.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-e4cfff-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/88af172c4a2dafb94197b67095c5ac/.command.log
Size: 52.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-e4cfff-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/b1eb0ae3d6b8e1f4cd5871edfe4a1e/fi_workdir/aih-tih-sc-e4cfff-R1_A23WJ53LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/88af172c4a2dafb94197b67095c5ac/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/88af172c4a2dafb94197b67095c5ac/.command.run
==> STAGING COMPLETE (3 inputs)

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 4206
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4206
=> 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:4206
  => 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: 
AC005972.3--C17orf64	HAVANA	gene	14908	19539	.	+	.	FI_gene_label "C17orf64^ENSG00000141371.13"  ; ID "AC005972.3--C17orf64^C17orf64^ENSG00000141371.13"  ; ccdsid "CCDS32698.2"  ; exon_id "ENSE00001899543.2"  ; exon_number 1 ; gene_id "AC005972.3--C17orf64^C17orf64^ENSG00000141371.13"  ; gene_name C17orf64 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157171.7"  ; havana_transcript "OTTHUMT00000347743.2"  ; hgnc_id "HGNC:26990"  ; level 1 ; orig_coord_info "chr17,60422593,60422643,+"  ; protein_id "ENSP00000269127.4"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "AC005972.3--C17orf64^ENST00000269127.5"  ; transcript_name "C17orf64-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC005972.3--C17orf64	HAVANA	mRNA	14908	19539	.	+	.	FI_gene_label "C17orf64^ENSG00000141371.13"  ; ID "AC005972.3--C17orf64^ENST00000269127.5"  ; Parent "AC005972.3--C17orf64^C17orf64^ENSG00000141371.13"  ; ccdsid "CCDS32698.2"  ; exon_id "ENSE00001899543.2"  ; exon_number 1 ; gene_id "AC005972.3--C17orf64^C17orf64^ENSG00000141371.13"  ; gene_name C17orf64 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157171.7"  ; havana_transcript "OTTHUMT00000347743.2"  ; hgnc_id "HGNC:26990"  ; level 1 ; orig_coord_info "chr17,60422593,60422643,+"  ; protein_id "ENSP00000269127.4"  ; tag basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "AC005972.3--C17orf64^ENST00000269127.5"  ; transcript_name "C17orf64-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ATF6--BRIP1	HAVANA	gene	38823	68971	.	+	.	FI_gene_label "BRIP1^ENSG00000136492.9"  ; ID "ATF6--BRIP1^BRIP1^ENSG00000136492.9"  ; ccdsid "CCDS11631.1"  ; exon_id "ENSE00001243809.3"  ; exon_number 2 ; gene_id "ATF6--BRIP1^BRIP1^ENSG00000136492.9"  ; gene_name BRIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179233.3"  ; havana_transcript "OTTHUMT00000445362.2"  ; hgnc_id "HGNC:20473"  ; level 2 ; orig_coord_info "chr17,61861447,61861539,-"  ; protein_id "ENSP00000259008.2"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ATF6--BRIP1^ENST00000259008.7"  ; transcript_name "BRIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATF6--BRIP1	HAVANA	mRNA	38823	68971	.	+	.	FI_gene_label "BRIP1^ENSG00000136492.9"  ; ID "ATF6--BRIP1^ENST00000259008.7"  ; Parent "ATF6--BRIP1^BRIP1^ENSG00000136492.9"  ; ccdsid "CCDS11631.1"  ; exon_id "ENSE00001243809.3"  ; exon_number 2 ; gene_id "ATF6--BRIP1^BRIP1^ENSG00000136492.9"  ; gene_name BRIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179233.3"  ; havana_transcript "OTTHUMT00000445362.2"  ; hgnc_id "HGNC:20473"  ; level 2 ; orig_coord_info "chr17,61861447,61861539,-"  ; protein_id "ENSP00000259008.2"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ATF6--BRIP1^ENST00000259008.7"  ; transcript_name "BRIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ATF6--BRIP1	HAVANA	gene	1023	32433	.	+	.	FI_gene_label "ATF6^ENSG00000118217.7"  ; ID "ATF6--BRIP1^ATF6^ENSG00000118217.7"  ; ccdsid "CCDS1235.1"  ; exon_id "ENSE00001445975.2"  ; exon_number 1 ; gene_id "ATF6--BRIP1^ATF6^ENSG00000118217.7"  ; gene_name ATF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023961.3"  ; havana_transcript "OTTHUMT00000060304.3"  ; hgnc_id "HGNC:791"  ; level 2 ; orig_coord_info "chr1,161766361,161766442,+"  ; protein_id "ENSP00000356919.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ATF6--BRIP1^ENST00000367942.4"  ; transcript_name "ATF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ATF6--BRIP1	HAVANA	mRNA	1023	32433	.	+	.	FI_gene_label "ATF6^ENSG00000118217.7"  ; ID "ATF6--BRIP1^ENST00000367942.4"  ; Parent "ATF6--BRIP1^ATF6^ENSG00000118217.7"  ; ccdsid "CCDS1235.1"  ; exon_id "ENSE00001445975.2"  ; exon_number 1 ; gene_id "ATF6--BRIP1^ATF6^ENSG00000118217.7"  ; gene_name ATF6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000023961.3"  ; havana_transcript "OTTHUMT00000060304.3"  ; hgnc_id "HGNC:791"  ; level 2 ; orig_coord_info "chr1,161766361,161766442,+"  ; protein_id "ENSP00000356919.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ATF6--BRIP1^ENST00000367942.4"  ; transcript_name "ATF6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HELZ--AL589765.4	HAVANA	gene	1794	48781	.	+	.	