENSG00000004142.12"  ; ccdsid "CCDS74018.1"  ; exon_id "ENSE00002245633.3"  ; exon_number 1 ; gene_id "MPRIP--POLDIP2^POLDIP2^ENSG00000004142.12"  ; gene_name POLDIP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132065.9"  ; havana_transcript "OTTHUMT00000446163.5"  ; hgnc_id "HGNC:23781"  ; level 2 ; orig_coord_info "chr17,28357288,28357448,-"  ; protein_id "ENSP00000475924.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MPRIP--POLDIP2^ENST00000540200.6"  ; transcript_name "POLDIP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MPRIP--POLDIP2	HAVANA	mRNA	50435	60323	.	+	.	FI_gene_label "POLDIP2^ENSG00000004142.12"  ; ID "MPRIP--POLDIP2^ENST00000540200.6"  ; Parent "MPRIP--POLDIP2^POLDIP2^ENSG00000004142.12"  ; ccdsid "CCDS74018.1"  ; exon_id "ENSE00002245633.3"  ; exon_number 1 ; gene_id "MPRIP--POLDIP2^POLDIP2^ENSG00000004142.12"  ; gene_name POLDIP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132065.9"  ; havana_transcript "OTTHUMT00000446163.5"  ; hgnc_id "HGNC:23781"  ; level 2 ; orig_coord_info "chr17,28357288,28357448,-"  ; protein_id "ENSP00000475924.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MPRIP--POLDIP2^ENST00000540200.6"  ; transcript_name "POLDIP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
POLR3E--BCLAF1P2	HAVANA	gene	1035	24635	.	+	.	FI_gene_label "POLR3E^ENSG00000058600.16"  ; ID "POLR3E--BCLAF1P2^POLR3E^ENSG00000058600.16"  ; ccdsid "CCDS10605.1"  ; exon_id "ENSE00003533384.1"  ; exon_number 2 ; gene_id "POLR3E--BCLAF1P2^POLR3E^ENSG00000058600.16"  ; gene_name POLR3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000094779.4"  ; havana_transcript "OTTHUMT00000211590.2"  ; hgnc_id "HGNC:30347"  ; level 2 ; orig_coord_info "chr16,22302969,22303004,+"  ; protein_id "ENSP00000299853.5"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "POLR3E--BCLAF1P2^ENST00000299853.10"  ; transcript_name "POLR3E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
POLR3E--BCLAF1P2	HAVANA	mRNA	1035	24635	.	+	.	FI_gene_label "POLR3E^ENSG00000058600.16"  ; ID "POLR3E--BCLAF1P2^ENST00000299853.10"  ; Parent "POLR3E--BCLAF1P2^POLR3E^ENSG00000058600.16"  ; ccdsid "CCDS10605.1"  ; exon_id "ENSE00003533384.1"  ; exon_number 2 ; gene_id "POLR3E--BCLAF1P2^POLR3E^ENSG00000058600.16"  ; gene_name POLR3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000094779.4"  ; havana_transcript "OTTHUMT00000211590.2"  ; hgnc_id "HGNC:30347"  ; level 2 ; orig_coord_info "chr16,22302969,22303004,+"  ; protein_id "ENSP00000299853.5"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "POLR3E--BCLAF1P2^ENST00000299853.10"  ; transcript_name "POLR3E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
POLR3E--RNA5-8SP2	HAVANA	gene	1035	24635	.	+	.	FI_gene_label "POLR3E^ENSG00000058600.16"  ; ID "POLR3E--RNA5-8SP2^POLR3E^ENSG00000058600.16"  ; ccdsid "CCDS10605.1"  ; exon_id "ENSE00003533384.1"  ; exon_number 2 ; gene_id "POLR3E--RNA5-8SP2^POLR3E^ENSG00000058600.16"  ; gene_name POLR3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000094779.4"  ; havana_transcript "OTTHUMT00000211590.2"  ; hgnc_id "HGNC:30347"  ; level 2 ; orig_coord_info "chr16,22302969,22303004,+"  ; protein_id "ENSP00000299853.5"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "POLR3E--RNA5-8SP2^ENST00000299853.10"  ; transcript_name "POLR3E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
