File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/e71b8256d1b9d7e25e09453f458153/.command.out
Size
38.2 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_bCu-T1-TRNA-1_A23MVY2LT4_2)
Attempt

Content

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

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 5535
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 5535
=> 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:5535
  => 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: 
ADAM23--HDAC4	HAVANA	gene	1001	32824	.	+	.	FI_gene_label "ADAM23^ENSG00000114948.13"  ; ID "ADAM23--HDAC4^ADAM23^ENSG00000114948.13"  ; ccdsid "CCDS2369.1"  ; exon_id "ENSE00001950784.2"  ; exon_number 1 ; gene_id "ADAM23--HDAC4^ADAM23^ENSG00000114948.13"  ; gene_name ADAM23 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132919.5"  ; havana_transcript "OTTHUMT00000256431.4"  ; hgnc_id "HGNC:202"  ; level 2 ; orig_coord_info "chr2,206443867,206444080,+"  ; protein_id "ENSP00000264377.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000264377.8"  ; transcript_name "ADAM23-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ADAM23--HDAC4	HAVANA	mRNA	1001	32824	.	+	.	FI_gene_label "ADAM23^ENSG00000114948.13"  ; ID "ADAM23--HDAC4^ENST00000264377.8"  ; Parent "ADAM23--HDAC4^ADAM23^ENSG00000114948.13"  ; ccdsid "CCDS2369.1"  ; exon_id "ENSE00001950784.2"  ; exon_number 1 ; gene_id "ADAM23--HDAC4^ADAM23^ENSG00000114948.13"  ; gene_name ADAM23 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132919.5"  ; havana_transcript "OTTHUMT00000256431.4"  ; hgnc_id "HGNC:202"  ; level 2 ; orig_coord_info "chr2,206443867,206444080,+"  ; protein_id "ENSP00000264377.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000264377.8"  ; transcript_name "ADAM23-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ADAM23--HDAC4	HAVANA	gene	36530	81643	.	+	.	FI_gene_label "HDAC4^ENSG00000068024.17"  ; ID "ADAM23--HDAC4^HDAC4^ENSG00000068024.17"  ; ccdsid "CCDS2529.1"  ; exon_id "ENSE00003664840.1"  ; exon_number 2 ; gene_id "ADAM23--HDAC4^HDAC4^ENSG00000068024.17"  ; gene_name HDAC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133344.7"  ; havana_transcript "OTTHUMT00000257174.2"  ; hgnc_id "HGNC:14063"  ; level 2 ; orig_coord_info "chr2,239352678,239352699,-"  ; protein_id "ENSP00000264606.3"  ; tag basic appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000345617.7"  ; transcript_name "HDAC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ADAM23--HDAC4	HAVANA	mRNA	36530	81643	.	+	.	FI_gene_label "HDAC4^ENSG00000068024.17"  ; ID "ADAM23--HDAC4^ENST00000345617.7"  ; Parent "ADAM23--HDAC4^HDAC4^ENSG00000068024.17"  ; ccdsid "CCDS2529.1"  ; exon_id "ENSE00003664840.1"  ; exon_number 2 ; gene_id "ADAM23--HDAC4^HDAC4^ENSG00000068024.17"  ; gene_name HDAC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133344.7"  ; havana_transcript "OTTHUMT00000257174.2"  ; hgnc_id "HGNC:14063"  ; level 2 ; orig_coord_info "chr2,239352678,239352699,-"  ; protein_id "ENSP00000264606.3"  ; tag basic appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000345617.7"  ; transcript_name "HDAC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AL845331.2--AFF3	ENSEMBL	gene	10488	55391	.	+	.	FI_gene_label "AFF3^ENSG00000144218.20"  ; ID "AL845331.2--AFF3^AFF3^ENSG00000144218.20"  ; ccdsid "CCDS42723.1"  ; exon_id "ENSE00003790625.1"  ; exon_number 3 ; gene_id "AL845331.2--AFF3^AFF3^ENSG00000144218.20"  ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13"  ; hgnc_id "HGNC:6473"  ; level 3 ; orig_coord_info "chr2,100104402,100104454,-"  ; protein_id "ENSP00000317421.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "AL845331.2--AFF3^ENST00000317233.8"  ; transcript_name "AFF3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AL845331.2--AFF3	ENSEMBL	mRNA	10488	55391	.	+	.	FI_gene_label "AFF3^ENSG00000144218.20"  ; ID "AL845331.2--AFF3^ENST00000317233.8"  ; Parent "AL845331.2--AFF3^AFF3^ENSG00000144218.20"  ; ccdsid "CCDS42723.1"  ; exon_id "ENSE00003790625.1"  ; exon_number 3 ; gene_id "AL845331.2--AFF3^AFF3^ENSG00000144218.20"  ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13"  ; hgnc_id "HGNC:6473"  ; level 3 ; orig_coord_info "chr2,100104402,100104454,-"  ; protein_id "ENSP00000317421.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "AL845331.2--AFF3^ENST00000317233.8"  ; transcript_name "AFF3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