FI_gene_label "HELZ^ENSG00000198265.12"  ; ID "HELZ--AL589765.4^HELZ^ENSG00000198265.12"  ; ccdsid "CCDS42374.1"  ; exon_id "ENSE00003483335.1"  ; exon_number 4 ; gene_id "HELZ--AL589765.4^HELZ^ENSG00000198265.12"  ; gene_name HELZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000179555.4"  ; havana_transcript "OTTHUMT00000447068.2"  ; hgnc_id "HGNC:16878"  ; level 2 ; orig_coord_info "chr17,67218595,67218804,-"  ; protein_id "ENSP00000351524.5"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "HELZ--AL589765.4^ENST00000358691.10"  ; transcript_name "HELZ-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HELZ--AL589765.4	HAVANA	mRNA	1794	48781	.	+	.	FI_gene_label "HELZ^ENSG00000198265.12"  ; ID "HELZ--AL589765.4^ENST00000358691.10"  ; Parent "HELZ--AL589765.4^HELZ^ENSG00000198265.12"  ; ccdsid "CCDS42374.1"  ; exon_id "ENSE00003483335.1"  ; exon_number 4 ; gene_id "HELZ--AL589765.4^HELZ^ENSG00000198265.12"  ; gene_name HELZ ; gene_type protein_coding ; havana_gene "OTTHUMG00000179555.4"  ; havana_transcript "OTTHUMT00000447068.2"  ; hgnc_id "HGNC:16878"  ; level 2 ; orig_coord_info "chr17,67218595,67218804,-"  ; protein_id "ENSP00000351524.5"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "HELZ--AL589765.4^ENST00000358691.10"  ; transcript_name "HELZ-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HHAT--SRGAP2	HAVANA	gene	1651	21351	.	+	.	FI_gene_label "HHAT^ENSG00000054392.13"  ; ID "HHAT--SRGAP2^HHAT^ENSG00000054392.13"  ; ccdsid "CCDS1495.1"  ; exon_id "ENSE00003476299.1"  ; exon_number 2 ; gene_id "HHAT--SRGAP2^HHAT^ENSG00000054392.13"  ; gene_name HHAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000036447.4"  ; havana_transcript "OTTHUMT00000088659.3"  ; hgnc_id "HGNC:18270"  ; level 2 ; orig_coord_info "chr1,210348976,210349066,+"  ; protein_id "ENSP00000261458.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "HHAT--SRGAP2^ENST00000261458.8"  ; transcript_name "HHAT-201"  ; transcript_support_level 2 ; transcript_type protein_coding
HHAT--SRGAP2	HAVANA	mRNA	1651	21351	.	+	.	FI_gene_label "HHAT^ENSG00000054392.13"  ; ID "HHAT--SRGAP2^ENST00000261458.8"  ; Parent "HHAT--SRGAP2^HHAT^ENSG00000054392.13"  ; ccdsid "CCDS1495.1"  ; exon_id "ENSE00003476299.1"  ; exon_number 2 ; gene_id "HHAT--SRGAP2^HHAT^ENSG00000054392.13"  ; gene_name HHAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000036447.4"  ; havana_transcript "OTTHUMT00000088659.3"  ; hgnc_id "HGNC:18270"  ; level 2 ; orig_coord_info "chr1,210348976,210349066,+"  ; protein_id "ENSP00000261458.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "HHAT--SRGAP2^ENST00000261458.8"  ; transcript_name "HHAT-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
HHAT--SRGAP2	ENSEMBL	gene	26639	42078	.	+	.	FI_gene_label "SRGAP2^ENSG00000266028.7"  ; ID "HHAT--SRGAP2^SRGAP2^ENSG00000266028.7"  ; exon_id "ENSE00002267225.2"  ; exon_number 2 ; gene_id "HHAT--SRGAP2^SRGAP2^ENSG00000266028.7"  ; gene_name SRGAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000184381.5"  ; hgnc_id "HGNC:19751"  ; level 3 ; orig_coord_info "chr1,206384050,206384076,+"  ; protein_id "ENSP00000397990.3"  ; tag basic ; transcript_id "HHAT--SRGAP2^ENST00000419187.6"  ; transcript_name "SRGAP2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
HHAT--SRGAP2	ENSEMBL	mRNA	26639	42078	.	+	.	FI_gene_label "SRGAP2^ENSG00000266028.7"  ; ID "HHAT--SRGAP2^ENST00000419187.6"  ; Parent "HHAT--SRGAP2^SRGAP2^ENSG00000266028.7"  ; exon_id "ENSE00002267225.2"  ; exon_number 2 ; gene_id "HHAT--SRGAP2^SRGAP2^ENSG00000266028.7"  ; gene_name SRGAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000184381.5"  ; hgnc_id "HGNC:19751"  ; level 3 ; orig_coord_info "chr1,206384050,206384076,+"  ; protein_id "ENSP00000397990.3"  ; tag basic ; transcript_id "HHAT--SRGAP2^ENST00000419187.6"  ; transcript_name "SRGAP2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
LGALS3--AL356020.1	HAVANA	gene	2050	8891	.	+	.	FI_gene_label "LGALS3^ENSG00000131981.16"  ; ID "LGALS3--AL356020.1^LGALS3^ENSG00000131981.16"  ; ccdsid "CCDS41956.1"  ; exon_id "ENSE00001536493.1"  ; exon_number 2 ; gene_id "LGALS3--AL356020.1^LGALS3^ENSG00000131981.16"  ; gene_name LGALS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171030.5"  ; havana_transcript "OTTHUMT00000411309.2"  ; hgnc_id "HGNC:6563"  ; level 2 ; orig_coord_info "chr14,55137374,55137391,+"  ; protein_id "ENSP00000254301.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LGALS3--AL356020.1^ENST00000254301.14"  ; transcript_name "LGALS3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LGALS3--AL356020.1	HAVANA	mRNA	2050	8891	.	+	.	FI_gene_label "LGALS3^ENSG00000131981.16"  ; ID "LGALS3--AL356020.1^ENST00000254301.14"  ; Parent "LGALS3--AL356020.1^LGALS3^ENSG00000131981.16"  ; ccdsid "CCDS41956.1"  ; exon_id "ENSE00001536493.1"  ; exon_number 2 ; gene_id "LGALS3--AL356020.1^LGALS3^ENSG00000131981.16"  ; gene_name LGALS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171030.5"  ; havana_transcript "OTTHUMT00000411309.2"  ; hgnc_id "HGNC:6563"  ; level 2 ; orig_coord_info "chr14,55137374,55137391,+"  ; protein_id "ENSP00000254301.