.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/437a99f1d473f24d2cb98a662d9e5a/.command.log
Size: 45.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/441ee15821de879298a1bdd22928d3/fi_workdir/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/437a99f1d473f24d2cb98a662d9e5a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/437a99f1d473f24d2cb98a662d9e5a/.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         |
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                          ------ 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: 2656
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2656
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => exon CDS
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:2656
  => 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: 
BMS1P7--PTPN20	ENSEMBL	gene	10618	29891	.	+	.	FI_gene_label "PTPN20^ENSG00000204179.10"  ; ID "BMS1P7--PTPN20^PTPN20^ENSG00000204179.10"  ; ccdsid "CCDS73114.1"  ; exon_id "ENSE00003719491.1"  ; exon_number 4 ; gene_id "BMS1P7--PTPN20^PTPN20^ENSG00000204179.10"  ; gene_name PTPN20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018094.10"  ; hgnc_id "HGNC:23423"  ; level 3 ; orig_coord_info "chr10,46946579,46946675,+"  ; protein_id "ENSP00000363335.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "BMS1P7--PTPN20^ENST00000374218.6"  ; transcript_name "PTPN20-201"  ; transcript_support_level 5 ; transcript_type protein_coding
BMS1P7--PTPN20	ENSEMBL	mRNA	10618	29891	.	+	.	FI_gene_label "PTPN20^ENSG00000204179.10"  ; ID "BMS1P7--PTPN20^ENST00000374218.6"  ; Parent "BMS1P7--PTPN20^PTPN20^ENSG00000204179.10"  ; ccdsid "CCDS73114.1"  ; exon_id "ENSE00003719491.1"  ; exon_number 4 ; gene_id "BMS1P7--PTPN20^PTPN20^ENSG00000204179.10"  ; gene_name PTPN20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018094.10"  ; hgnc_id "HGNC:23423"  ; level 3 ; orig_coord_info "chr10,46946579,46946675,+"  ; protein_id "ENSP00000363335.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "BMS1P7--PTPN20^ENST00000374218.6"  ; transcript_name "PTPN20-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
E2F3--TMEM241	HAVANA	gene	1001	13190	.	+	.	FI_gene_label "E2F3^ENSG00000112242.15"  ; ID "E2F3--TMEM241^E2F3^ENSG00000112242.15"  ; ccdsid "CCDS4545.1"  ; exon_id "ENSE00001148453.4"  ; exon_number 1 ; gene_id "E2F3--TMEM241^E2F3^ENSG00000112242.15"  ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3"  ; havana_transcript "OTTHUMT00000043828.3"  ; hgnc_id "HGNC:3115"  ; level 2 ; orig_coord_info "chr6,20402233,20402625,+"  ; protein_id "ENSP00000262904.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "E2F3--TMEM241^ENST00000346618.8"  ; transcript_name "E2F3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
E2F3--TMEM241	HAVANA	mRNA	1001	13190	.	+	.	FI_gene_label "E2F3^ENSG00000112242.15"  ; ID "E2F3--TMEM241^ENST00000346618.8"  ; Parent "E2F3--TMEM241^E2F3^ENSG00000112242.15"  ; ccdsid "CCDS4545.1"  ; exon_id "ENSE00001148453.4"  ; exon_number 1 ; gene_id "E2F3--TMEM241^E2F3^ENSG00000112242.15"  ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3"  ; havana_transcript "OTTHUMT00000043828.3"  ; hgnc_id "HGNC:3115"  ; level 2 ; orig_coord_info "chr6,20402233,20402625,+"  ; protein_id "ENSP00000262904.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "E2F3--TMEM241^ENST00000346618.8"  ; transcript_name "E2F3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
E2F3--TMEM241	HAVANA	gene	16191	35568	.	+	.	FI_gene_label "TMEM241^ENSG00000134490.14"  ; ID "E2F3--TMEM241^TMEM241^ENSG00000134490.14"  ; ccdsid "CCDS11876.2"  ; exon_id "ENSE00002168027.1"  ; exon_number 1 ; gene_id "E2F3--TMEM241^TMEM241^ENSG00000134490.14"  ; gene_name TMEM241 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131771.8"  ; havana_transcript "OTTHUMT00000254702.4"  ; hgnc_id "HGNC:31723"  ; level 2 ; orig_coord_info "chr18,23437781,23437852,-"  ; protein_id "ENSP00000372720.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "E2F3--TMEM241^ENST00000383233.8"  ; transcript_name "TMEM241-201"  ; transcript_support_level 1 ; transcript_type protein_coding