POLR3E--RNA5-8SP2	HAVANA	mRNA	1035	24635	.	+	.	FI_gene_label "POLR3E^ENSG00000058600.16"  ; ID "POLR3E--RNA5-8SP2^ENST00000299853.10"  ; Parent "POLR3E--RNA5-8SP2^POLR3E^ENSG00000058600.16"  ; ccdsid "CCDS10605.1"  ; exon_id "ENSE00003533384.1"  ; exon_number 2 ; gene_id "POLR3E--RNA5-8SP2^POLR3E^ENSG00000058600.16"  ; gene_name POLR3E ; gene_type protein_coding ; havana_gene "OTTHUMG00000094779.4"  ; havana_transcript "OTTHUMT00000211590.2"  ; hgnc_id "HGNC:30347"  ; level 2 ; orig_coord_info "chr16,22302969,22303004,+"  ; protein_id "ENSP00000299853.5"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "POLR3E--RNA5-8SP2^ENST00000299853.10"  ; transcript_name "POLR3E-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PURB--CDHR3	HAVANA	gene	24617	49038	.	+	.	FI_gene_label "CDHR3^ENSG00000128536.16"  ; ID "PURB--CDHR3^CDHR3^ENSG00000128536.16"  ; ccdsid "CCDS47684.1"  ; exon_id "ENSE00001844362.2"  ; exon_number 1 ; gene_id "PURB--CDHR3^CDHR3^ENSG00000128536.16"  ; gene_name CDHR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157520.3"  ; havana_transcript "OTTHUMT00000349025.3"  ; hgnc_id "HGNC:26308"  ; level 2 ; orig_coord_info "chr7,105963319,105963364,+"  ; protein_id "ENSP00000325954.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PURB--CDHR3^ENST00000317716.14"  ; transcript_name "CDHR3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PURB--CDHR3	HAVANA	mRNA	24617	49038	.	+	.	FI_gene_label "CDHR3^ENSG00000128536.16"  ; ID "PURB--CDHR3^ENST00000317716.14"  ; Parent "PURB--CDHR3^CDHR3^ENSG00000128536.16"  ; ccdsid "CCDS47684.1"  ; exon_id "ENSE00001844362.2"  ; exon_number 1 ; gene_id "PURB--CDHR3^CDHR3^ENSG00000128536.16"  ; gene_name CDHR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157520.3"  ; havana_transcript "OTTHUMT00000349025.3"  ; hgnc_id "HGNC:26308"  ; level 2 ; orig_coord_info "chr7,105963319,105963364,+"  ; protein_id "ENSP00000325954.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PURB--CDHR3^ENST00000317716.14"  ; transcript_name "CDHR3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PURB--CDHR3	HAVANA	gene	1001	10232	.	+	.	FI_gene_label "PURB^ENSG00000146676.10"  ; ID "PURB--CDHR3^PURB^ENSG00000146676.10"  ; ccdsid "CCDS5499.1"  ; exon_id "ENSE00001522527.5"  ; exon_number 1 ; gene_id "PURB--CDHR3^PURB^ENSG00000146676.10"  ; gene_name PURB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023578.6"  ; havana_transcript "OTTHUMT00000251332.4"  ; hgnc_id "HGNC:9702"  ; level 2 ; orig_coord_info "chr7,44884413,44885348,-"  ; protein_id "ENSP00000379051.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PURB--CDHR3^ENST00000395699.5"  ; transcript_name "PURB-201"  ; transcript_support_level NA ; transcript_type protein_coding
PURB--CDHR3	HAVANA	mRNA	1001	10232	.	+	.	FI_gene_label "PURB^ENSG00000146676.10"  ; ID "PURB--CDHR3^ENST00000395699.5"  ; Parent "PURB--CDHR3^PURB^ENSG00000146676.10"  ; ccdsid "CCDS5499.1"  ; exon_id "ENSE00001522527.5"  ; exon_number 1 ; gene_id "PURB--CDHR3^PURB^ENSG00000146676.10"  ; gene_name PURB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023578.6"  ; havana_transcript "OTTHUMT00000251332.4"  ; hgnc_id "HGNC:9702"  ; level 2 ; orig_coord_info "chr7,44884413,44885348,-"  ; protein_id "ENSP00000379051.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PURB--CDHR3^ENST00000395699.5"  ; transcript_name "PURB-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