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LGALS3--AL356020.1^ENST00000254301.14"  ; transcript_name "LGALS3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LGALS3--AL365295.1	HAVANA	gene	2050	8891	.	+	.	FI_gene_label "LGALS3^ENSG00000131981.16"  ; ID "LGALS3--AL365295.1^LGALS3^ENSG00000131981.16"  ; ccdsid "CCDS41956.1"  ; exon_id "ENSE00001536493.1"  ; exon_number 2 ; gene_id "LGALS3--AL365295.1^LGALS3^ENSG00000131981.16"  ; gene_name LGALS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171030.5"  ; havana_transcript "OTTHUMT00000411309.2"  ; hgnc_id "HGNC:6563"  ; level 2 ; orig_coord_info "chr14,55137374,55137391,+"  ; protein_id "ENSP00000254301.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LGALS3--AL365295.1^ENST00000254301.14"  ; transcript_name "LGALS3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LGALS3--AL365295.1	HAVANA	mRNA	2050	8891	.	+	.	FI_gene_label "LGALS3^ENSG00000131981.16"  ; ID "LGALS3--AL365295.1^ENST00000254301.14"  ; Parent "LGALS3--AL365295.1^LGALS3^ENSG00000131981.16"  ; ccdsid "CCDS41956.1"  ; exon_id "ENSE00001536493.1"  ; exon_number 2 ; gene_id "LGALS3--AL365295.1^LGALS3^ENSG00000131981.16"  ; gene_name LGALS3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171030.5"  ; havana_transcript "OTTHUMT00000411309.2"  ; hgnc_id "HGNC:6563"  ; level 2 ; orig_coord_info "chr14,55137374,55137391,+"  ; protein_id "ENSP00000254301.9"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "LGALS3--AL365295.1^ENST00000254301.14"  ; transcript_name "LGALS3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MCM3AP--NCAM2	ENSEMBL	gene	36669	59540	.	+	.	FI_gene_label "NCAM2^ENSG00000154654.15"  ; ID "MCM3AP--NCAM2^NCAM2^ENSG00000154654.15"  ; exon_id "ENSE00003749383.1"  ; exon_number 1 ; gene_id "MCM3AP--NCAM2^NCAM2^ENSG00000154654.15"  ; gene_name NCAM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000078121.4"  ; hgnc_id "HGNC:7657"  ; level 3 ; orig_coord_info "chr21,21280577,21280652,+"  ; protein_id "ENSP00000284894.8"  ; tag basic ; transcript_id "MCM3AP--NCAM2^ENST00000284894.8"  ; transcript_name "NCAM2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
MCM3AP--NCAM2	ENSEMBL	mRNA	36669	59540	.	+	.	FI_gene_label "NCAM2^ENSG00000154654.15"  ; ID "MCM3AP--NCAM2^ENST00000284894.8"  ; Parent "MCM3AP--NCAM2^NCAM2^ENSG00000154654.15"  ; exon_id "ENSE00003749383.1"  ; exon_number 1 ; gene_id "MCM3AP--NCAM2^NCAM2^ENSG00000154654.15"  ; gene_name NCAM2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000078121.4"  ; hgnc_id "HGNC:7657"  ; level 3 ; orig_coord_info "chr21,21280577,21280652,+"  ; protein_id "ENSP00000284894.8"  ; tag basic ; transcript_id "MCM3AP--NCAM2^ENST00000284894.8"  ; transcript_name "NCAM2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
MCM3AP--NCAM2	HAVANA	gene	1687	31388	.	+	.	FI_gene_label "MCM3AP^ENSG00000160294.11"  ; ID "MCM3AP--NCAM2^MCM3AP^ENSG00000160294.11"  ; ccdsid "CCDS13734.1"  ; exon_id "ENSE00003847161.1"  ; exon_number 1 ; gene_id "MCM3AP--NCAM2^MCM3AP^ENSG00000160294.11"  ; gene_name MCM3AP ; gene_type protein_coding ; havana_gene "OTTHUMG00000090630.5"  ; havana_transcript "OTTHUMT00000504450.2"  ; hgnc_id "HGNC:6946"  ; level 2 ; orig_coord_info "chr21,46284068,46285286,-"  ; protein_id "ENSP00000291688.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MCM3AP--NCAM2^ENST00000291688.6"  ; transcript_name "MCM3AP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MCM3AP--NCAM2	HAVANA	mRNA	1687	31388	.	+	.	FI_gene_label "MCM3AP^ENSG00000160294.11"  ; ID "MCM3AP--NCAM2^ENST00000291688.6"  ; Parent "MCM3AP--NCAM2^MCM3AP^ENSG00000160294.11"  ; ccdsid "CCDS13734.1"  ; exon_id "ENSE00003847161.1"  ; exon_number 1 ; gene_id "MCM3AP--NCAM2^MCM3AP^ENSG00000160294.11"  ; gene_name MCM3AP ; gene_type protein_coding ; havana_gene "OTTHUMG00000090630.5"  ; havana_transcript "OTTHUMT00000504450.2"  ; hgnc_id "HGNC:6946"  ; level 2 ; orig_coord_info "chr21,46284068,46285286,-"  ; protein_id "ENSP00000291688.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MCM3AP--NCAM2^ENST00000291688.6"  ; transcript_name "MCM3AP-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MIPOL1--GPR137C	HAVANA	gene	47488	61155	.	+	.	FI_gene_label "GPR137C^ENSG00000180998.12"  ; ID "MIPOL1--GPR137C^GPR137C^ENSG00000180998.12"  ; ccdsid "CCDS45106.1"  ; exon_id "ENSE00001282180.7"  ; exon_number 1 ; gene_id "MIPOL1--GPR137C^GPR137C^ENSG00000180998.12"  ; gene_name GPR137C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171104.3"  ; havana_transcript "OTTHUMT00000411685.2"  ; hgnc_id "HGNC:25445"  ; level 2 ; orig_coord_info "chr14,52553148,52553591,+"  ; protein_id "ENSP00000315106.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MIPOL1--GPR137C^ENST00000321662.11"  ; transcript_name "GPR137C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MIPOL1--GPR137C	HAVANA	mRNA	47488	61155	.	+	.	