E2F3--TMEM241	HAVANA	mRNA	16191	35568	.	+	.	FI_gene_label "TMEM241^ENSG00000134490.14"  ; ID "E2F3--TMEM241^ENST00000383233.8"  ; Parent "E2F3--TMEM241^TMEM241^ENSG00000134490.14"  ; ccdsid "CCDS11876.2"  ; exon_id "ENSE00002168027.1"  ; exon_number 1 ; gene_id "E2F3--TMEM241^TMEM241^ENSG00000134490.14"  ; gene_name TMEM241 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131771.8"  ; havana_transcript "OTTHUMT00000254702.4"  ; hgnc_id "HGNC:31723"  ; level 2 ; orig_coord_info "chr18,23437781,23437852,-"  ; protein_id "ENSP00000372720.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "E2F3--TMEM241^ENST00000383233.8"  ; transcript_name "TMEM241-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ESR1--SCAF8	HAVANA	gene	7250	25560	.	+	.	FI_gene_label "ESR1^ENSG00000091831.24"  ; ID "ESR1--SCAF8^ESR1^ENSG00000091831.24"  ; ccdsid "CCDS5234.1"  ; exon_id "ENSE00001877305.2"  ; exon_number 1 ; gene_id "ESR1--SCAF8^ESR1^ENSG00000091831.24"  ; gene_name ESR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016103.7"  ; havana_transcript "OTTHUMT00000043308.2"  ; hgnc_id "HGNC:3467"  ; level 2 ; orig_coord_info "chr6,151807913,151808364,+"  ; protein_id "ENSP00000206249.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ESR1--SCAF8^ENST00000206249.8"  ; transcript_name "ESR1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ESR1--SCAF8	HAVANA	mRNA	7250	25560	.	+	.	FI_gene_label "ESR1^ENSG00000091831.24"  ; ID "ESR1--SCAF8^ENST00000206249.8"  ; Parent "ESR1--SCAF8^ESR1^ENSG00000091831.24"  ; ccdsid "CCDS5234.1"  ; exon_id "ENSE00001877305.2"  ; exon_number 1 ; gene_id "ESR1--SCAF8^ESR1^ENSG00000091831.24"  ; gene_name ESR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016103.7"  ; havana_transcript "OTTHUMT00000043308.2"  ; hgnc_id "HGNC:3467"  ; level 2 ; orig_coord_info "chr6,151807913,151808364,+"  ; protein_id "ENSP00000206249.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ESR1--SCAF8^ENST00000206249.8"  ; transcript_name "ESR1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ESR1--SCAF8	HAVANA	gene	35090	60239	.	+	.	FI_gene_label "SCAF8^ENSG00000213079.10"  ; ID "ESR1--SCAF8^SCAF8^ENSG00000213079.10"  ; ccdsid "CCDS5247.1"  ; exon_id "ENSE00001428900.4"  ; exon_number 1 ; gene_id "ESR1--SCAF8^SCAF8^ENSG00000213079.10"  ; gene_name SCAF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015877.2"  ; havana_transcript "OTTHUMT00000042798.2"  ; hgnc_id "HGNC:20959"  ; level 2 ; orig_coord_info "chr6,154733901,154733930,+"  ; protein_id "ENSP00000356146.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ESR1--SCAF8^ENST00000367178.8"  ; transcript_name "SCAF8-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ESR1--SCAF8	HAVANA	mRNA	35090	60239	.	+	.	FI_gene_label "SCAF8^ENSG00000213079.10"  ; ID "ESR1--SCAF8^ENST00000367178.8"  ; Parent "ESR1--SCAF8^SCAF8^ENSG00000213079.10"  ; ccdsid "CCDS5247.1"  ; exon_id "ENSE00001428900.4"  ; exon_number 1 ; gene_id "ESR1--SCAF8^SCAF8^ENSG00000213079.10"  ; gene_name SCAF8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015877.2"  ; havana_transcript "OTTHUMT00000042798.2"  ; hgnc_id "HGNC:20959"  ; level 2 ; orig_coord_info "chr6,154733901,154733930,+"  ; protein_id "ENSP00000356146.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ESR1--SCAF8^ENST00000367178.8"  ; transcript_name "SCAF8-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
GOLGA6L10--GOLGA2P6	HAVANA	gene	1001	9781	.	+	.	FI_gene_label "GOLGA6L10^ENSG00000278662.5"  ; ID "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5"  ; ccdsid "CCDS45325.2"  ; exon_id "ENSE00002255247.2"  ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5"  ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4"  ; havana_transcript "OTTHUMT00000419277.4"  ; hgnc_id "HGNC:37228"  ; level 2 ; orig_coord_info "chr15,82349292,82349375,-"  ; protein_id "ENSP00000479362.1"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000610657.2"  ; transcript_name "GOLGA6L10-207"  ; transcript_support_level 2 ; transcript_type protein_coding