BMS1P23--AFF3	ENSEMBL	gene	12133	57036	.	+	.	FI_gene_label "AFF3^ENSG00000144218.20"  ; ID "BMS1P23--AFF3^AFF3^ENSG00000144218.20"  ; ccdsid "CCDS42723.1"  ; exon_id "ENSE00003790625.1"  ; exon_number 3 ; gene_id "BMS1P23--AFF3^AFF3^ENSG00000144218.20"  ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13"  ; hgnc_id "HGNC:6473"  ; level 3 ; orig_coord_info "chr2,100104402,100104454,-"  ; protein_id "ENSP00000317421.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "BMS1P23--AFF3^ENST00000317233.8"  ; transcript_name "AFF3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
BMS1P23--AFF3	ENSEMBL	mRNA	12133	57036	.	+	.	FI_gene_label "AFF3^ENSG00000144218.20"  ; ID "BMS1P23--AFF3^ENST00000317233.8"  ; Parent "BMS1P23--AFF3^AFF3^ENSG00000144218.20"  ; ccdsid "CCDS42723.1"  ; exon_id "ENSE00003790625.1"  ; exon_number 3 ; gene_id "BMS1P23--AFF3^AFF3^ENSG00000144218.20"  ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13"  ; hgnc_id "HGNC:6473"  ; level 3 ; orig_coord_info "chr2,100104402,100104454,-"  ; protein_id "ENSP00000317421.4"  ; tag basic appris_alternative_2 CCDS ; transcript_id "BMS1P23--AFF3^ENST00000317233.8"  ; transcript_name "AFF3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
IRAG1--ZNF143	HAVANA	gene	33464	53054	.	+	.	FI_gene_label "ZNF143^ENSG00000166478.10"  ; ID "IRAG1--ZNF143^ZNF143^ENSG00000166478.10"  ; exon_id "ENSE00002140238.1"  ; exon_number 2 ; gene_id "IRAG1--ZNF143^ZNF143^ENSG00000166478.10"  ; gene_name ZNF143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149922.5"  ; havana_transcript "OTTHUMT00000313923.1"  ; hgnc_id "HGNC:12928"  ; level 1 ; orig_coord_info "chr11,9471309,9471420,+"  ; protein_id "ENSP00000299606.2"  ; tag dotter_confirmed not_organism_supported basic exp_conf ; transcript_id "IRAG1--ZNF143^ENST00000299606.6"  ; transcript_name "ZNF143-201"  ; transcript_support_level 5 ; transcript_type protein_coding
IRAG1--ZNF143	HAVANA	mRNA	33464	53054	.	+	.	FI_gene_label "ZNF143^ENSG00000166478.10"  ; ID "IRAG1--ZNF143^ENST00000299606.6"  ; Parent "IRAG1--ZNF143^ZNF143^ENSG00000166478.10"  ; exon_id "ENSE00002140238.1"  ; exon_number 2 ; gene_id "IRAG1--ZNF143^ZNF143^ENSG00000166478.10"  ; gene_name ZNF143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149922.5"  ; havana_transcript "OTTHUMT00000313923.1"  ; hgnc_id "HGNC:12928"  ; level 1 ; orig_coord_info "chr11,9471309,9471420,+"  ; protein_id "ENSP00000299606.2"  ; tag dotter_confirmed not_organism_supported basic exp_conf ; transcript_id "IRAG1--ZNF143^ENST00000299606.6"  ; transcript_name "ZNF143-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
IRAG1--ZNF143	HAVANA	gene	1237	29755	.	+	.	FI_gene_label "IRAG1^ENSG00000072952.19"  ; ID "IRAG1--ZNF143^IRAG1^ENSG00000072952.19"  ; ccdsid "CCDS55746.1"  ; exon_id "ENSE00002197128.1"  ; exon_number 1 ; gene_id "IRAG1--ZNF143^IRAG1^ENSG00000072952.19"  ; gene_name IRAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165773.7"  ; havana_transcript "OTTHUMT00000386137.2"  ; hgnc_id "HGNC:7237"  ; level 2 ; orig_coord_info "chr11,10693536,10693602,-"  ; protein_id "ENSP00000412130.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "IRAG1--ZNF143^ENST00000423302.6"  ; transcript_name "IRAG1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