SMG1P1--GAS7	HAVANA	gene	32022	61058	.	+	.	FI_gene_label "GAS7^ENSG00000007237.19"  ; ID "SMG1P1--GAS7^GAS7^ENSG00000007237.19"  ; exon_id "ENSE00002725781.1"  ; exon_number 2 ; gene_id "SMG1P1--GAS7^GAS7^ENSG00000007237.19"  ; gene_name GAS7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177945.15"  ; havana_transcript "OTTHUMT00000439868.3"  ; hgnc_id "HGNC:4169"  ; level 2 ; orig_coord_info "chr17,10039742,10039744,-"  ; protein_id "ENSP00000322608.5"  ; tag CAGE_supported_TSS basic ; transcript_id "SMG1P1--GAS7^ENST00000323816.8"  ; transcript_name "GAS7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SMG1P1--GAS7	HAVANA	mRNA	32022	61058	.	+	.	FI_gene_label "GAS7^ENSG00000007237.19"  ; ID "SMG1P1--GAS7^ENST00000323816.8"  ; Parent "SMG1P1--GAS7^GAS7^ENSG00000007237.19"  ; exon_id "ENSE00002725781.1"  ; exon_number 2 ; gene_id "SMG1P1--GAS7^GAS7^ENSG00000007237.19"  ; gene_name GAS7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177945.15"  ; havana_transcript "OTTHUMT00000439868.3"  ; hgnc_id "HGNC:4169"  ; level 2 ; orig_coord_info "chr17,10039742,10039744,-"  ; protein_id "ENSP00000322608.5"  ; tag CAGE_supported_TSS basic ; transcript_id "SMG1P1--GAS7^ENST00000323816.8"  ; transcript_name "GAS7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SPNS1--ABCC1	HAVANA	gene	1558	9863	.	+	.	FI_gene_label "SPNS1^ENSG00000169682.18"  ; ID "SPNS1--ABCC1^SPNS1^ENSG00000169682.18"  ; ccdsid "CCDS10646.1"  ; exon_id "ENSE00001614308.2"  ; exon_number 1 ; gene_id "SPNS1--ABCC1^SPNS1^ENSG00000169682.18"  ; gene_name SPNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131762.4"  ; havana_transcript "OTTHUMT00000254690.3"  ; hgnc_id "HGNC:30621"  ; level 2 ; orig_coord_info "chr16,28975152,28975392,+"  ; protein_id "ENSP00000309945.11"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPNS1--ABCC1^ENST00000311008.16"  ; transcript_name "SPNS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SPNS1--ABCC1	HAVANA	mRNA	1558	9863	.	+	.	FI_gene_label "SPNS1^ENSG00000169682.18"  ; ID "SPNS1--ABCC1^ENST00000311008.16"  ; Parent "SPNS1--ABCC1^SPNS1^ENSG00000169682.18"  ; ccdsid "CCDS10646.1"  ; exon_id "ENSE00001614308.2"  ; exon_number 1 ; gene_id "SPNS1--ABCC1^SPNS1^ENSG00000169682.18"  ; gene_name SPNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131762.4"  ; havana_transcript "OTTHUMT00000254690.3"  ; hgnc_id "HGNC:30621"  ; level 2 ; orig_coord_info "chr16,28975152,28975392,+"  ; protein_id "ENSP00000309945.11"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPNS1--ABCC1^ENST00000311008.16"  ; transcript_name "SPNS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SPNS1--ABCC1	HAVANA	gene	13308	55493	.	+	.	FI_gene_label "ABCC1^ENSG00000103222.20"  ; ID "SPNS1--ABCC1^ABCC1^ENSG00000103222.20"  ; exon_id "ENSE00003713334.1"  ; exon_number 1 ; gene_id "SPNS1--ABCC1^ABCC1^ENSG00000103222.20"  ; gene_name ABCC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048267.6"  ; hgnc_id "HGNC:51"  ; level 2 ; orig_coord_info "chr16,15949752,15949799,+"  ; protein_id "ENSP00000382340.4"  ; tag basic appris_alternative_2 ; transcript_id "SPNS1--ABCC1^ENST00000399408.7"  ; transcript_name "ABCC1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SPNS1--ABCC1	HAVANA	mRNA	13308	55493	.	+	.	FI_gene_label "ABCC1^ENSG00000103222.20"  ; ID "SPNS1--ABCC1^ENST00000399408.7"  ; Parent "SPNS1--ABCC1^ABCC1^ENSG00000103222.20"  ; exon_id "ENSE00003713334.1"  ; exon_number 1 ; gene_id "SPNS1--ABCC1^ABCC1^ENSG00000103222.20"  ; gene_name ABCC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048267.6"  ; hgnc_id "HGNC:51"  ; level 2 ; orig_coord_info "chr16,15949752,15949799,+"  ; protein_id "ENSP00000382340.4"  ; tag basic appris_alternative_2 ; transcript_id "SPNS1--ABCC1^ENST00000399408.7"  ; transcript_name "ABCC1-201"  ; 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: 