GOLGA6L10--GOLGA2P6	HAVANA	mRNA	1001	9781	.	+	.	FI_gene_label "GOLGA6L10^ENSG00000278662.5"  ; ID "GOLGA6L10--GOLGA2P6^ENST00000610657.2"  ; Parent "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5"  ; ccdsid "CCDS45325.2"  ; exon_id "ENSE00002255247.2"  ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA6L10^ENSG00000278662.5"  ; gene_name GOLGA6L10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172580.4"  ; havana_transcript "OTTHUMT00000419277.4"  ; hgnc_id "HGNC:37228"  ; level 2 ; orig_coord_info "chr15,82349292,82349375,-"  ; protein_id "ENSP00000479362.1"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000610657.2"  ; transcript_name "GOLGA6L10-207"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NVL--CNIH4	HAVANA	gene	1018	28933	.	+	.	FI_gene_label "NVL^ENSG00000143748.18"  ; ID "NVL--CNIH4^NVL^ENSG00000143748.18"  ; ccdsid "CCDS1541.1"  ; exon_id "ENSE00001847692.2"  ; exon_number 1 ; gene_id "NVL--CNIH4^NVL^ENSG00000143748.18"  ; gene_name NVL ; gene_type protein_coding ; havana_gene "OTTHUMG00000037536.9"  ; havana_transcript "OTTHUMT00000091453.4"  ; hgnc_id "HGNC:8070"  ; level 2 ; orig_coord_info "chr1,224330071,224330127,-"  ; protein_id "ENSP00000281701.6"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "NVL--CNIH4^ENST00000281701.11"  ; transcript_name "NVL-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NVL--CNIH4	HAVANA	mRNA	1018	28933	.	+	.	FI_gene_label "NVL^ENSG00000143748.18"  ; ID "NVL--CNIH4^ENST00000281701.11"  ; Parent "NVL--CNIH4^NVL^ENSG00000143748.18"  ; ccdsid "CCDS1541.1"  ; exon_id "ENSE00001847692.2"  ; exon_number 1 ; gene_id "NVL--CNIH4^NVL^ENSG00000143748.18"  ; gene_name NVL ; gene_type protein_coding ; havana_gene "OTTHUMG00000037536.9"  ; havana_transcript "OTTHUMT00000091453.4"  ; hgnc_id "HGNC:8070"  ; level 2 ; orig_coord_info "chr1,224330071,224330127,-"  ; protein_id "ENSP00000281701.6"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "NVL--CNIH4^ENST00000281701.11"  ; transcript_name "NVL-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NVL--CNIH4	HAVANA	gene	31980	42027	.	+	.	FI_gene_label "CNIH4^ENSG00000143771.12"  ; ID "NVL--CNIH4^CNIH4^ENSG00000143771.12"  ; ccdsid "CCDS60429.1"  ; exon_id "ENSE00001862204.1"  ; exon_number 1 ; gene_id "NVL--CNIH4^CNIH4^ENSG00000143771.12"  ; gene_name CNIH4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037635.4"  ; havana_transcript "OTTHUMT00000091758.1"  ; hgnc_id "HGNC:25013"  ; level 2 ; orig_coord_info "chr1,224356925,224356993,+"  ; protein_id "ENSP00000355821.3"  ; tag basic CCDS ; transcript_id "NVL--CNIH4^ENST00000366856.3"  ; transcript_name "CNIH4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
NVL--CNIH4	HAVANA	mRNA	31980	42027	.	+	.	FI_gene_label "CNIH4^ENSG00000143771.12"  ; ID "NVL--CNIH4^ENST00000366856.3"  ; Parent "NVL--CNIH4^CNIH4^ENSG00000143771.12"  ; ccdsid "CCDS60429.1"  ; exon_id "ENSE00001862204.1"  ; exon_number 1 ; gene_id "NVL--CNIH4^CNIH4^ENSG00000143771.12"  ; gene_name CNIH4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000037635.4"  ; havana_transcript "OTTHUMT00000091758.1"  ; hgnc_id "HGNC:25013"  ; level 2 ; orig_coord_info "chr1,224356925,224356993,+"  ; protein_id "ENSP00000355821.3"  ; tag basic CCDS ; transcript_id "NVL--CNIH4^ENST00000366856.3"  ; transcript_name "CNIH4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
RBM14--RBM4	HAVANA	gene	15043	21268	.	+	.	FI_gene_label "RBM4^ENSG00000173933.21"  ; ID "RBM14--RBM4^RBM4^ENSG00000173933.21"  ; ccdsid "CCDS41676.1"  ; exon_id "ENSE00003513724.1"  ; exon_number 2 ; gene_id "RBM14--RBM4^RBM4^ENSG00000173933.21"  ; gene_name RBM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154171.7"  ; havana_transcript "OTTHUMT00000334210.2"  ; hgnc_id "HGNC:9901"  ; level 2 ; orig_coord_info "chr11,66639712,66640123,+"  ; protein_id "ENSP00000309166.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310092.12"  ; transcript_name "RBM4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4	HAVANA	mRNA	15043	21268	.	+	.	