IRAG1--ZNF143	HAVANA	mRNA	1237	29755	.	+	.	FI_gene_label "IRAG1^ENSG00000072952.19"  ; ID "IRAG1--ZNF143^ENST00000423302.6"  ; Parent "IRAG1--ZNF143^IRAG1^ENSG00000072952.19"  ; ccdsid "CCDS55746.1"  ; exon_id "ENSE00002197128.1"  ; exon_number 1 ; gene_id "IRAG1--ZNF143^IRAG1^ENSG00000072952.19"  ; gene_name IRAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165773.7"  ; havana_transcript "OTTHUMT00000386137.2"  ; hgnc_id "HGNC:7237"  ; level 2 ; orig_coord_info "chr11,10693536,10693602,-"  ; protein_id "ENSP00000412130.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "IRAG1--ZNF143^ENST00000423302.6"  ; transcript_name "IRAG1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NAV2--NELL1	HAVANA	gene	60558	91777	.	+	.	FI_gene_label "NELL1^ENSG00000165973.19"  ; ID "NAV2--NELL1^NELL1^ENSG00000165973.19"  ; ccdsid "CCDS73267.1"  ; exon_id "ENSE00001311201.5"  ; exon_number 1 ; gene_id "NAV2--NELL1^NELL1^ENSG00000165973.19"  ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3"  ; havana_transcript "OTTHUMT00000387587.1"  ; hgnc_id "HGNC:7750"  ; level 1 ; orig_coord_info "chr11,20669724,20669778,+"  ; protein_id "ENSP00000298925.5"  ; tag basic exp_conf CCDS ; transcript_id "NAV2--NELL1^ENST00000298925.9"  ; transcript_name "NELL1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
NAV2--NELL1	HAVANA	mRNA	60558	91777	.	+	.	FI_gene_label "NELL1^ENSG00000165973.19"  ; ID "NAV2--NELL1^ENST00000298925.9"  ; Parent "NAV2--NELL1^NELL1^ENSG00000165973.19"  ; ccdsid "CCDS73267.1"  ; exon_id "ENSE00001311201.5"  ; exon_number 1 ; gene_id "NAV2--NELL1^NELL1^ENSG00000165973.19"  ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3"  ; havana_transcript "OTTHUMT00000387587.1"  ; hgnc_id "HGNC:7750"  ; level 1 ; orig_coord_info "chr11,20669724,20669778,+"  ; protein_id "ENSP00000298925.5"  ; tag basic exp_conf CCDS ; transcript_id "NAV2--NELL1^ENST00000298925.9"  ; transcript_name "NELL1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NAV2--NELL1	HAVANA	gene	2305	57537	.	+	.	FI_gene_label "NAV2^ENSG00000166833.22"  ; ID "NAV2--NELL1^NAV2^ENSG00000166833.22"  ; ccdsid "CCDS7850.1"  ; exon_id "ENSE00003846126.1"  ; exon_number 1 ; gene_id "NAV2--NELL1^NAV2^ENSG00000166833.22"  ; gene_name NAV2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151837.7"  ; havana_transcript "OTTHUMT00000324114.1"  ; hgnc_id "HGNC:15997"  ; level 2 ; orig_coord_info "chr11,19713696,19713962,+"  ; protein_id "ENSP00000309577.6"  ; tag basic MANE_Select CCDS ; transcript_id "NAV2--NELL1^ENST00000349880.9"  ; transcript_name "NAV2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NAV2--NELL1	HAVANA	mRNA	2305	57537	.	+	.	FI_gene_label "NAV2^ENSG00000166833.22"  ; ID "NAV2--NELL1^ENST00000349880.9"  ; Parent "NAV2--NELL1^NAV2^ENSG00000166833.22"  ; ccdsid "CCDS7850.1"  ; exon_id "ENSE00003846126.1"  ; exon_number 1 ; gene_id "NAV2--NELL1^NAV2^ENSG00000166833.22"  ; gene_name NAV2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151837.7"  ; havana_transcript "OTTHUMT00000324114.1"  ; hgnc_id "HGNC:15997"  ; level 2 ; orig_coord_info "chr11,19713696,19713962,+"  ; protein_id "ENSP00000309577.6"  ; tag basic MANE_Select CCDS ; transcript_id "NAV2--NELL1^ENST00000349880.9"  ; transcript_name "NAV2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NELL1--INSC	HAVANA	gene	1021	32240	.	+	.	FI_gene_label "NELL1^ENSG00000165973.19"  ; ID "NELL1--INSC^NELL1^ENSG00000165973.19"  ; ccdsid "CCDS73267.1"  ; exon_id "ENSE00001311201.5"  ; exon_number 1 ; gene_id "NELL1--INSC^NELL1^ENSG00000165973.19"  ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3"  ; havana_transcript "OTTHUMT00000387587.1"  ; hgnc_id "HGNC:7750"  ; level 1 ; orig_coord_info "chr11,20669724,20669778,+"  ; protein_id "ENSP00000298925.5"  ; tag basic exp_conf CCDS ; transcript_id "NELL1--INSC^ENST00000298925.9"  ; transcript_name "NELL1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
