.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_bua-T1-TRNA-1_B23MHV2LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/2aab80a40f7709497dbee04ef6102c/.command.log
Size: 47.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_bua-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/4470cf5f35d6936be3232d643d81dc/fi_workdir/659_bua-T1-TRNA-1_B23MHV2LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/2aab80a40f7709497dbee04ef6102c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/2aab80a40f7709497dbee04ef6102c/.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: 4237
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 4237
=> 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:4237
  => 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: 
AC013268.1--MALL	HAVANA	gene	16390	22812	.	+	.	FI_gene_label "MALL^ENSG00000144063.4"  ; ID "AC013268.1--MALL^MALL^ENSG00000144063.4"  ; ccdsid "CCDS2085.1"  ; exon_id "ENSE00001129113.3"  ; exon_number 1 ; gene_id "AC013268.1--MALL^MALL^ENSG00000144063.4"  ; gene_name MALL ; gene_type protein_coding ; havana_gene "OTTHUMG00000131196.3"  ; havana_transcript "OTTHUMT00000253921.2"  ; hgnc_id "HGNC:6818"  ; level 2 ; orig_coord_info "chr2,110115688,110115792,-"  ; protein_id "ENSP00000272462.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC013268.1--MALL^ENST00000272462.3"  ; transcript_name "MALL-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC013268.1--MALL	HAVANA	mRNA	16390	22812	.	+	.	FI_gene_label "MALL^ENSG00000144063.4"  ; ID "AC013268.1--MALL^ENST00000272462.3"  ; Parent "AC013268.1--MALL^MALL^ENSG00000144063.4"  ; ccdsid "CCDS2085.1"  ; exon_id "ENSE00001129113.3"  ; exon_number 1 ; gene_id "AC013268.1--MALL^MALL^ENSG00000144063.4"  ; gene_name MALL ; gene_type protein_coding ; havana_gene "OTTHUMG00000131196.3"  ; havana_transcript "OTTHUMT00000253921.2"  ; hgnc_id "HGNC:6818"  ; level 2 ; orig_coord_info "chr2,110115688,110115792,-"  ; protein_id "ENSP00000272462.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC013268.1--MALL^ENST00000272462.3"  ; transcript_name "MALL-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC092807.3--DDAH1	HAVANA	gene	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1	HAVANA	mRNA	13647	23704	.	+	.	FI_gene_label "DDAH1^ENSG00000153904.21"  ; ID "AC092807.3--DDAH1^ENST00000284031.13"  ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; ccdsid "CCDS705.1"  ; exon_id "ENSE00001013010.7"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21"  ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3"  ; havana_transcript "OTTHUMT00000029189.3"  ; hgnc_id "HGNC:2715"  ; level 2 ; orig_coord_info "chr1,85464743,85465045,-"  ; protein_id "ENSP00000284031.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13"  ; transcript_name "DDAH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ADAMTS2--RARS1	HAVANA	gene	32835	48962	.	+	.	