FI_gene_label "RBM4^ENSG00000173933.21"  ; ID "RBM14--RBM4^ENST00000310092.12"  ; Parent "RBM14--RBM4^RBM4^ENSG00000173933.21"  ; ccdsid "CCDS41676.1"  ; exon_id "ENSE00003513724.1"  ; exon_number 2 ; gene_id "RBM14--RBM4^RBM4^ENSG00000173933.21"  ; gene_name RBM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154171.7"  ; havana_transcript "OTTHUMT00000334210.2"  ; hgnc_id "HGNC:9901"  ; level 2 ; orig_coord_info "chr11,66639712,66640123,+"  ; protein_id "ENSP00000309166.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310092.12"  ; transcript_name "RBM4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RBM14--RBM4	HAVANA	gene	1005	12006	.	+	.	FI_gene_label "RBM14^ENSG00000239306.5"  ; ID "RBM14--RBM4^RBM14^ENSG00000239306.5"  ; ccdsid "CCDS8147.1"  ; exon_id "ENSE00003902856.1"  ; exon_number 1 ; gene_id "RBM14--RBM4^RBM14^ENSG00000239306.5"  ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5"  ; havana_transcript "OTTHUMT00000277128.1"  ; hgnc_id "HGNC:14219"  ; level 2 ; orig_coord_info "chr11,66616721,66617057,+"  ; protein_id "ENSP00000311747.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310137.5"  ; transcript_name "RBM14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4	HAVANA	mRNA	1005	12006	.	+	.	FI_gene_label "RBM14^ENSG00000239306.5"  ; ID "RBM14--RBM4^ENST00000310137.5"  ; Parent "RBM14--RBM4^RBM14^ENSG00000239306.5"  ; ccdsid "CCDS8147.1"  ; exon_id "ENSE00003902856.1"  ; exon_number 1 ; gene_id "RBM14--RBM4^RBM14^ENSG00000239306.5"  ; gene_name RBM14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140380.5"  ; havana_transcript "OTTHUMT00000277128.1"  ; hgnc_id "HGNC:14219"  ; level 2 ; orig_coord_info "chr11,66616721,66617057,+"  ; protein_id "ENSP00000311747.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4^ENST00000310137.5"  ; transcript_name "RBM14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	1021	7754	.	+	.	FI_gene_label "STX16^ENSG00000124222.22"  ; ID "STX16--NPEPL1^ENST00000312283.12"  ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; exon_id "ENSE00003459479.1"  ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22"  ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8"  ; havana_transcript "OTTHUMT00000267911.2"  ; hgnc_id "HGNC:11431"  ; level 2 ; orig_coord_info "chr20,58667505,58667597,+"  ; protein_id "ENSP00000312086.8"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12"  ; transcript_name "STX16-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
STX16--NPEPL1	HAVANA	gene	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1	HAVANA	mRNA	18353	29399	.	+	.	FI_gene_label "NPEPL1^ENSG00000215440.12"  ; ID "STX16--NPEPL1^ENST00000356091.11"  ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; ccdsid "CCDS46621.1"  ; exon_id "ENSE00001408052.7"  ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12"  ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8"  ; havana_transcript "OTTHUMT00000080402.7"  ; hgnc_id "HGNC:16244"  ; level 2 ; orig_coord_info "chr20,58692901,58693050,+"  ; protein_id "ENSP00000348395.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11"  ; transcript_name "NPEPL1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TMEM241--E2F3	HAVANA	gene	29898	42087	.	+	.	FI_gene_label "E2F3^ENSG00000112242.15"  ; ID "TMEM241--E2F3^E2F3^ENSG00000112242.15"  ; ccdsid "CCDS4545.1"  ; exon_id "ENSE00001148453.4"  ; exon_number 1 ; gene_id "TMEM241--E2F3^E2F3^ENSG00000112242.15"  ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3"  ; havana_transcript "OTTHUMT00000043828.3"  ; hgnc_id "HGNC:3115"  ; level 2 ; orig_coord_info "chr6,20402233,20402625,+"  ; protein_id "ENSP00000262904.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TMEM241--E2F3^ENST00000346618.8"  ; transcript_name "E2F3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMEM241--E2F3	HAVANA	mRNA	29898	42087	.	+	.	FI_gene_label "E2F3^ENSG00000112242.15"  ; ID "TMEM241--E2F3^ENST00000346618.8"  ; Parent "TMEM241--E2F3^E2F3^ENSG00000112242.15"  ; ccdsid "CCDS4545.1"  ; exon_id "ENSE00001148453.4"  ; exon_number 1 ; gene_id "TMEM241--E2F3^E2F3^ENSG00000112242.15"  ; gene_name E2F3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016389.3"  ; havana_transcript "OTTHUMT00000043828.3"  ; hgnc_id "HGNC:3115"  ; level 2 ; orig_coord_info "chr6,20402233,20402625,+"  ; protein_id "ENSP00000262904.4"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "TMEM241--E2F3^ENST00000346618.8"  ; transcript_name "E2F3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TMEM241--E2F3	HAVANA	gene	1001	20378	.	