FI_gene_label "GPR137C^ENSG00000180998.12"  ; ID "MIPOL1--GPR137C^ENST00000321662.11"  ; Parent "MIPOL1--GPR137C^GPR137C^ENSG00000180998.12"  ; ccdsid "CCDS45106.1"  ; exon_id "ENSE00001282180.7"  ; exon_number 1 ; gene_id "MIPOL1--GPR137C^GPR137C^ENSG00000180998.12"  ; gene_name GPR137C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171104.3"  ; havana_transcript "OTTHUMT00000411685.2"  ; hgnc_id "HGNC:25445"  ; level 2 ; orig_coord_info "chr14,52553148,52553591,+"  ; protein_id "ENSP00000315106.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MIPOL1--GPR137C^ENST00000321662.11"  ; transcript_name "GPR137C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MIPOL1--GPR137C	HAVANA	gene	1038	44487	.	+	.	FI_gene_label "MIPOL1^ENSG00000151338.18"  ; ID "MIPOL1--GPR137C^MIPOL1^ENSG00000151338.18"  ; ccdsid "CCDS9664.1"  ; exon_id "ENSE00003679602.1"  ; exon_number 4 ; gene_id "MIPOL1--GPR137C^MIPOL1^ENSG00000151338.18"  ; gene_name MIPOL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140252.3"  ; havana_transcript "OTTHUMT00000276734.1"  ; hgnc_id "HGNC:21460"  ; level 2 ; orig_coord_info "chr14,37247889,37247907,+"  ; protein_id "ENSP00000333539.7"  ; tag basic appris_principal_2 CCDS ; transcript_id "MIPOL1--GPR137C^ENST00000327441.11"  ; transcript_name "MIPOL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MIPOL1--GPR137C	HAVANA	mRNA	1038	44487	.	+	.	FI_gene_label "MIPOL1^ENSG00000151338.18"  ; ID "MIPOL1--GPR137C^ENST00000327441.11"  ; Parent "MIPOL1--GPR137C^MIPOL1^ENSG00000151338.18"  ; ccdsid "CCDS9664.1"  ; exon_id "ENSE00003679602.1"  ; exon_number 4 ; gene_id "MIPOL1--GPR137C^MIPOL1^ENSG00000151338.18"  ; gene_name MIPOL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140252.3"  ; havana_transcript "OTTHUMT00000276734.1"  ; hgnc_id "HGNC:21460"  ; level 2 ; orig_coord_info "chr14,37247889,37247907,+"  ; protein_id "ENSP00000333539.7"  ; tag basic appris_principal_2 CCDS ; transcript_id "MIPOL1--GPR137C^ENST00000327441.11"  ; transcript_name "MIPOL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MSI2--NUP58	HAVANA	gene	1673	54046	.	+	.	FI_gene_label "MSI2^ENSG00000153944.12"  ; ID "MSI2--NUP58^MSI2^ENSG00000153944.12"  ; ccdsid "CCDS11596.1"  ; exon_id "ENSE00002219180.3"  ; exon_number 1 ; gene_id "MSI2--NUP58^MSI2^ENSG00000153944.12"  ; gene_name MSI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178398.4"  ; havana_transcript "OTTHUMT00000441813.2"  ; hgnc_id "HGNC:18585"  ; level 2 ; orig_coord_info "chr17,57256743,57256804,+"  ; protein_id "ENSP00000284073.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--NUP58^ENST00000284073.7"  ; transcript_name "MSI2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MSI2--NUP58	HAVANA	mRNA	1673	54046	.	+	.	FI_gene_label "MSI2^ENSG00000153944.12"  ; ID "MSI2--NUP58^ENST00000284073.7"  ; Parent "MSI2--NUP58^MSI2^ENSG00000153944.12"  ; ccdsid "CCDS11596.1"  ; exon_id "ENSE00002219180.3"  ; exon_number 1 ; gene_id "MSI2--NUP58^MSI2^ENSG00000153944.12"  ; gene_name MSI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178398.4"  ; havana_transcript "OTTHUMT00000441813.2"  ; hgnc_id "HGNC:18585"  ; level 2 ; orig_coord_info "chr17,57256743,57256804,+"  ; protein_id "ENSP00000284073.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--NUP58^ENST00000284073.7"  ; transcript_name "MSI2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MSI2--NUP58	HAVANA	gene	57124	80934	.	+	.	FI_gene_label "NUP58^ENSG00000139496.16"  ; ID "MSI2--NUP58^NUP58^ENSG00000139496.16"  ; ccdsid "CCDS31949.1"  ; exon_id "ENSE00001866306.1"  ; exon_number 1 ; gene_id "MSI2--NUP58^NUP58^ENSG00000139496.16"  ; gene_name NUP58 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016608.6"  ; havana_transcript "OTTHUMT00000354750.1"  ; hgnc_id "HGNC:20261"  ; level 2 ; orig_coord_info "chr13,25301774,25301880,+"  ; protein_id "ENSP00000371137.3"  ; tag basic CCDS ; transcript_id "MSI2--NUP58^ENST00000381718.7"  ; transcript_name "NUP58-201"  ; transcript_support_level 2 ; transcript_type protein_coding
MSI2--NUP58	HAVANA	mRNA	57124	80934	.	+	.	FI_gene_label "NUP58^ENSG00000139496.16"  ; ID "MSI2--NUP58^ENST00000381718.7"  ; Parent "MSI2--NUP58^NUP58^ENSG00000139496.16"  ; ccdsid "CCDS31949.1"  ; exon_id "ENSE00001866306.1"  ; exon_number 1 ; gene_id "MSI2--NUP58^NUP58^ENSG00000139496.16"  ; gene_name NUP58 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016608.6"  ; havana_transcript "OTTHUMT00000354750.1"  ; hgnc_id "HGNC:20261"  ; level 2 ; orig_coord_info "chr13,25301774,25301880,+"  ; protein_id "ENSP00000371137.3"  ; tag basic CCDS ; transcript_id "MSI2--NUP58^ENST00000381718.7"  ; transcript_name "NUP58-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
OTUD7B--CTSS	HAVANA	gene	26267	40735	.	+	.	FI_gene_label "CTSS^ENSG00000163131.12"  ; ID "OTUD7B--CTSS^CTSS^ENSG00000163131.12"  ; ccdsid "CCDS968.1"  ; exon_id "ENSE00001448523.1"  ; exon_number 2 ; gene_id "OTUD7B--CTSS^CTSS^ENSG00000163131.12"  ; gene_name CTSS ; gene_type protein_coding ; havana_gene "OTTHUMG00000035010.3"  ; havana_transcript "OTTHUMT00000084737.2"  ; hgnc_id "HGNC:2545"  ; level 2 ; orig_coord_info "chr1,150764638,150764763,-"  ; protein_id "ENSP00000357981.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "OTUD7B--CTSS^ENST00000368985.8"  ; transcript_name "CTSS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