NELL1--INSC	HAVANA	mRNA	1021	32240	.	+	.	FI_gene_label "NELL1^ENSG00000165973.19"  ; ID "NELL1--INSC^ENST00000298925.9"  ; Parent "NELL1--INSC^NELL1^ENSG00000165973.19"  ; ccdsid "CCDS73267.1"  ; exon_id "ENSE00001311201.5"  ; exon_number 1 ; gene_id "NELL1--INSC^NELL1^ENSG00000165973.19"  ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3"  ; havana_transcript "OTTHUMT00000387587.1"  ; hgnc_id "HGNC:7750"  ; level 1 ; orig_coord_info "chr11,20669724,20669778,+"  ; protein_id "ENSP00000298925.5"  ; tag basic exp_conf CCDS ; transcript_id "NELL1--INSC^ENST00000298925.9"  ; transcript_name "NELL1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NELL1--INSC	HAVANA	gene	35246	55096	.	+	.	FI_gene_label "INSC^ENSG00000188487.12"  ; ID "NELL1--INSC^INSC^ENSG00000188487.12"  ; ccdsid "CCDS41621.1"  ; exon_id "ENSE00001538117.1"  ; exon_number 1 ; gene_id "NELL1--INSC^INSC^ENSG00000188487.12"  ; gene_name INSC ; gene_type protein_coding ; havana_gene "OTTHUMG00000165838.3"  ; havana_transcript "OTTHUMT00000386590.1"  ; hgnc_id "HGNC:33116"  ; level 2 ; orig_coord_info "chr11,15112470,15112565,+"  ; protein_id "ENSP00000368872.3"  ; tag basic appris_principal_4 CCDS ; transcript_id "NELL1--INSC^ENST00000379554.7"  ; transcript_name "INSC-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NELL1--INSC	HAVANA	mRNA	35246	55096	.	+	.	FI_gene_label "INSC^ENSG00000188487.12"  ; ID "NELL1--INSC^ENST00000379554.7"  ; Parent "NELL1--INSC^INSC^ENSG00000188487.12"  ; ccdsid "CCDS41621.1"  ; exon_id "ENSE00001538117.1"  ; exon_number 1 ; gene_id "NELL1--INSC^INSC^ENSG00000188487.12"  ; gene_name INSC ; gene_type protein_coding ; havana_gene "OTTHUMG00000165838.3"  ; havana_transcript "OTTHUMT00000386590.1"  ; hgnc_id "HGNC:33116"  ; level 2 ; orig_coord_info "chr11,15112470,15112565,+"  ; protein_id "ENSP00000368872.3"  ; tag basic appris_principal_4 CCDS ; transcript_id "NELL1--INSC^ENST00000379554.7"  ; transcript_name "INSC-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PPFIBP2--PARVA	HAVANA	gene	1702	37120	.	+	.	FI_gene_label "PPFIBP2^ENSG00000166387.13"  ; ID "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13"  ; ccdsid "CCDS31419.1"  ; exon_id "ENSE00001278528.6"  ; exon_number 2 ; gene_id "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13"  ; gene_name PPFIBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165617.10"  ; havana_transcript "OTTHUMT00000385345.3"  ; hgnc_id "HGNC:9250"  ; level 2 ; orig_coord_info "chr11,7549476,7549539,+"  ; protein_id "ENSP00000299492.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PPFIBP2--PARVA^ENST00000299492.9"  ; transcript_name "PPFIBP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PPFIBP2--PARVA	HAVANA	mRNA	1702	37120	.	+	.	FI_gene_label "PPFIBP2^ENSG00000166387.13"  ; ID "PPFIBP2--PARVA^ENST00000299492.9"  ; Parent "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13"  ; ccdsid "CCDS31419.1"  ; exon_id "ENSE00001278528.6"  ; exon_number 2 ; gene_id "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13"  ; gene_name PPFIBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165617.10"  ; havana_transcript "OTTHUMT00000385345.3"  ; hgnc_id "HGNC:9250"  ; level 2 ; orig_coord_info "chr11,7549476,7549539,+"  ; protein_id "ENSP00000299492.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PPFIBP2--PARVA^ENST00000299492.9"  ; transcript_name "PPFIBP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PPFIBP2--PARVA	HAVANA	gene	42627	67717	.	+	.	FI_gene_label "PARVA^ENSG00000197702.14"  ; ID "PPFIBP2--PARVA^PARVA^ENSG00000197702.14"  ; exon_id "ENSE00003840507.2"  ; exon_number 1 ; gene_id "PPFIBP2--PARVA^PARVA^ENSG00000197702.14"  ; gene_name PARVA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165778.6"  ; havana_transcript "OTTHUMT00000386165.5"  ; hgnc_id "HGNC:14652"  ; level 2 ; orig_coord_info "chr11,12377648,12377783,+"  ; protein_id "ENSP00000334008.9"  ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "PPFIBP2--PARVA^ENST00000334956.15"  ; transcript_name "PARVA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PPFIBP2--PARVA	HAVANA	mRNA	42627	67717	.	+	.	