+	.	FI_gene_label "TMEM241^ENSG00000134490.14"  ; ID "TMEM241--E2F3^TMEM241^ENSG00000134490.14"  ; ccdsid "CCDS11876.2"  ; exon_id "ENSE00002168027.1"  ; exon_number 1 ; gene_id "TMEM241--E2F3^TMEM241^ENSG00000134490.14"  ; gene_name TMEM241 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131771.8"  ; havana_transcript "OTTHUMT00000254702.4"  ; hgnc_id "HGNC:31723"  ; level 2 ; orig_coord_info "chr18,23437781,23437852,-"  ; protein_id "ENSP00000372720.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM241--E2F3^ENST00000383233.8"  ; transcript_name "TMEM241-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMEM241--E2F3	HAVANA	mRNA	1001	20378	.	+	.	FI_gene_label "TMEM241^ENSG00000134490.14"  ; ID "TMEM241--E2F3^ENST00000383233.8"  ; Parent "TMEM241--E2F3^TMEM241^ENSG00000134490.14"  ; ccdsid "CCDS11876.2"  ; exon_id "ENSE00002168027.1"  ; exon_number 1 ; gene_id "TMEM241--E2F3^TMEM241^ENSG00000134490.14"  ; gene_name TMEM241 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131771.8"  ; havana_transcript "OTTHUMT00000254702.4"  ; hgnc_id "HGNC:31723"  ; level 2 ; orig_coord_info "chr18,23437781,23437852,-"  ; protein_id "ENSP00000372720.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM241--E2F3^ENST00000383233.8"  ; transcript_name "TMEM241-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	1052	15760	.	+	.	FI_gene_label "TVP23C^ENSG00000175106.17"  ; ID "TVP23C--CDRT4^ENST00000225576.7"  ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; ccdsid "CCDS11170.1"  ; exon_id "ENSE00001105678.2"  ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17"  ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10"  ; havana_transcript "OTTHUMT00000130705.3"  ; hgnc_id "HGNC:30453"  ; level 2 ; orig_coord_info "chr17,15563437,15563448,-"  ; protein_id "ENSP00000225576.3"  ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7"  ; transcript_name "TVP23C-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TVP23C--CDRT4	HAVANA	gene	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4	HAVANA	mRNA	19889	25887	.	+	.	FI_gene_label "CDRT4^ENSG00000239704.11"  ; ID "TVP23C--CDRT4^ENST00000619038.5"  ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; ccdsid "CCDS73995.1"  ; exon_id "ENSE00003735347.1"  ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11"  ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14"  ; havana_transcript "OTTHUMT00000130383.9"  ; hgnc_id "HGNC:14383"  ; level 2 ; orig_coord_info "chr17,15440208,15440238,-"  ; protein_id "ENSP00000482523.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5"  ; transcript_name "CDRT4-204"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF528--ZNF610	HAVANA	gene	17953	27667	.	+	.	FI_gene_label "ZNF610^ENSG00000167554.15"  ; ID "ZNF528--ZNF610^ZNF610^ENSG00000167554.15"  ; ccdsid "CCDS12851.1"  ; exon_id "ENSE00002470175.1"  ; exon_number 3 ; gene_id "ZNF528--ZNF610^ZNF610^ENSG00000167554.15"  ; gene_name ZNF610 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182645.4"  ; havana_transcript "OTTHUMT00000462863.1"  ; hgnc_id "HGNC:26687"  ; level 2 ; orig_coord_info "chr19,52349173,52349235,+"  ; protein_id "ENSP00000324441.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "ZNF528--ZNF610^ENST00000321287.12"  ; transcript_name "ZNF610-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF528--ZNF610	HAVANA	mRNA	17953	27667	.	+	.	FI_gene_label "ZNF610^ENSG00000167554.15"  ; ID "ZNF528--ZNF610^ENST00000321287.12"  ; Parent "ZNF528--ZNF610^ZNF610^ENSG00000167554.15"  ; ccdsid "CCDS12851.1"  ; exon_id "ENSE00002470175.1"  ; exon_number 3 ; gene_id "ZNF528--ZNF610^ZNF610^ENSG00000167554.15"  ; gene_name ZNF610 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182645.4"  ; havana_transcript "OTTHUMT00000462863.1"  ; hgnc_id "HGNC:26687"  ; level 2 ; orig_coord_info "chr19,52349173,52349235,+"  ; protein_id "ENSP00000324441.8"  ; tag basic appris_principal_2 CCDS ; transcript_id "ZNF528--ZNF610^ENST00000321287.12"  ; transcript_name "ZNF610-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF528--ZNF610	HAVANA	gene	1001	14939	.	