OTUD7B--CTSS	HAVANA	mRNA	26267	40735	.	+	.	FI_gene_label "CTSS^ENSG00000163131.12"  ; ID "OTUD7B--CTSS^ENST00000368985.8"  ; Parent "OTUD7B--CTSS^CTSS^ENSG00000163131.12"  ; ccdsid "CCDS968.1"  ; exon_id "ENSE00001448523.1"  ; exon_number 2 ; gene_id "OTUD7B--CTSS^CTSS^ENSG00000163131.12"  ; gene_name CTSS ; gene_type protein_coding ; havana_gene "OTTHUMG00000035010.3"  ; havana_transcript "OTTHUMT00000084737.2"  ; hgnc_id "HGNC:2545"  ; level 2 ; orig_coord_info "chr1,150764638,150764763,-"  ; protein_id "ENSP00000357981.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "OTUD7B--CTSS^ENST00000368985.8"  ; transcript_name "CTSS-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
OTUD7B--CTSS	HAVANA	gene	1052	14793	.	+	.	FI_gene_label "OTUD7B^ENSG00000264522.6"  ; ID "OTUD7B--CTSS^OTUD7B^ENSG00000264522.6"  ; exon_id "ENSE00001666491.1"  ; exon_number 2 ; gene_id "OTUD7B--CTSS^OTUD7B^ENSG00000264522.6"  ; gene_name OTUD7B ; gene_type protein_coding ; havana_gene "OTTHUMG00000012291.7"  ; havana_transcript "OTTHUMT00000034148.2"  ; hgnc_id "HGNC:16683"  ; level 2 ; orig_coord_info "chr1,149977426,149977510,-"  ; protein_id "ENSP00000408231.1"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "OTUD7B--CTSS^ENST00000417191.2"  ; transcript_name "OTUD7B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
OTUD7B--CTSS	HAVANA	mRNA	1052	14793	.	+	.	FI_gene_label "OTUD7B^ENSG00000264522.6"  ; ID "OTUD7B--CTSS^ENST00000417191.2"  ; Parent "OTUD7B--CTSS^OTUD7B^ENSG00000264522.6"  ; exon_id "ENSE00001666491.1"  ; exon_number 2 ; gene_id "OTUD7B--CTSS^OTUD7B^ENSG00000264522.6"  ; gene_name OTUD7B ; gene_type protein_coding ; havana_gene "OTTHUMG00000012291.7"  ; havana_transcript "OTTHUMT00000034148.2"  ; hgnc_id "HGNC:16683"  ; level 2 ; orig_coord_info "chr1,149977426,149977510,-"  ; protein_id "ENSP00000408231.1"  ; tag mRNA_end_NF cds_end_NF ; transcript_id "OTUD7B--CTSS^ENST00000417191.2"  ; transcript_name "OTUD7B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RPS6KB1--LINC01483	HAVANA	gene	1076	21996	.	+	.	FI_gene_label "RPS6KB1^ENSG00000108443.14"  ; ID "RPS6KB1--LINC01483^RPS6KB1^ENSG00000108443.14"  ; ccdsid "CCDS11621.1"  ; exon_id "ENSE00001823154.2"  ; exon_number 1 ; gene_id "RPS6KB1--LINC01483^RPS6KB1^ENSG00000108443.14"  ; gene_name RPS6KB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150642.5"  ; havana_transcript "OTTHUMT00000319324.2"  ; hgnc_id "HGNC:10436"  ; level 2 ; orig_coord_info "chr17,59893185,59893325,+"  ; protein_id "ENSP00000225577.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "RPS6KB1--LINC01483^ENST00000225577.9"  ; transcript_name "RPS6KB1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RPS6KB1--LINC01483	HAVANA	mRNA	1076	21996	.	+	.	FI_gene_label "RPS6KB1^ENSG00000108443.14"  ; ID "RPS6KB1--LINC01483^ENST00000225577.9"  ; Parent "RPS6KB1--LINC01483^RPS6KB1^ENSG00000108443.14"  ; ccdsid "CCDS11621.1"  ; exon_id "ENSE00001823154.2"  ; exon_number 1 ; gene_id "RPS6KB1--LINC01483^RPS6KB1^ENSG00000108443.14"  ; gene_name RPS6KB1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150642.5"  ; havana_transcript "OTTHUMT00000319324.2"  ; hgnc_id "HGNC:10436"  ; level 2 ; orig_coord_info "chr17,59893185,59893325,+"  ; protein_id "ENSP00000225577.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "RPS6KB1--LINC01483^ENST00000225577.9"  ; transcript_name "RPS6KB1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SPOCK1--CWC27	ENSEMBL	gene	8877	21636	.	+	.	FI_gene_label "SPOCK1^ENSG00000152377.14"  ; ID "SPOCK1--CWC27^SPOCK1^ENSG00000152377.14"  ; exon_id "ENSE00003594531.1"  ; exon_number 1 ; gene_id "SPOCK1--CWC27^SPOCK1^ENSG00000152377.14"  ; gene_name SPOCK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129157.7"  ; hgnc_id "HGNC:11251"  ; level 3 ; orig_coord_info "chr5,137267010,137267055,-"  ; protein_id "ENSP00000282223.9"  ; tag basic ; transcript_id "SPOCK1--CWC27^ENST00000282223.11"  ; transcript_name "SPOCK1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SPOCK1--CWC27	ENSEMBL	mRNA	8877	21636	.	+	.	FI_gene_label "SPOCK1^ENSG00000152377.14"  ; ID "SPOCK1--CWC27^ENST00000282223.11"  ; Parent "SPOCK1--CWC27^SPOCK1^ENSG00000152377.14"  ; exon_id "ENSE00003594531.1"  ; exon_number 1 ; gene_id "SPOCK1--CWC27^SPOCK1^ENSG00000152377.14"  ; gene_name SPOCK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129157.7"  ; hgnc_id "HGNC:11251"  ; level 3 ; orig_coord_info "chr5,137267010,137267055,-"  ; protein_id "ENSP00000282223.9"  ; tag basic ; transcript_id "SPOCK1--CWC27^ENST00000282223.11"  ; transcript_name "SPOCK1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SPOCK1--CWC27	HAVANA	gene	24639	44078	.	+	.	FI_gene_label "CWC27^ENSG00000153015.16"  ; ID "SPOCK1--CWC27^CWC27^ENSG00000153015.16"  ; ccdsid "CCDS3982.2"  ; exon_id "ENSE00001487414.2"  ; exon_number 1 ; gene_id "SPOCK1--CWC27^CWC27^ENSG00000153015.16"  ; gene_name CWC27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074069.8"  ; havana_transcript "OTTHUMT00000157247.5"  ; hgnc_id "HGNC:10664"  ; level 2 ; orig_coord_info "chr5,64769147,64769188,+"  ; protein_id "ENSP00000370460.