FI_gene_label "PARVA^ENSG00000197702.14"  ; ID "PPFIBP2--PARVA^ENST00000334956.15"  ; Parent "PPFIBP2--PARVA^PARVA^ENSG00000197702.14"  ; exon_id "ENSE00003840507.2"  ; exon_number 1 ; gene_id "PPFIBP2--PARVA^PARVA^ENSG00000197702.14"  ; gene_name PARVA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165778.6"  ; havana_transcript "OTTHUMT00000386165.5"  ; hgnc_id "HGNC:14652"  ; level 2 ; orig_coord_info "chr11,12377648,12377783,+"  ; protein_id "ENSP00000334008.9"  ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "PPFIBP2--PARVA^ENST00000334956.15"  ; transcript_name "PARVA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RHOG--SBF2	HAVANA	gene	8810	67621	.	+	.	FI_gene_label "SBF2^ENSG00000133812.17"  ; ID "RHOG--SBF2^SBF2^ENSG00000133812.17"  ; ccdsid "CCDS31427.1"  ; exon_id "ENSE00003900171.1"  ; exon_number 1 ; gene_id "RHOG--SBF2^SBF2^ENSG00000133812.17"  ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3"  ; havana_transcript "OTTHUMT00000386911.2"  ; hgnc_id "HGNC:2135"  ; level 2 ; orig_coord_info "chr11,10294015,10294069,-"  ; protein_id "ENSP00000256190.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "RHOG--SBF2^ENST00000256190.13"  ; transcript_name "SBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RHOG--SBF2	HAVANA	mRNA	8810	67621	.	+	.	FI_gene_label "SBF2^ENSG00000133812.17"  ; ID "RHOG--SBF2^ENST00000256190.13"  ; Parent "RHOG--SBF2^SBF2^ENSG00000133812.17"  ; ccdsid "CCDS31427.1"  ; exon_id "ENSE00003900171.1"  ; exon_number 1 ; gene_id "RHOG--SBF2^SBF2^ENSG00000133812.17"  ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3"  ; havana_transcript "OTTHUMT00000386911.2"  ; hgnc_id "HGNC:2135"  ; level 2 ; orig_coord_info "chr11,10294015,10294069,-"  ; protein_id "ENSP00000256190.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "RHOG--SBF2^ENST00000256190.13"  ; transcript_name "SBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RHOG--SBF2	HAVANA	gene	1001	5809	.	+	.	FI_gene_label "RHOG^ENSG00000177105.10"  ; ID "RHOG--SBF2^RHOG^ENSG00000177105.10"  ; ccdsid "CCDS7748.1"  ; exon_id "ENSE00001393048.2"  ; exon_number 2 ; gene_id "RHOG--SBF2^RHOG^ENSG00000177105.10"  ; gene_name RHOG ; gene_type protein_coding ; havana_gene "OTTHUMG00000012287.4"  ; havana_transcript "OTTHUMT00000034125.3"  ; hgnc_id "HGNC:672"  ; level 2 ; orig_coord_info "chr11,3827566,3828138,-"  ; protein_id "ENSP00000339467.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RHOG--SBF2^ENST00000351018.5"  ; transcript_name "RHOG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RHOG--SBF2	HAVANA	mRNA	1001	5809	.	+	.	FI_gene_label "RHOG^ENSG00000177105.10"  ; ID "RHOG--SBF2^ENST00000351018.5"  ; Parent "RHOG--SBF2^RHOG^ENSG00000177105.10"  ; ccdsid "CCDS7748.1"  ; exon_id "ENSE00001393048.2"  ; exon_number 2 ; gene_id "RHOG--SBF2^RHOG^ENSG00000177105.10"  ; gene_name RHOG ; gene_type protein_coding ; havana_gene "OTTHUMG00000012287.4"  ; havana_transcript "OTTHUMT00000034125.3"  ; hgnc_id "HGNC:672"  ; level 2 ; orig_coord_info "chr11,3827566,3828138,-"  ; protein_id "ENSP00000339467.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RHOG--SBF2^ENST00000351018.5"  ; transcript_name "RHOG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SBF2--AC009869.1	HAVANA	gene	1001	59812	.	+	.	FI_gene_label "SBF2^ENSG00000133812.17"  ; ID "SBF2--AC009869.1^SBF2^ENSG00000133812.17"  ; ccdsid "CCDS31427.1"  ; exon_id "ENSE00003900171.1"  ; exon_number 1 ; gene_id "SBF2--AC009869.1^SBF2^ENSG00000133812.17"  ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3"  ; havana_transcript "OTTHUMT00000386911.2"  ; hgnc_id "HGNC:2135"  ; level 2 ; orig_coord_info "chr11,10294015,10294069,-"  ; protein_id "ENSP00000256190.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--AC009869.1^ENST00000256190.13"  ; transcript_name "SBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SBF2--AC009869.1	HAVANA	mRNA	1001	59812	.	+	.	FI_gene_label "SBF2^ENSG00000133812.17"  ; ID "SBF2--AC009869.1^ENST00000256190.13"  ; Parent "SBF2--AC009869.1^SBF2^ENSG00000133812.17"  ; ccdsid "CCDS31427.1"  ; exon_id "ENSE00003900171.1"  ; exon_number 1 ; gene_id "SBF2--AC009869.1^SBF2^ENSG00000133812.17"  ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3"  ; havana_transcript "OTTHUMT00000386911.2"  ; hgnc_id "HGNC:2135"  ; level 2 ; orig_coord_info "chr11,10294015,10294069,-"  ; protein_id "ENSP00000256190.