FI_gene_label "RARS1^ENSG00000113643.9"  ; ID "ADAMTS2--RARS1^RARS1^ENSG00000113643.9"  ; ccdsid "CCDS4367.1"  ; exon_id "ENSE00001148323.6"  ; exon_number 1 ; gene_id "ADAMTS2--RARS1^RARS1^ENSG00000113643.9"  ; gene_name RARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130411.4"  ; havana_transcript "OTTHUMT00000252794.3"  ; hgnc_id "HGNC:9870"  ; level 2 ; orig_coord_info "chr5,168486499,168486543,+"  ; protein_id "ENSP00000231572.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAMTS2--RARS1^ENST00000231572.8"  ; transcript_name "RARS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ADAMTS2--RARS1	HAVANA	mRNA	32835	48962	.	+	.	FI_gene_label "RARS1^ENSG00000113643.9"  ; ID "ADAMTS2--RARS1^ENST00000231572.8"  ; Parent "ADAMTS2--RARS1^RARS1^ENSG00000113643.9"  ; ccdsid "CCDS4367.1"  ; exon_id "ENSE00001148323.6"  ; exon_number 1 ; gene_id "ADAMTS2--RARS1^RARS1^ENSG00000113643.9"  ; gene_name RARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130411.4"  ; havana_transcript "OTTHUMT00000252794.3"  ; hgnc_id "HGNC:9870"  ; level 2 ; orig_coord_info "chr5,168486499,168486543,+"  ; protein_id "ENSP00000231572.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAMTS2--RARS1^ENST00000231572.8"  ; transcript_name "RARS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ADAMTS2--RARS1	HAVANA	gene	1001	29814	.	+	.	FI_gene_label "ADAMTS2^ENSG00000087116.16"  ; ID "ADAMTS2--RARS1^ADAMTS2^ENSG00000087116.16"  ; ccdsid "CCDS4444.1"  ; exon_id "ENSE00003847948.1"  ; exon_number 1 ; gene_id "ADAMTS2--RARS1^ADAMTS2^ENSG00000087116.16"  ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7"  ; havana_transcript "OTTHUMT00000253507.2"  ; hgnc_id "HGNC:218"  ; level 2 ; orig_coord_info "chr5,179345190,179345328,-"  ; protein_id "ENSP00000251582.7"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAMTS2--RARS1^ENST00000251582.12"  ; transcript_name "ADAMTS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ADAMTS2--RARS1	HAVANA	mRNA	1001	29814	.	+	.	FI_gene_label "ADAMTS2^ENSG00000087116.16"  ; ID "ADAMTS2--RARS1^ENST00000251582.12"  ; Parent "ADAMTS2--RARS1^ADAMTS2^ENSG00000087116.16"  ; ccdsid "CCDS4444.1"  ; exon_id "ENSE00003847948.1"  ; exon_number 1 ; gene_id "ADAMTS2--RARS1^ADAMTS2^ENSG00000087116.16"  ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7"  ; havana_transcript "OTTHUMT00000253507.2"  ; hgnc_id "HGNC:218"  ; level 2 ; orig_coord_info "chr5,179345190,179345328,-"  ; protein_id "ENSP00000251582.7"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAMTS2--RARS1^ENST00000251582.12"  ; transcript_name "ADAMTS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AVL9--RNU6-1085P	HAVANA	gene	1064	30635	.	+	.	FI_gene_label "AVL9^ENSG00000105778.19"  ; ID "AVL9--RNU6-1085P^AVL9^ENSG00000105778.19"  ; ccdsid "CCDS34613.1"  ; exon_id "ENSE00001944463.1"  ; exon_number 1 ; gene_id "AVL9--RNU6-1085P^AVL9^ENSG00000105778.19"  ; gene_name AVL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152929.2"  ; havana_transcript "OTTHUMT00000328643.2"  ; hgnc_id "HGNC:28994"  ; level 2 ; orig_coord_info "chr7,32495710,32495802,+"  ; protein_id "ENSP00000315568.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "AVL9--RNU6-1085P^ENST00000318709.9"  ; transcript_name "AVL9-201"  ; transcript_support_level 2 ; transcript_type protein_coding