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPOCK1--CWC27^ENST00000381070.8"  ; transcript_name "CWC27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SPOCK1--CWC27	HAVANA	mRNA	24639	44078	.	+	.	FI_gene_label "CWC27^ENSG00000153015.16"  ; ID "SPOCK1--CWC27^ENST00000381070.8"  ; Parent "SPOCK1--CWC27^CWC27^ENSG00000153015.16"  ; ccdsid "CCDS3982.2"  ; exon_id "ENSE00001487414.2"  ; exon_number 1 ; gene_id "SPOCK1--CWC27^CWC27^ENSG00000153015.16"  ; gene_name CWC27 ; gene_type protein_coding ; havana_gene "OTTHUMG00000074069.8"  ; havana_transcript "OTTHUMT00000157247.5"  ; hgnc_id "HGNC:10664"  ; level 2 ; orig_coord_info "chr5,64769147,64769188,+"  ; protein_id "ENSP00000370460.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SPOCK1--CWC27^ENST00000381070.8"  ; transcript_name "CWC27-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SRGAP2--HHAT	HAVANA	gene	43383	63083	.	+	.	FI_gene_label "HHAT^ENSG00000054392.13"  ; ID "SRGAP2--HHAT^HHAT^ENSG00000054392.13"  ; ccdsid "CCDS1495.1"  ; exon_id "ENSE00003476299.1"  ; exon_number 2 ; gene_id "SRGAP2--HHAT^HHAT^ENSG00000054392.13"  ; gene_name HHAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000036447.4"  ; havana_transcript "OTTHUMT00000088659.3"  ; hgnc_id "HGNC:18270"  ; level 2 ; orig_coord_info "chr1,210348976,210349066,+"  ; protein_id "ENSP00000261458.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SRGAP2--HHAT^ENST00000261458.8"  ; transcript_name "HHAT-201"  ; transcript_support_level 2 ; transcript_type protein_coding
SRGAP2--HHAT	HAVANA	mRNA	43383	63083	.	+	.	FI_gene_label "HHAT^ENSG00000054392.13"  ; ID "SRGAP2--HHAT^ENST00000261458.8"  ; Parent "SRGAP2--HHAT^HHAT^ENSG00000054392.13"  ; ccdsid "CCDS1495.1"  ; exon_id "ENSE00003476299.1"  ; exon_number 2 ; gene_id "SRGAP2--HHAT^HHAT^ENSG00000054392.13"  ; gene_name HHAT ; gene_type protein_coding ; havana_gene "OTTHUMG00000036447.4"  ; havana_transcript "OTTHUMT00000088659.3"  ; hgnc_id "HGNC:18270"  ; level 2 ; orig_coord_info "chr1,210348976,210349066,+"  ; protein_id "ENSP00000261458.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "SRGAP2--HHAT^ENST00000261458.8"  ; transcript_name "HHAT-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
SRGAP2--HHAT	ENSEMBL	gene	3282	18721	.	+	.	FI_gene_label "SRGAP2^ENSG00000266028.7"  ; ID "SRGAP2--HHAT^SRGAP2^ENSG00000266028.7"  ; exon_id "ENSE00002267225.2"  ; exon_number 2 ; gene_id "SRGAP2--HHAT^SRGAP2^ENSG00000266028.7"  ; gene_name SRGAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000184381.5"  ; hgnc_id "HGNC:19751"  ; level 3 ; orig_coord_info "chr1,206384050,206384076,+"  ; protein_id "ENSP00000397990.3"  ; tag basic ; transcript_id "SRGAP2--HHAT^ENST00000419187.6"  ; transcript_name "SRGAP2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SRGAP2--HHAT	ENSEMBL	mRNA	3282	18721	.	+	.	FI_gene_label "SRGAP2^ENSG00000266028.7"  ; ID "SRGAP2--HHAT^ENST00000419187.6"  ; Parent "SRGAP2--HHAT^SRGAP2^ENSG00000266028.7"  ; exon_id "ENSE00002267225.2"  ; exon_number 2 ; gene_id "SRGAP2--HHAT^SRGAP2^ENSG00000266028.7"  ; gene_name SRGAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000184381.5"  ; hgnc_id "HGNC:19751"  ; level 3 ; orig_coord_info "chr1,206384050,206384076,+"  ; protein_id "ENSP00000397990.3"  ; tag basic ; transcript_id "SRGAP2--HHAT^ENST00000419187.6"  ; transcript_name "SRGAP2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SUCO--IKZF3	HAVANA	gene	1802	28233	.	+	.	FI_gene_label "SUCO^ENSG00000094975.14"  ; ID "SUCO--IKZF3^SUCO^ENSG00000094975.14"  ; ccdsid "CCDS1303.1"  ; exon_id "ENSE00001906524.2"  ; exon_number 1 ; gene_id "SUCO--IKZF3^SUCO^ENSG00000094975.14"  ; gene_name SUCO ; gene_type protein_coding ; havana_gene "OTTHUMG00000034839.5"  ; havana_transcript "OTTHUMT00000084273.3"  ; hgnc_id "HGNC:1240"  ; level 2 ; orig_coord_info "chr1,172533436,172533497,+"  ; protein_id "ENSP00000263688.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SUCO--IKZF3^ENST00000263688.4"  ; transcript_name "SUCO-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SUCO--IKZF3	HAVANA	mRNA	1802	28233	.	+	.	FI_gene_label "SUCO^ENSG00000094975.14"  ; ID "SUCO--IKZF3^ENST00000263688.4"  ; Parent "SUCO--IKZF3^SUCO^ENSG00000094975.14"  ; ccdsid "CCDS1303.1"  ; exon_id "ENSE00001906524.2"  ; exon_number 1 ; gene_id "SUCO--IKZF3^SUCO^ENSG00000094975.14"  ; gene_name SUCO ; gene_type protein_coding ; havana_gene "OTTHUMG00000034839.5"  ; havana_transcript "OTTHUMT00000084273.3"  ; hgnc_id "HGNC:1240"  ; level 2 ; orig_coord_info "chr1,172533436,172533497,+"  ; protein_id "ENSP00000263688.3"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "SUCO--IKZF3^ENST00000263688.4"  ; transcript_name "SUCO-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SUCO--IKZF3	HAVANA	gene	31358	40913	.	+	.	FI_gene_label "IKZF3^ENSG00000161405.17"  ; ID "SUCO--IKZF3^IKZF3^ENSG00000161405.17"  ; exon_id "ENSE00002692875.1"  ; exon_number 1 ; gene_id "SUCO--IKZF3^IKZF3^ENSG00000161405.17"  ; gene_name IKZF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133250.5"  ; havana_transcript "OTTHUMT00000257011.2"  ; hgnc_id "HGNC:13178"  ; level 2 ; orig_coord_info "chr17,39864120,39864126,-"  ; protein_id "ENSP00000462791.1"  ; transcript_id "SUCO--IKZF3^ENST00000293068.9"  ; transcript_name "IKZF3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