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--AC009869.1^ENST00000256190.13"  ; transcript_name "SBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SBF2--AC087379.1	HAVANA	gene	1001	59812	.	+	.	FI_gene_label "SBF2^ENSG00000133812.17"  ; ID "SBF2--AC087379.1^SBF2^ENSG00000133812.17"  ; ccdsid "CCDS31427.1"  ; exon_id "ENSE00003900171.1"  ; exon_number 1 ; gene_id "SBF2--AC087379.1^SBF2^ENSG00000133812.17"  ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3"  ; havana_transcript "OTTHUMT00000386911.2"  ; hgnc_id "HGNC:2135"  ; level 2 ; orig_coord_info "chr11,10294015,10294069,-"  ; protein_id "ENSP00000256190.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--AC087379.1^ENST00000256190.13"  ; transcript_name "SBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SBF2--AC087379.1	HAVANA	mRNA	1001	59812	.	+	.	FI_gene_label "SBF2^ENSG00000133812.17"  ; ID "SBF2--AC087379.1^ENST00000256190.13"  ; Parent "SBF2--AC087379.1^SBF2^ENSG00000133812.17"  ; ccdsid "CCDS31427.1"  ; exon_id "ENSE00003900171.1"  ; exon_number 1 ; gene_id "SBF2--AC087379.1^SBF2^ENSG00000133812.17"  ; gene_name SBF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165890.3"  ; havana_transcript "OTTHUMT00000386911.2"  ; hgnc_id "HGNC:2135"  ; level 2 ; orig_coord_info "chr11,10294015,10294069,-"  ; protein_id "ENSP00000256190.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "SBF2--AC087379.1^ENST00000256190.13"  ; transcript_name "SBF2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TNS1--ALK	HAVANA	gene	8232	56093	.	+	.	FI_gene_label "TNS1^ENSG00000079308.19"  ; ID "TNS1--ALK^TNS1^ENSG00000079308.19"  ; ccdsid "CCDS2407.1"  ; exon_id "ENSE00003622889.1"  ; exon_number 6 ; gene_id "TNS1--ALK^TNS1^ENSG00000079308.19"  ; gene_name TNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133056.10"  ; havana_transcript "OTTHUMT00000256672.2"  ; hgnc_id "HGNC:11973"  ; level 2 ; orig_coord_info "chr2,217897798,217897965,-"  ; protein_id "ENSP00000171887.4"  ; tag basic CCDS ; transcript_id "TNS1--ALK^ENST00000171887.8"  ; transcript_name "TNS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TNS1--ALK	HAVANA	mRNA	8232	56093	.	+	.	FI_gene_label "TNS1^ENSG00000079308.19"  ; ID "TNS1--ALK^ENST00000171887.8"  ; Parent "TNS1--ALK^TNS1^ENSG00000079308.19"  ; ccdsid "CCDS2407.1"  ; exon_id "ENSE00003622889.1"  ; exon_number 6 ; gene_id "TNS1--ALK^TNS1^ENSG00000079308.19"  ; gene_name TNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133056.10"  ; havana_transcript "OTTHUMT00000256672.2"  ; hgnc_id "HGNC:11973"  ; level 2 ; orig_coord_info "chr2,217897798,217897965,-"  ; protein_id "ENSP00000171887.4"  ; tag basic CCDS ; transcript_id "TNS1--ALK^ENST00000171887.8"  ; transcript_name "TNS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TNS1--ALK	HAVANA	gene	59295	94299	.	+	.	FI_gene_label "ALK^ENSG00000171094.18"  ; ID "TNS1--ALK^ALK^ENSG00000171094.18"  ; ccdsid "CCDS33172.1"  ; exon_id "ENSE00001794937.2"  ; exon_number 1 ; gene_id "TNS1--ALK^ALK^ENSG00000171094.18"  ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4"  ; havana_transcript "OTTHUMT00000324994.2"  ; hgnc_id "HGNC:427"  ; level 2 ; orig_coord_info "chr2,29919993,29920659,-"  ; protein_id "ENSP00000373700.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS1--ALK^ENST00000389048.8"  ; transcript_name "ALK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TNS1--ALK	HAVANA	mRNA	59295	94299	.	+	.	FI_gene_label "ALK^ENSG00000171094.18"  ; ID "TNS1--ALK^ENST00000389048.8"  ; Parent "TNS1--ALK^ALK^ENSG00000171094.18"  ; ccdsid "CCDS33172.1"  ; exon_id "ENSE00001794937.2"  ; exon_number 1 ; gene_id "TNS1--ALK^ALK^ENSG00000171094.18"  ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4"  ; havana_transcript "OTTHUMT00000324994.2"  ; hgnc_id "HGNC:427"  ; level 2 ; orig_coord_info "chr2,29919993,29920659,-"  ; protein_id "ENSP00000373700.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS1--ALK^ENST00000389048.8"  ; transcript_name "ALK-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TRPC2--WEE1	HAVANA	gene	21081	33282	.	