TXNDC11--AC025277.1	HAVANA	gene	1001	17381	.	+	.	FI_gene_label "TXNDC11^ENSG00000153066.13"  ; ID "TXNDC11--AC025277.1^TXNDC11^ENSG00000153066.13"  ; ccdsid "CCDS32387.1"  ; exon_id "ENSE00002633581.2"  ; exon_number 1 ; gene_id "TXNDC11--AC025277.1^TXNDC11^ENSG00000153066.13"  ; gene_name TXNDC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177467.2"  ; havana_transcript "OTTHUMT00000437054.1"  ; hgnc_id "HGNC:28030"  ; level 2 ; orig_coord_info "chr16,11742477,11742730,-"  ; protein_id "ENSP00000283033.5"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TXNDC11--AC025277.1^ENST00000283033.10"  ; transcript_name "TXNDC11-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TXNDC11--AC025277.1	HAVANA	mRNA	1001	17381	.	+	.	FI_gene_label "TXNDC11^ENSG00000153066.13"  ; ID "TXNDC11--AC025277.1^ENST00000283033.10"  ; Parent "TXNDC11--AC025277.1^TXNDC11^ENSG00000153066.13"  ; ccdsid "CCDS32387.1"  ; exon_id "ENSE00002633581.2"  ; exon_number 1 ; gene_id "TXNDC11--AC025277.1^TXNDC11^ENSG00000153066.13"  ; gene_name TXNDC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177467.2"  ; havana_transcript "OTTHUMT00000437054.1"  ; hgnc_id "HGNC:28030"  ; level 2 ; orig_coord_info "chr16,11742477,11742730,-"  ; protein_id "ENSP00000283033.5"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TXNDC11--AC025277.1^ENST00000283033.10"  ; transcript_name "TXNDC11-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
TXNDC11--AC109495.1	HAVANA	gene	1001	17381	.	+	.	FI_gene_label "TXNDC11^ENSG00000153066.13"  ; ID "TXNDC11--AC109495.1^TXNDC11^ENSG00000153066.13"  ; ccdsid "CCDS32387.1"  ; exon_id "ENSE00002633581.2"  ; exon_number 1 ; gene_id "TXNDC11--AC109495.1^TXNDC11^ENSG00000153066.13"  ; gene_name TXNDC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177467.2"  ; havana_transcript "OTTHUMT00000437054.1"  ; hgnc_id "HGNC:28030"  ; level 2 ; orig_coord_info "chr16,11742477,11742730,-"  ; protein_id "ENSP00000283033.5"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TXNDC11--AC109495.1^ENST00000283033.10"  ; transcript_name "TXNDC11-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TXNDC11--AC109495.1	HAVANA	mRNA	1001	17381	.	+	.	FI_gene_label "TXNDC11^ENSG00000153066.13"  ; ID "TXNDC11--AC109495.1^ENST00000283033.10"  ; Parent "TXNDC11--AC109495.1^TXNDC11^ENSG00000153066.13"  ; ccdsid "CCDS32387.1"  ; exon_id "ENSE00002633581.2"  ; exon_number 1 ; gene_id "TXNDC11--AC109495.1^TXNDC11^ENSG00000153066.13"  ; gene_name TXNDC11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177467.2"  ; havana_transcript "OTTHUMT00000437054.1"  ; hgnc_id "HGNC:28030"  ; level 2 ; orig_coord_info "chr16,11742477,11742730,-"  ; protein_id "ENSP00000283033.5"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TXNDC11--AC109495.1^ENST00000283033.10"  ; transcript_name "TXNDC11-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ULK2--ANKRD30BP1	HAVANA	gene	1001	37290	.	+	.	