SUCO--IKZF3	HAVANA	mRNA	31358	40913	.	+	.	FI_gene_label "IKZF3^ENSG00000161405.17"  ; ID "SUCO--IKZF3^ENST00000293068.9"  ; Parent "SUCO--IKZF3^IKZF3^ENSG00000161405.17"  ; exon_id "ENSE00002692875.1"  ; exon_number 1 ; gene_id "SUCO--IKZF3^IKZF3^ENSG00000161405.17"  ; gene_name IKZF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133250.5"  ; havana_transcript "OTTHUMT00000257011.2"  ; hgnc_id "HGNC:13178"  ; level 2 ; orig_coord_info "chr17,39864120,39864126,-"  ; protein_id "ENSP00000462791.1"  ; transcript_id "SUCO--IKZF3^ENST00000293068.9"  ; transcript_name "IKZF3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
TANC2--DDX59-AS1	HAVANA	gene	1005	42292	.	+	.	FI_gene_label "TANC2^ENSG00000170921.15"  ; ID "TANC2--DDX59-AS1^TANC2^ENSG00000170921.15"  ; exon_id "ENSE00002709640.1"  ; exon_number 1 ; gene_id "TANC2--DDX59-AS1^TANC2^ENSG00000170921.15"  ; gene_name TANC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179103.2"  ; havana_transcript "OTTHUMT00000444766.1"  ; hgnc_id "HGNC:30212"  ; level 2 ; orig_coord_info "chr17,63009560,63009626,+"  ; protein_id "ENSP00000374171.4"  ; tag basic appris_alternative_2 ; transcript_id "TANC2--DDX59-AS1^ENST00000389520.8"  ; transcript_name "TANC2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TANC2--DDX59-AS1	HAVANA	mRNA	1005	42292	.	+	.	FI_gene_label "TANC2^ENSG00000170921.15"  ; ID "TANC2--DDX59-AS1^ENST00000389520.8"  ; Parent "TANC2--DDX59-AS1^TANC2^ENSG00000170921.15"  ; exon_id "ENSE00002709640.1"  ; exon_number 1 ; gene_id "TANC2--DDX59-AS1^TANC2^ENSG00000170921.15"  ; gene_name TANC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179103.2"  ; havana_transcript "OTTHUMT00000444766.1"  ; hgnc_id "HGNC:30212"  ; level 2 ; orig_coord_info "chr17,63009560,63009626,+"  ; protein_id "ENSP00000374171.4"  ; tag basic appris_alternative_2 ; transcript_id "TANC2--DDX59-AS1^ENST00000389520.8"  ; transcript_name "TANC2-201"  ; 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: 
AC005972.3--C17orf64	HAVANA	gene	1001	2733	.	+	.	FI_gene_label "AC005972.3^ENSG00000283538.3"  ; ID "AC005972.3--C17orf64^AC005972.3^ENSG00000283538.3"  ; exon_id "ENSE00003837708.1"  ; exon_number 1 ; gene_id "AC005972.3--C17orf64^AC005972.3^ENSG00000283538.3"  ; gene_name "AC005972.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000179100.4"  ; havana_transcript "OTTHUMT00000444764.1"  ; level 2 ; orig_coord_info "chr17,62968500,62968549,-"  ; tag basic ; transcript_id "AC005972.3--C17orf64^ENST00000581596.1"  ; transcript_name "AC005972.3-203"  ; transcript_support_level 1 ; transcript_type lncRNA
AC005972.3--C17orf64	HAVANA	RNA	1001	2733	.	+	.	FI_gene_label "AC005972.3^ENSG00000283538.3"  ; ID "AC005972.3--C17orf64^ENST00000581596.1"  ; Parent "AC005972.3--C17orf64^AC005972.3^ENSG00000283538.3"  ; exon_id "ENSE00003837708.1"  ; exon_number 1 ; gene_id "AC005972.3--C17orf64^AC005972.3^ENSG00000283538.3"  ; gene_name "AC005972.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000179100.4"  ; havana_transcript "OTTHUMT00000444764.1"  ; level 2 ; orig_coord_info "chr17,62968500,62968549,-"  ; tag basic ; transcript_id "AC005972.3--C17orf64^ENST00000581596.1"  ; transcript_name "AC005972.3-203"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
HELZ--AL589765.4	HAVANA	gene	51782	54163	.	+	.	FI_gene_label "AL589765.4^ENSG00000249602.1"  ; ID "HELZ--AL589765.4^AL589765.4^ENSG00000249602.1"  ; exon_id "ENSE00002019324.1"  ; exon_number 1 ; gene_id "HELZ--AL589765.4^AL589765.4^ENSG00000249602.1"  ; gene_name "AL589765.4"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000045374.2"  ; havana_transcript "OTTHUMT00000105378.2"  ; level 2 ; orig_coord_info "chr1,151769344,151769501,-"  ; tag basic ; transcript_id "HELZ--AL589765.4^ENST00000512280.1"  ; transcript_name "AL589765.4-201"  ; transcript_support_level 3 ; transcript_type lncRNA
HELZ--AL589765.4	HAVANA	RNA	51782	54163	.	+	.	FI_gene_label "AL589765.4^ENSG00000249602.1"  ; ID "HELZ--AL589765.4^ENST00000512280.1"  ; Parent "HELZ--AL589765.4^AL589765.4^ENSG00000249602.1"  ; exon_id "ENSE00002019324.1"  ; exon_number 1 ; gene_id "HELZ--AL589765.4^AL589765.4^ENSG00000249602.1"  ; gene_name "AL589765.4"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000045374.2"  ; havana_transcript "OTTHUMT00000105378.2"  ; level 2 ; orig_coord_info "chr1,151769344,151769501,-"  ; tag basic ; transcript_id "HELZ--AL589765.4^ENST00000512280.1"  ; transcript_name "AL589765.4-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