+	.	FI_gene_label "WEE1^ENSG00000166483.12"  ; ID "TRPC2--WEE1^WEE1^ENSG00000166483.12"  ; ccdsid "CCDS44536.1"  ; exon_id "ENSE00003609415.1"  ; exon_number 2 ; gene_id "TRPC2--WEE1^WEE1^ENSG00000166483.12"  ; gene_name WEE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165863.4"  ; havana_transcript "OTTHUMT00000386758.2"  ; hgnc_id "HGNC:12761"  ; level 2 ; orig_coord_info "chr11,9575954,9576093,+"  ; protein_id "ENSP00000299613.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "TRPC2--WEE1^ENST00000299613.10"  ; transcript_name "WEE1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TRPC2--WEE1	HAVANA	mRNA	21081	33282	.	+	.	FI_gene_label "WEE1^ENSG00000166483.12"  ; ID "TRPC2--WEE1^ENST00000299613.10"  ; Parent "TRPC2--WEE1^WEE1^ENSG00000166483.12"  ; ccdsid "CCDS44536.1"  ; exon_id "ENSE00003609415.1"  ; exon_number 2 ; gene_id "TRPC2--WEE1^WEE1^ENSG00000166483.12"  ; gene_name WEE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165863.4"  ; havana_transcript "OTTHUMT00000386758.2"  ; hgnc_id "HGNC:12761"  ; level 2 ; orig_coord_info "chr11,9575954,9576093,+"  ; protein_id "ENSP00000299613.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "TRPC2--WEE1^ENST00000299613.10"  ; transcript_name "WEE1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
AL845331.2--AFF3	HAVANA	gene	1001	6028	.	+	.	FI_gene_label "AL845331.2^ENSG00000261522.5"  ; ID "AL845331.2--AFF3^AL845331.2^ENSG00000261522.5"  ; exon_id "ENSE00002584959.1"  ; exon_number 1 ; gene_id "AL845331.2--AFF3^AL845331.2^ENSG00000261522.5"  ; gene_name "AL845331.2"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000175551.1"  ; havana_transcript "OTTHUMT00000430470.1"  ; level 2 ; orig_coord_info "chr2,94587081,94587183,-"  ; tag basic ; transcript_id "AL845331.2--AFF3^ENST00000562821.5"  ; transcript_name "AL845331.2-201"  ; transcript_support_level 2 ; transcript_type processed_transcript
AL845331.2--AFF3	HAVANA	RNA	1001	6028	.	+	.	FI_gene_label "AL845331.2^ENSG00000261522.5"  ; ID "AL845331.2--AFF3^ENST00000562821.5"  ; Parent "AL845331.2--AFF3^AL845331.2^ENSG00000261522.5"  ; exon_id "ENSE00002584959.1"  ; exon_number 1 ; gene_id "AL845331.2--AFF3^AL845331.2^ENSG00000261522.5"  ; gene_name "AL845331.2"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000175551.1"  ; havana_transcript "OTTHUMT00000430470.1"  ; level 2 ; orig_coord_info "chr2,94587081,94587183,-"  ; tag basic ; transcript_id "AL845331.2--AFF3^ENST00000562821.5"  ; transcript_name "AL845331.2-201"  ; transcript_support_level 2 ; transcript_type processed_transcript
L1 and L2 created: 
BMS1P23--AFF3	HAVANA	gene	2071	7422	.	+	.	FI_gene_label "BMS1P23^ENSG00000286156.1"  ; ID "BMS1P23--AFF3^BMS1P23^ENSG00000286156.1"  ; exon_id "ENSE00003847039.1"  ; exon_number 1 ; gene_id "BMS1P23--AFF3^BMS1P23^ENSG00000286156.1"  ; gene_name BMS1P23 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193495.2"  ; havana_transcript "OTTHUMT00000502279.1"  ; hgnc_id "HGNC:55088"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr2,94203214,94203287,-"  ; tag basic ; transcript_id "BMS1P23--AFF3^ENST00000651108.1"  ; transcript_name "BMS1P23-201"  ; transcript_type transcribed_unprocessed_pseudogene
BMS1P23--AFF3	HAVANA	RNA	2071	7422	.	+	.	FI_gene_label "BMS1P23^ENSG00000286156.1"  ; ID "BMS1P23--AFF3^ENST00000651108.1"  ; Parent "BMS1P23--AFF3^BMS1P23^ENSG00000286156.1"  ; exon_id "ENSE00003847039.1"  ; exon_number 1 ; gene_id "BMS1P23--AFF3^BMS1P23^ENSG00000286156.1"  ; gene_name BMS1P23 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193495.2"  ; havana_transcript "OTTHUMT00000502279.1"  ; hgnc_id "HGNC:55088"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr2,94203214,94203287,-"  ; tag basic ; transcript_id "BMS1P23--AFF3^ENST00000651108.1"  ; transcript_name "BMS1P23-201"  ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