AVL9--RNU6-1085P	HAVANA	mRNA	1064	30635	.	+	.	FI_gene_label "AVL9^ENSG00000105778.19"  ; ID "AVL9--RNU6-1085P^ENST00000318709.9"  ; Parent "AVL9--RNU6-1085P^AVL9^ENSG00000105778.19"  ; ccdsid "CCDS34613.1"  ; exon_id "ENSE00001944463.1"  ; exon_number 1 ; gene_id "AVL9--RNU6-1085P^AVL9^ENSG00000105778.19"  ; gene_name AVL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152929.2"  ; havana_transcript "OTTHUMT00000328643.2"  ; hgnc_id "HGNC:28994"  ; level 2 ; orig_coord_info "chr7,32495710,32495802,+"  ; protein_id "ENSP00000315568.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "AVL9--RNU6-1085P^ENST00000318709.9"  ; transcript_name "AVL9-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
AVL9--SEPTIN7	HAVANA	gene	1064	30635	.	+	.	FI_gene_label "AVL9^ENSG00000105778.19"  ; ID "AVL9--SEPTIN7^AVL9^ENSG00000105778.19"  ; ccdsid "CCDS34613.1"  ; exon_id "ENSE00001944463.1"  ; exon_number 1 ; gene_id "AVL9--SEPTIN7^AVL9^ENSG00000105778.19"  ; gene_name AVL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152929.2"  ; havana_transcript "OTTHUMT00000328643.2"  ; hgnc_id "HGNC:28994"  ; level 2 ; orig_coord_info "chr7,32495710,32495802,+"  ; protein_id "ENSP00000315568.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "AVL9--SEPTIN7^ENST00000318709.9"  ; transcript_name "AVL9-201"  ; transcript_support_level 2 ; transcript_type protein_coding
AVL9--SEPTIN7	HAVANA	mRNA	1064	30635	.	+	.	FI_gene_label "AVL9^ENSG00000105778.19"  ; ID "AVL9--SEPTIN7^ENST00000318709.9"  ; Parent "AVL9--SEPTIN7^AVL9^ENSG00000105778.19"  ; ccdsid "CCDS34613.1"  ; exon_id "ENSE00001944463.1"  ; exon_number 1 ; gene_id "AVL9--SEPTIN7^AVL9^ENSG00000105778.19"  ; gene_name AVL9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152929.2"  ; havana_transcript "OTTHUMT00000328643.2"  ; hgnc_id "HGNC:28994"  ; level 2 ; orig_coord_info "chr7,32495710,32495802,+"  ; protein_id "ENSP00000315568.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "AVL9--SEPTIN7^ENST00000318709.9"  ; transcript_name "AVL9-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
AVL9--SEPTIN7	ENSEMBL	gene	33690	63614	.	+	.	FI_gene_label "SEPTIN7^ENSG00000122545.20"  ; ID "AVL9--SEPTIN7^SEPTIN7^ENSG00000122545.20"  ; exon_id "ENSE00003749079.1"  ; exon_number 1 ; gene_id "AVL9--SEPTIN7^SEPTIN7^ENSG00000122545.20"  ; gene_name SEPTIN7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155063.6"  ; hgnc_id "HGNC:1717"  ; level 3 ; orig_coord_info "chr7,35801210,35801270,+"  ; protein_id "ENSP00000344868.7"  ; tag basic appris_alternative_1 ; transcript_id "AVL9--SEPTIN7^ENST00000350320.10"  ; transcript_name "SEPTIN7-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AVL9--SEPTIN7	ENSEMBL	mRNA	33690	63614	.	+	.	FI_gene_label "SEPTIN7^ENSG00000122545.20"  ; ID "AVL9--SEPTIN7^ENST00000350320.10"  ; Parent "AVL9--SEPTIN7^SEPTIN7^ENSG00000122545.20"  ; exon_id "ENSE00003749079.1"  ; exon_number 1 ; gene_id "AVL9--SEPTIN7^SEPTIN7^ENSG00000122545.20"  ; gene_name SEPTIN7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155063.6"  ; hgnc_id "HGNC:1717"  ; level 3 ; orig_coord_info "chr7,35801210,35801270,+"  ; protein_id "ENSP00000344868.7"  ; tag basic appris_alternative_1 ; transcript_id "AVL9--SEPTIN7^ENST00000350320.10"  ; transcript_name "SEPTIN7-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