+	.	FI_gene_label "ZNF528^ENSG00000167555.14"  ; ID "ZNF528--ZNF610^ZNF528^ENSG00000167555.14"  ; ccdsid "CCDS33091.1"  ; exon_id "ENSE00003647276.1"  ; exon_number 4 ; gene_id "ZNF528--ZNF610^ZNF528^ENSG00000167555.14"  ; gene_name ZNF528 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156494.9"  ; havana_transcript "OTTHUMT00000344336.2"  ; hgnc_id "HGNC:29384"  ; level 2 ; orig_coord_info "chr19,52402014,52402028,+"  ; protein_id "ENSP00000353652.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF528--ZNF610^ENST00000360465.8"  ; transcript_name "ZNF528-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF528--ZNF610	HAVANA	mRNA	1001	14939	.	+	.	FI_gene_label "ZNF528^ENSG00000167555.14"  ; ID "ZNF528--ZNF610^ENST00000360465.8"  ; Parent "ZNF528--ZNF610^ZNF528^ENSG00000167555.14"  ; ccdsid "CCDS33091.1"  ; exon_id "ENSE00003647276.1"  ; exon_number 4 ; gene_id "ZNF528--ZNF610^ZNF528^ENSG00000167555.14"  ; gene_name ZNF528 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156494.9"  ; havana_transcript "OTTHUMT00000344336.2"  ; hgnc_id "HGNC:29384"  ; level 2 ; orig_coord_info "chr19,52402014,52402028,+"  ; protein_id "ENSP00000353652.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF528--ZNF610^ENST00000360465.8"  ; transcript_name "ZNF528-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF528--ZNF880	HAVANA	gene	17973	21182	.	+	.	FI_gene_label "ZNF880^ENSG00000221923.9"  ; ID "ZNF528--ZNF880^ZNF880^ENSG00000221923.9"  ; exon_id "ENSE00001665096.1"  ; exon_number 1 ; gene_id "ZNF528--ZNF880^ZNF880^ENSG00000221923.9"  ; gene_name ZNF880 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167972.3"  ; havana_transcript "OTTHUMT00000397373.1"  ; hgnc_id "HGNC:37249"  ; level 2 ; orig_coord_info "chr19,52369966,52369977,+"  ; protein_id "ENSP00000343625.5"  ; tag basic ; transcript_id "ZNF528--ZNF880^ENST00000344085.9"  ; transcript_name "ZNF880-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF528--ZNF880	HAVANA	mRNA	17973	21182	.	+	.	FI_gene_label "ZNF880^ENSG00000221923.9"  ; ID "ZNF528--ZNF880^ENST00000344085.9"  ; Parent "ZNF528--ZNF880^ZNF880^ENSG00000221923.9"  ; exon_id "ENSE00001665096.1"  ; exon_number 1 ; gene_id "ZNF528--ZNF880^ZNF880^ENSG00000221923.9"  ; gene_name ZNF880 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167972.3"  ; havana_transcript "OTTHUMT00000397373.1"  ; hgnc_id "HGNC:37249"  ; level 2 ; orig_coord_info "chr19,52369966,52369977,+"  ; protein_id "ENSP00000343625.5"  ; tag basic ; transcript_id "ZNF528--ZNF880^ENST00000344085.9"  ; transcript_name "ZNF880-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF528--ZNF880	HAVANA	gene	1001	14939	.	+	.	FI_gene_label "ZNF528^ENSG00000167555.14"  ; ID "ZNF528--ZNF880^ZNF528^ENSG00000167555.14"  ; ccdsid "CCDS33091.1"  ; exon_id "ENSE00003647276.1"  ; exon_number 4 ; gene_id "ZNF528--ZNF880^ZNF528^ENSG00000167555.14"  ; gene_name ZNF528 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156494.9"  ; havana_transcript "OTTHUMT00000344336.2"  ; hgnc_id "HGNC:29384"  ; level 2 ; orig_coord_info "chr19,52402014,52402028,+"  ; protein_id "ENSP00000353652.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF528--ZNF880^ENST00000360465.8"  ; transcript_name "ZNF528-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF528--ZNF880	HAVANA	mRNA	1001	14939	.	+	.	FI_gene_label "ZNF528^ENSG00000167555.14"  ; ID "ZNF528--ZNF880^ENST00000360465.8"  ; Parent "ZNF528--ZNF880^ZNF528^ENSG00000167555.14"  ; ccdsid "CCDS33091.1"  ; exon_id "ENSE00003647276.1"  ; exon_number 4 ; gene_id "ZNF528--ZNF880^ZNF528^ENSG00000167555.14"  ; gene_name ZNF528 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156494.9"  ; havana_transcript "OTTHUMT00000344336.2"  ; hgnc_id "HGNC:29384"  ; level 2 ; orig_coord_info "chr19,52402014,52402028,+"  ; protein_id "ENSP00000353652.