FI_gene_label "ULK2^ENSG00000083290.20"  ; ID "ULK2--ANKRD30BP1^ULK2^ENSG00000083290.20"  ; ccdsid "CCDS11213.1"  ; exon_id "ENSE00001415890.1"  ; exon_number 1 ; gene_id "ULK2--ANKRD30BP1^ULK2^ENSG00000083290.20"  ; gene_name ULK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059511.7"  ; havana_transcript "OTTHUMT00000132376.2"  ; hgnc_id "HGNC:13480"  ; level 2 ; orig_coord_info "chr17,19867328,19867417,-"  ; protein_id "ENSP00000354877.2"  ; tag alternative_3_UTR basic appris_principal_1 CCDS ; transcript_id "ULK2--ANKRD30BP1^ENST00000361658.6"  ; transcript_name "ULK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ULK2--ANKRD30BP1	HAVANA	mRNA	1001	37290	.	+	.	FI_gene_label "ULK2^ENSG00000083290.20"  ; ID "ULK2--ANKRD30BP1^ENST00000361658.6"  ; Parent "ULK2--ANKRD30BP1^ULK2^ENSG00000083290.20"  ; ccdsid "CCDS11213.1"  ; exon_id "ENSE00001415890.1"  ; exon_number 1 ; gene_id "ULK2--ANKRD30BP1^ULK2^ENSG00000083290.20"  ; gene_name ULK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059511.7"  ; havana_transcript "OTTHUMT00000132376.2"  ; hgnc_id "HGNC:13480"  ; level 2 ; orig_coord_info "chr17,19867328,19867417,-"  ; protein_id "ENSP00000354877.2"  ; tag alternative_3_UTR basic appris_principal_1 CCDS ; transcript_id "ULK2--ANKRD30BP1^ENST00000361658.6"  ; transcript_name "ULK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CRK--AC004253.2	HAVANA	gene	11065	12084	.	+	.	FI_gene_label "AC004253.2^ENSG00000265046.1"  ; ID "CRK--AC004253.2^AC004253.2^ENSG00000265046.1"  ; exon_id "ENSE00002734663.1"  ; exon_number 1 ; gene_id "CRK--AC004253.2^AC004253.2^ENSG00000265046.1"  ; gene_name "AC004253.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000179321.1"  ; havana_transcript "OTTHUMT00000445734.1"  ; level 2 ; orig_coord_info "chr17,31830731,31830790,+"  ; tag basic ; transcript_id "CRK--AC004253.2^ENST00000585025.1"  ; transcript_name "AC004253.2-201"  ; transcript_support_level 3 ; transcript_type lncRNA
CRK--AC004253.2	HAVANA	RNA	11065	12084	.	+	.	FI_gene_label "AC004253.2^ENSG00000265046.1"  ; ID "CRK--AC004253.2^ENST00000585025.1"  ; Parent "CRK--AC004253.2^AC004253.2^ENSG00000265046.1"  ; exon_id "ENSE00002734663.1"  ; exon_number 1 ; gene_id "CRK--AC004253.2^AC004253.2^ENSG00000265046.1"  ; gene_name "AC004253.2"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000179321.1"  ; havana_transcript "OTTHUMT00000445734.1"  ; level 2 ; orig_coord_info "chr17,31830731,31830790,+"  ; tag basic ; transcript_id "CRK--AC004253.2^ENST00000585025.1"  ; transcript_name "AC004253.2-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
POLR3E--BCLAF1P2	HAVANA	gene	27641	30249	.	+	.	FI_gene_label "BCLAF1P2^ENSG00000279800.2"  ; ID "POLR3E--BCLAF1P2^BCLAF1P2^ENSG00000279800.2"  ; exon_id "ENSE00003755616.2"  ; exon_number 1 ; gene_id "POLR3E--BCLAF1P2^BCLAF1P2^ENSG00000279800.2"  ; gene_name BCLAF1P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000191386.1"  ; havana_transcript "OTTHUMT00000487743.1"  ; hgnc_id "HGNC:51807"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr16,34266041,34268649,-"  ; tag pseudo_consens basic ; transcript_id "POLR3E--BCLAF1P2^ENST00000624956.2"  ; transcript_name "BCLAF1P2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