SBF2--AC009869.1	HAVANA	gene	62814	67704	.	+	.	FI_gene_label "AC009869.1^ENSG00000286960.1"  ; ID "SBF2--AC009869.1^AC009869.1^ENSG00000286960.1"  ; exon_id "ENSE00003867542.1"  ; exon_number 1 ; gene_id "SBF2--AC009869.1^AC009869.1^ENSG00000286960.1"  ; gene_name "AC009869.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000195097.1"  ; havana_transcript "OTTHUMT00000524440.1"  ; level 2 ; orig_coord_info "chr11,15864452,15866497,+"  ; tag basic TAGENE ; transcript_id "SBF2--AC009869.1^ENST00000659436.1"  ; transcript_name "AC009869.1-201"  ; transcript_type lncRNA
SBF2--AC009869.1	HAVANA	RNA	62814	67704	.	+	.	FI_gene_label "AC009869.1^ENSG00000286960.1"  ; ID "SBF2--AC009869.1^ENST00000659436.1"  ; Parent "SBF2--AC009869.1^AC009869.1^ENSG00000286960.1"  ; exon_id "ENSE00003867542.1"  ; exon_number 1 ; gene_id "SBF2--AC009869.1^AC009869.1^ENSG00000286960.1"  ; gene_name "AC009869.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000195097.1"  ; havana_transcript "OTTHUMT00000524440.1"  ; level 2 ; orig_coord_info "chr11,15864452,15866497,+"  ; tag basic TAGENE ; transcript_id "SBF2--AC009869.1^ENST00000659436.1"  ; transcript_name "AC009869.1-201"  ; transcript_type lncRNA
L1 and L2 created: 
SBF2--AC087379.1	HAVANA	gene	62814	71750	.	+	.	FI_gene_label "AC087379.1^ENSG00000254645.2"  ; ID "SBF2--AC087379.1^AC087379.1^ENSG00000254645.2"  ; exon_id "ENSE00002159676.1"  ; exon_number 1 ; gene_id "SBF2--AC087379.1^AC087379.1^ENSG00000254645.2"  ; gene_name "AC087379.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000166009.2"  ; havana_transcript "OTTHUMT00000387434.1"  ; level 2 ; orig_coord_info "chr11,15758712,15758898,-"  ; tag basic ; transcript_id "SBF2--AC087379.1^ENST00000524613.1"  ; transcript_name "AC087379.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
SBF2--AC087379.1	HAVANA	RNA	62814	71750	.	+	.	FI_gene_label "AC087379.1^ENSG00000254645.2"  ; ID "SBF2--AC087379.1^ENST00000524613.1"  ; Parent "SBF2--AC087379.1^AC087379.1^ENSG00000254645.2"  ; exon_id "ENSE00002159676.1"  ; exon_number 1 ; gene_id "SBF2--AC087379.1^AC087379.1^ENSG00000254645.2"  ; gene_name "AC087379.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000166009.2"  ; havana_transcript "OTTHUMT00000387434.1"  ; level 2 ; orig_coord_info "chr11,15758712,15758898,-"  ; tag basic ; transcript_id "SBF2--AC087379.1^ENST00000524613.1"  ; transcript_name "AC087379.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TRPC2--WEE1	HAVANA	gene	1001	17053	.	+	.	FI_gene_label "TRPC2^ENSG00000182048.11"  ; ID "TRPC2--WEE1^TRPC2^ENSG00000182048.11"  ; exon_id "ENSE00001745449.1"  ; exon_number 1 ; gene_id "TRPC2--WEE1^TRPC2^ENSG00000182048.11"  ; gene_name TRPC2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000011712.2"  ; havana_transcript "OTTHUMT00000032350.2"  ; hgnc_id "HGNC:12334"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr11,3609901,3609989,+"  ; tag basic ; transcript_id "TRPC2--WEE1^ENST00000451043.6"  ; transcript_name "TRPC2-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TRPC2--WEE1	HAVANA	RNA	1001	17053	.	+	.	FI_gene_label "TRPC2^ENSG00000182048.11"  ; ID "TRPC2--WEE1^ENST00000451043.6"  ; Parent "TRPC2--WEE1^TRPC2^ENSG00000182048.11"  ; exon_id "ENSE00001745449.1"  ; exon_number 1 ; gene_id "TRPC2--WEE1^TRPC2^ENSG00000182048.11"  ; gene_name TRPC2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000011712.2"  ; havana_transcript "OTTHUMT00000032350.2"  ; hgnc_id "HGNC:12334"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr11,3609901,3609989,+"  ; tag basic ; transcript_id "TRPC2--WEE1^ENST00000451043.6"  ; transcript_name "TRPC2-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
295 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 ------------------------------
532 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------

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

------------------------ Check12: all level1 locations -------------------------
We fixed 18 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------

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


GFF3 file parsed