LGALS3--AL356020.1	HAVANA	gene	11892	14555	.	+	.	FI_gene_label "AL356020.1^ENSG00000258731.1"  ; ID "LGALS3--AL356020.1^AL356020.1^ENSG00000258731.1"  ; exon_id "ENSE00002472010.1"  ; exon_number 1 ; gene_id "LGALS3--AL356020.1^AL356020.1^ENSG00000258731.1"  ; gene_name "AL356020.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000171155.2"  ; havana_transcript "OTTHUMT00000411965.1"  ; level 2 ; orig_coord_info "chr14,53153354,53153731,+"  ; tag basic ; transcript_id "LGALS3--AL356020.1^ENST00000554235.1"  ; transcript_name "AL356020.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
LGALS3--AL356020.1	HAVANA	RNA	11892	14555	.	+	.	FI_gene_label "AL356020.1^ENSG00000258731.1"  ; ID "LGALS3--AL356020.1^ENST00000554235.1"  ; Parent "LGALS3--AL356020.1^AL356020.1^ENSG00000258731.1"  ; exon_id "ENSE00002472010.1"  ; exon_number 1 ; gene_id "LGALS3--AL356020.1^AL356020.1^ENSG00000258731.1"  ; gene_name "AL356020.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000171155.2"  ; havana_transcript "OTTHUMT00000411965.1"  ; level 2 ; orig_coord_info "chr14,53153354,53153731,+"  ; tag basic ; transcript_id "LGALS3--AL356020.1^ENST00000554235.1"  ; transcript_name "AL356020.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
LGALS3--AL365295.1	HAVANA	gene	28190	36751	.	+	.	FI_gene_label "AL365295.1^ENSG00000237356.7"  ; ID "LGALS3--AL365295.1^AL365295.1^ENSG00000237356.7"  ; exon_id "ENSE00001653377.1"  ; exon_number 1 ; gene_id "LGALS3--AL365295.1^AL365295.1^ENSG00000237356.7"  ; gene_name "AL365295.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000133700.25"  ; havana_transcript "OTTHUMT00000316369.1"  ; level 2 ; orig_coord_info "chr14,53369381,53369501,+"  ; transcript_id "LGALS3--AL365295.1^ENST00000425648.1"  ; transcript_name "AL365295.1-205"  ; transcript_support_level 4 ; transcript_type lncRNA
LGALS3--AL365295.1	HAVANA	RNA	28190	36751	.	+	.	FI_gene_label "AL365295.1^ENSG00000237356.7"  ; ID "LGALS3--AL365295.1^ENST00000425648.1"  ; Parent "LGALS3--AL365295.1^AL365295.1^ENSG00000237356.7"  ; exon_id "ENSE00001653377.1"  ; exon_number 1 ; gene_id "LGALS3--AL365295.1^AL365295.1^ENSG00000237356.7"  ; gene_name "AL365295.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000133700.25"  ; havana_transcript "OTTHUMT00000316369.1"  ; level 2 ; orig_coord_info "chr14,53369381,53369501,+"  ; transcript_id "LGALS3--AL365295.1^ENST00000425648.1"  ; transcript_name "AL365295.1-205"  ; transcript_support_level 4 ; transcript_type lncRNA
L1 and L2 created: 
RPS6KB1--LINC01483	HAVANA	gene	26870	31707	.	+	.	FI_gene_label "LINC01483^ENSG00000227517.7"  ; ID "RPS6KB1--LINC01483^LINC01483^ENSG00000227517.7"  ; exon_id "ENSE00001802669.1"  ; exon_number 1 ; gene_id "RPS6KB1--LINC01483^LINC01483^ENSG00000227517.7"  ; gene_name LINC01483 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132249.5"  ; havana_transcript "OTTHUMT00000255327.1"  ; hgnc_id "HGNC:51130"  ; level 2 ; orig_coord_info "chr17,69594785,69594940,+"  ; tag basic ; transcript_id "RPS6KB1--LINC01483^ENST00000433856.5"  ; transcript_name "LINC01483-201"  ; transcript_support_level 2 ; transcript_type lncRNA
RPS6KB1--LINC01483	HAVANA	RNA	26870	31707	.	+	.	FI_gene_label "LINC01483^ENSG00000227517.7"  ; ID "RPS6KB1--LINC01483^ENST00000433856.5"  ; Parent "RPS6KB1--LINC01483^LINC01483^ENSG00000227517.7"  ; exon_id "ENSE00001802669.1"  ; exon_number 1 ; gene_id "RPS6KB1--LINC01483^LINC01483^ENSG00000227517.7"  ; gene_name LINC01483 ; gene_type lncRNA ; havana_gene "OTTHUMG00000132249.5"  ; havana_transcript "OTTHUMT00000255327.1"  ; hgnc_id "HGNC:51130"  ; level 2 ; orig_coord_info "chr17,69594785,69594940,+"  ; tag basic ; transcript_id "RPS6KB1--LINC01483^ENST00000433856.5"  ; transcript_name "LINC01483-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
TANC2--DDX59-AS1	HAVANA	gene	50636	53371	.	+	.	FI_gene_label "DDX59-AS1^ENSG00000260088.1"  ; ID "TANC2--DDX59-AS1^DDX59-AS1^ENSG00000260088.1"  ; exon_id "ENSE00002576725.1"  ; exon_number 1 ; gene_id "TANC2--DDX59-AS1^DDX59-AS1^ENSG00000260088.1"  ; gene_name "DDX59-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000035741.1"  ; havana_transcript "OTTHUMT00000086957.1"  ; hgnc_id "HGNC:41094"  ; level 2 ; orig_coord_info "chr1,200669507,200669622,+"  ; tag basic ; transcript_id "TANC2--DDX59-AS1^ENST00000568695.1"  ; transcript_name "DDX59-AS1-201"  ; transcript_support_level 1 ; transcript_type lncRNA
TANC2--DDX59-AS1	HAVANA	RNA	50636	53371	.	+	.	FI_gene_label "DDX59-AS1^ENSG00000260088.1"  ; ID "TANC2--DDX59-AS1^ENST00000568695.1"  ; Parent "TANC2--DDX59-AS1^DDX59-AS1^ENSG00000260088.1"  ; exon_id "ENSE00002576725.1"  ; exon_number 1 ; gene_id "TANC2--DDX59-AS1^DDX59-AS1^ENSG00000260088.1"  ; gene_name "DDX59-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000035741.1"  ; havana_transcript "OTTHUMT00000086957.1"  ; hgnc_id "HGNC:41094"  ; level 2 ; orig_coord_info "chr1,200669507,200669622,+"  ; tag basic ; transcript_id "TANC2--DDX59-AS1^ENST00000568695.1"  ; transcript_name "DDX59-AS1-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
332 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 ------------------------------
566 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 26 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