POLR3E--BCLAF1P2	HAVANA	RNA	27641	30249	.	+	.	FI_gene_label "BCLAF1P2^ENSG00000279800.2"  ; ID "POLR3E--BCLAF1P2^ENST00000624956.2"  ; Parent "POLR3E--BCLAF1P2^BCLAF1P2^ENSG00000279800.2"  ; exon_id "ENSE00003755616.2"  ; exon_number 1 ; gene_id "POLR3E--BCLAF1P2^BCLAF1P2^ENSG00000279800.2"  ; gene_name BCLAF1P2 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000191386.1"  ; havana_transcript "OTTHUMT00000487743.1"  ; hgnc_id "HGNC:51807"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr16,34266041,34268649,-"  ; tag pseudo_consens basic ; transcript_id "POLR3E--BCLAF1P2^ENST00000624956.2"  ; transcript_name "BCLAF1P2-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
POLR3E--RNA5-8SP2	ENSEMBL	gene	27641	27792	.	+	.	FI_gene_label "RNA5-8SP2^ENSG00000200434.1"  ; ID "POLR3E--RNA5-8SP2^RNA5-8SP2^ENSG00000200434.1"  ; exon_id "ENSE00001806843.1"  ; exon_number 1 ; gene_id "POLR3E--RNA5-8SP2^RNA5-8SP2^ENSG00000200434.1"  ; gene_name "RNA5-8SP2"  ; gene_type rRNA_pseudogene ; hgnc_id "HGNC:41956"  ; level 3 ; orig_coord_info "chr16,34162959,34163110,+"  ; tag basic ; transcript_id "POLR3E--RNA5-8SP2^ENST00000363564.1"  ; transcript_name "RNA5-8SP2-201"  ; transcript_support_level NA ; transcript_type rRNA_pseudogene
POLR3E--RNA5-8SP2	ENSEMBL	RNA	27641	27792	.	+	.	FI_gene_label "RNA5-8SP2^ENSG00000200434.1"  ; ID "POLR3E--RNA5-8SP2^ENST00000363564.1"  ; Parent "POLR3E--RNA5-8SP2^RNA5-8SP2^ENSG00000200434.1"  ; exon_id "ENSE00001806843.1"  ; exon_number 1 ; gene_id "POLR3E--RNA5-8SP2^RNA5-8SP2^ENSG00000200434.1"  ; gene_name "RNA5-8SP2"  ; gene_type rRNA_pseudogene ; hgnc_id "HGNC:41956"  ; level 3 ; orig_coord_info "chr16,34162959,34163110,+"  ; tag basic ; transcript_id "POLR3E--RNA5-8SP2^ENST00000363564.1"  ; transcript_name "RNA5-8SP2-201"  ; transcript_support_level NA ; transcript_type rRNA_pseudogene
L1 and L2 created: 
SMG1P1--GAS7	HAVANA	gene	1578	10727	.	+	.	FI_gene_label "SMG1P1^ENSG00000237296.9"  ; ID "SMG1P1--GAS7^SMG1P1^ENSG00000237296.9"  ; exon_id "ENSE00001654077.1"  ; exon_number 1 ; gene_id "SMG1P1--GAS7^SMG1P1^ENSG00000237296.9"  ; gene_name SMG1P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000156797.2"  ; havana_transcript "OTTHUMT00000345868.1"  ; hgnc_id "HGNC:44186"  ; level 2 ; orig_coord_info "chr16,22437585,22437737,+"  ; transcript_id "SMG1P1--GAS7^ENST00000308347.10"  ; transcript_name "SMG1P1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
SMG1P1--GAS7	HAVANA	RNA	1578	10727	.	+	.	FI_gene_label "SMG1P1^ENSG00000237296.9"  ; ID "SMG1P1--GAS7^ENST00000308347.10"  ; Parent "SMG1P1--GAS7^SMG1P1^ENSG00000237296.9"  ; exon_id "ENSE00001654077.1"  ; exon_number 1 ; gene_id "SMG1P1--GAS7^SMG1P1^ENSG00000237296.9"  ; gene_name SMG1P1 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000156797.2"  ; havana_transcript "OTTHUMT00000345868.1"  ; hgnc_id "HGNC:44186"  ; level 2 ; orig_coord_info "chr16,22437585,22437737,+"  ; transcript_id "SMG1P1--GAS7^ENST00000308347.10"  ; transcript_name "SMG1P1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
TXNDC11--AC025277.1	HAVANA	gene	20382	22036	.	+	.	FI_gene_label "AC025277.1^ENSG00000261555.1"  ; ID "TXNDC11--AC025277.1^AC025277.1^ENSG00000261555.1"  ; exon_id "ENSE00002589454.1"  ; exon_number 1 ; gene_id "TXNDC11--AC025277.1^AC025277.1^ENSG00000261555.1"  ; gene_name "AC025277.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000177267.1"  ; havana_transcript "OTTHUMT00000436068.1"  ; level 2 ; orig_coord_info "chr16,17825252,17826906,+"  ; tag basic ; transcript_id "TXNDC11--AC025277.1^ENST00000564852.1"  ; transcript_name "AC025277.1-201"  ; transcript_support_level NA ; transcript_type lncRNA