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF528--ZNF880^ENST00000360465.8"  ; transcript_name "ZNF528-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF737--AC010329.5	HAVANA	gene	1029	14652	.	+	.	FI_gene_label "ZNF737^ENSG00000237440.9"  ; ID "ZNF737--AC010329.5^ZNF737^ENSG00000237440.9"  ; ccdsid "CCDS54238.1"  ; exon_id "ENSE00002317806.3"  ; exon_number 1 ; gene_id "ZNF737--AC010329.5^ZNF737^ENSG00000237440.9"  ; gene_name ZNF737 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179732.5"  ; havana_transcript "OTTHUMT00000447844.4"  ; hgnc_id "HGNC:32468"  ; level 2 ; orig_coord_info "chr19,20565638,20565640,-"  ; protein_id "ENSP00000395733.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF737--AC010329.5^ENST00000427401.9"  ; transcript_name "ZNF737-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ZNF737--AC010329.5	HAVANA	mRNA	1029	14652	.	+	.	FI_gene_label "ZNF737^ENSG00000237440.9"  ; ID "ZNF737--AC010329.5^ENST00000427401.9"  ; Parent "ZNF737--AC010329.5^ZNF737^ENSG00000237440.9"  ; ccdsid "CCDS54238.1"  ; exon_id "ENSE00002317806.3"  ; exon_number 1 ; gene_id "ZNF737--AC010329.5^ZNF737^ENSG00000237440.9"  ; gene_name ZNF737 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179732.5"  ; havana_transcript "OTTHUMT00000447844.4"  ; hgnc_id "HGNC:32468"  ; level 2 ; orig_coord_info "chr19,20565638,20565640,-"  ; protein_id "ENSP00000395733.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF737--AC010329.5^ENST00000427401.9"  ; transcript_name "ZNF737-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
AP001347.1--ANKRD20A11P	HAVANA	gene	8798	22852	.	+	.	FI_gene_label "ANKRD20A11P^ENSG00000215559.8"  ; ID "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; exon_id "ENSE00002284794.1"  ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; gene_name ANKRD20A11P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074237.2"  ; havana_transcript "OTTHUMT00000157750.1"  ; hgnc_id "HGNC:42024"  ; level 2 ; orig_coord_info "chr21,13979702,13980437,-"  ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000344693.5"  ; transcript_name "ANKRD20A11P-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
AP001347.1--ANKRD20A11P	HAVANA	RNA	8798	22852	.	+	.	FI_gene_label "ANKRD20A11P^ENSG00000215559.8"  ; ID "AP001347.1--ANKRD20A11P^ENST00000344693.5"  ; Parent "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; exon_id "ENSE00002284794.1"  ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^ANKRD20A11P^ENSG00000215559.8"  ; gene_name ANKRD20A11P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000074237.2"  ; havana_transcript "OTTHUMT00000157750.1"  ; hgnc_id "HGNC:42024"  ; level 2 ; orig_coord_info "chr21,13979702,13980437,-"  ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000344693.5"  ; transcript_name "ANKRD20A11P-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
AP001347.1--ANKRD20A11P	HAVANA	gene	1003	5797	.	+	.	FI_gene_label "AP001347.1^ENSG00000224905.7"  ; ID "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7"  ; exon_id "ENSE00001608016.1"  ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7"  ; gene_name "AP001347.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000074260.3"  ; havana_transcript "OTTHUMT00000157812.1"  ; level 2 ; orig_coord_info "chr21,14027421,14027597,+"  ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000428809.5"  ; transcript_name "AP001347.1-202"  ; transcript_support_level 1 ; transcript_type lncRNA
AP001347.1--ANKRD20A11P	HAVANA	RNA	1003	5797	.	+	.	FI_gene_label "AP001347.1^ENSG00000224905.7"  ; ID "AP001347.1--ANKRD20A11P^ENST00000428809.5"  ; Parent "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7"  ; exon_id "ENSE00001608016.1"  ; exon_number 1 ; gene_id "AP001347.1--ANKRD20A11P^AP001347.1^ENSG00000224905.7"  ; gene_name "AP001347.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000074260.3"  ; havana_transcript "OTTHUMT00000157812.1"  ; level 2 ; orig_coord_info "chr21,14027421,14027597,+"  ; tag basic ; transcript_id "AP001347.1--ANKRD20A11P^ENST00000428809.5"  ; transcript_name "AP001347.1-202"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