TXNDC11--AC025277.1	HAVANA	RNA	20382	22036	.	+	.	FI_gene_label "AC025277.1^ENSG00000261555.1"  ; ID "TXNDC11--AC025277.1^ENST00000564852.1"  ; Parent "TXNDC11--AC025277.1^AC025277.1^ENSG00000261555.1"  ; exon_id "ENSE00002589454.1"  ; exon_number 1 ; gene_id "TXNDC11--AC025277.1^AC025277.1^ENSG00000261555.1"  ; gene_name "AC025277.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000177267.1"  ; havana_transcript "OTTHUMT00000436068.1"  ; level 2 ; orig_coord_info "chr16,17825252,17826906,+"  ; tag basic ; transcript_id "TXNDC11--AC025277.1^ENST00000564852.1"  ; transcript_name "AC025277.1-201"  ; transcript_support_level NA ; transcript_type lncRNA
L1 and L2 created: 
TXNDC11--AC109495.1	HAVANA	gene	20382	21036	.	+	.	FI_gene_label "AC109495.1^ENSG00000260945.1"  ; ID "TXNDC11--AC109495.1^AC109495.1^ENSG00000260945.1"  ; exon_id "ENSE00002597322.1"  ; exon_number 1 ; gene_id "TXNDC11--AC109495.1^AC109495.1^ENSG00000260945.1"  ; gene_name "AC109495.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000177266.1"  ; havana_transcript "OTTHUMT00000436067.1"  ; level 2 ; orig_coord_info "chr16,17540947,17540985,-"  ; tag basic ; transcript_id "TXNDC11--AC109495.1^ENST00000568026.1"  ; transcript_name "AC109495.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
TXNDC11--AC109495.1	HAVANA	RNA	20382	21036	.	+	.	FI_gene_label "AC109495.1^ENSG00000260945.1"  ; ID "TXNDC11--AC109495.1^ENST00000568026.1"  ; Parent "TXNDC11--AC109495.1^AC109495.1^ENSG00000260945.1"  ; exon_id "ENSE00002597322.1"  ; exon_number 1 ; gene_id "TXNDC11--AC109495.1^AC109495.1^ENSG00000260945.1"  ; gene_name "AC109495.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000177266.1"  ; havana_transcript "OTTHUMT00000436067.1"  ; level 2 ; orig_coord_info "chr16,17540947,17540985,-"  ; tag basic ; transcript_id "TXNDC11--AC109495.1^ENST00000568026.1"  ; transcript_name "AC109495.1-201"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
ULK2--ANKRD30BP1	HAVANA	gene	40292	55178	.	+	.	FI_gene_label "ANKRD30BP1^ENSG00000175302.5"  ; ID "ULK2--ANKRD30BP1^ANKRD30BP1^ENSG00000175302.5"  ; exon_id "ENSE00001690047.1"  ; exon_number 1 ; gene_id "ULK2--ANKRD30BP1^ANKRD30BP1^ENSG00000175302.5"  ; gene_name ANKRD30BP1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000074201.1"  ; havana_transcript "OTTHUMT00000157664.1"  ; hgnc_id "HGNC:19722"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chr21,13427745,13427773,-"  ; tag pseudo_consens basic ; transcript_id "ULK2--ANKRD30BP1^ENST00000451052.1"  ; transcript_name "ANKRD30BP1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
ULK2--ANKRD30BP1	HAVANA	RNA	40292	55178	.	+	.	FI_gene_label "ANKRD30BP1^ENSG00000175302.5"  ; ID "ULK2--ANKRD30BP1^ENST00000451052.1"  ; Parent "ULK2--ANKRD30BP1^ANKRD30BP1^ENSG00000175302.5"  ; exon_id "ENSE00001690047.1"  ; exon_number 1 ; gene_id "ULK2--ANKRD30BP1^ANKRD30BP1^ENSG00000175302.5"  ; gene_name ANKRD30BP1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000074201.1"  ; havana_transcript "OTTHUMT00000157664.1"  ; hgnc_id "HGNC:19722"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chr21,13427745,13427773,-"  ; tag pseudo_consens basic ; transcript_id "ULK2--ANKRD30BP1^ENST00000451052.1"  ; transcript_name "ANKRD30BP1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
268 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 ------------------------------
432 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