BMS1P7--PTPN20	HAVANA	gene	1001	7575	.	+	.	FI_gene_label "BMS1P7^ENSG00000270025.2"  ; ID "BMS1P7--PTPN20^BMS1P7^ENSG00000270025.2"  ; exon_id "ENSE00001675840.2"  ; exon_number 1 ; gene_id "BMS1P7--PTPN20^BMS1P7^ENSG00000270025.2"  ; gene_name BMS1P7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018163.3"  ; havana_transcript "OTTHUMT00000047911.2"  ; hgnc_id "HGNC:23655"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr10,48059827,48060016,-"  ; tag basic ; transcript_id "BMS1P7--PTPN20^ENST00000602440.2"  ; transcript_name "BMS1P7-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
BMS1P7--PTPN20	HAVANA	RNA	1001	7575	.	+	.	FI_gene_label "BMS1P7^ENSG00000270025.2"  ; ID "BMS1P7--PTPN20^ENST00000602440.2"  ; Parent "BMS1P7--PTPN20^BMS1P7^ENSG00000270025.2"  ; exon_id "ENSE00001675840.2"  ; exon_number 1 ; gene_id "BMS1P7--PTPN20^BMS1P7^ENSG00000270025.2"  ; gene_name BMS1P7 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000018163.3"  ; havana_transcript "OTTHUMT00000047911.2"  ; hgnc_id "HGNC:23655"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr10,48059827,48060016,-"  ; tag basic ; transcript_id "BMS1P7--PTPN20^ENST00000602440.2"  ; transcript_name "BMS1P7-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
GOLGA6L10--GOLGA2P6	HAVANA	gene	12782	20364	.	+	.	FI_gene_label "GOLGA2P6^ENSG00000241621.1"  ; ID "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1"  ; exon_id "ENSE00001603136.1"  ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1"  ; gene_name GOLGA2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000017890.1"  ; havana_transcript "OTTHUMT00000047421.1"  ; hgnc_id "HGNC:44948"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chr10,30374327,30374386,-"  ; tag pseudo_consens basic ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000340929.4"  ; transcript_name "GOLGA2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
GOLGA6L10--GOLGA2P6	HAVANA	RNA	12782	20364	.	+	.	FI_gene_label "GOLGA2P6^ENSG00000241621.1"  ; ID "GOLGA6L10--GOLGA2P6^ENST00000340929.4"  ; Parent "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1"  ; exon_id "ENSE00001603136.1"  ; exon_number 1 ; gene_id "GOLGA6L10--GOLGA2P6^GOLGA2P6^ENSG00000241621.1"  ; gene_name GOLGA2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000017890.1"  ; havana_transcript "OTTHUMT00000047421.1"  ; hgnc_id "HGNC:44948"  ; level 1 ; ont "PGO:0000005"  ; orig_coord_info "chr10,30374327,30374386,-"  ; tag pseudo_consens basic ; transcript_id "GOLGA6L10--GOLGA2P6^ENST00000340929.4"  ; transcript_name "GOLGA2P6-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
ZNF737--AC010329.5	HAVANA	gene	18979	24152	.	+	.	FI_gene_label "AC010329.5^ENSG00000280171.1"  ; ID "ZNF737--AC010329.5^AC010329.5^ENSG00000280171.1"  ; exon_id "ENSE00003758367.1"  ; exon_number 1 ; gene_id "ZNF737--AC010329.5^AC010329.5^ENSG00000280171.1"  ; gene_name "AC010329.5"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000189491.1"  ; havana_transcript "OTTHUMT00000479791.1"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr19,20674923,20675043,+"  ; tag basic ; transcript_id "ZNF737--AC010329.5^ENST00000623497.1"  ; transcript_name "AC010329.5-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
ZNF737--AC010329.5	HAVANA	RNA	18979	24152	.	+	.	FI_gene_label "AC010329.5^ENSG00000280171.1"  ; ID "ZNF737--AC010329.5^ENST00000623497.1"  ; Parent "ZNF737--AC010329.5^AC010329.5^ENSG00000280171.1"  ; exon_id "ENSE00003758367.1"  ; exon_number 1 ; gene_id "ZNF737--AC010329.5^AC010329.5^ENSG00000280171.1"  ; gene_name "AC010329.5"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000189491.1"  ; havana_transcript "OTTHUMT00000479791.1"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr19,20674923,20675043,+"  ; tag basic ; transcript_id "ZNF737--AC010329.5^ENST00000623497.1"  ; transcript_name "AC010329.5-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
250 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 ------------------------------
654 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 20 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