CRACD--THEGL	HAVANA	gene	2941	23980	.	+	.	FI_gene_label "CRACD^ENSG00000109265.14"  ; ID "CRACD--THEGL^CRACD^ENSG00000109265.14"  ; ccdsid "CCDS43230.1"  ; exon_id "ENSE00003562187.1"  ; exon_number 4 ; gene_id "CRACD--THEGL^CRACD^ENSG00000109265.14"  ; gene_name CRACD ; gene_type protein_coding ; havana_gene "OTTHUMG00000160749.7"  ; havana_transcript "OTTHUMT00000362097.3"  ; hgnc_id "HGNC:29219"  ; level 2 ; orig_coord_info "chr4,56298230,56298349,+"  ; protein_id "ENSP00000264229.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRACD--THEGL^ENST00000264229.11"  ; transcript_name "CRACD-201"  ; transcript_support_level 2 ; transcript_type protein_coding
CRACD--THEGL	HAVANA	mRNA	2941	23980	.	+	.	FI_gene_label "CRACD^ENSG00000109265.14"  ; ID "CRACD--THEGL^ENST00000264229.11"  ; Parent "CRACD--THEGL^CRACD^ENSG00000109265.14"  ; ccdsid "CCDS43230.1"  ; exon_id "ENSE00003562187.1"  ; exon_number 4 ; gene_id "CRACD--THEGL^CRACD^ENSG00000109265.14"  ; gene_name CRACD ; gene_type protein_coding ; havana_gene "OTTHUMG00000160749.7"  ; havana_transcript "OTTHUMT00000362097.3"  ; hgnc_id "HGNC:29219"  ; level 2 ; orig_coord_info "chr4,56298230,56298349,+"  ; protein_id "ENSP00000264229.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRACD--THEGL^ENST00000264229.11"  ; transcript_name "CRACD-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CRACD--THEGL	HAVANA	gene	26981	37776	.	+	.	FI_gene_label "THEGL^ENSG00000249693.3"  ; ID "CRACD--THEGL^THEGL^ENSG00000249693.3"  ; ccdsid "CCDS58899.1"  ; exon_id "ENSE00002081975.2"  ; exon_number 1 ; gene_id "CRACD--THEGL^THEGL^ENSG00000249693.3"  ; gene_name THEGL ; gene_type protein_coding ; havana_gene "OTTHUMG00000160770.3"  ; havana_transcript "OTTHUMT00000362201.3"  ; hgnc_id "HGNC:43771"  ; level 1 ; orig_coord_info "chr4,56530677,56531169,+"  ; protein_id "ENSP00000456850.1"  ; tag not_organism_supported basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "CRACD--THEGL^ENST00000512175.3"  ; transcript_name "THEGL-202"  ; transcript_support_level 5 ; transcript_type protein_coding
CRACD--THEGL	HAVANA	mRNA	26981	37776	.	+	.	FI_gene_label "THEGL^ENSG00000249693.3"  ; ID "CRACD--THEGL^ENST00000512175.3"  ; Parent "CRACD--THEGL^THEGL^ENSG00000249693.3"  ; ccdsid "CCDS58899.1"  ; exon_id "ENSE00002081975.2"  ; exon_number 1 ; gene_id "CRACD--THEGL^THEGL^ENSG00000249693.3"  ; gene_name THEGL ; gene_type protein_coding ; havana_gene "OTTHUMG00000160770.3"  ; havana_transcript "OTTHUMT00000362201.3"  ; hgnc_id "HGNC:43771"  ; level 1 ; orig_coord_info "chr4,56530677,56531169,+"  ; protein_id "ENSP00000456850.1"  ; tag not_organism_supported basic MANE_Select appris_principal_1 exp_conf CCDS ; transcript_id "CRACD--THEGL^ENST00000512175.3"  ; transcript_name "THEGL-202"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ERBIN--ARHGAP26	HAVANA	gene	38475	91117	.	+	.	FI_gene_label "ARHGAP26^ENSG00000145819.18"  ; ID "ERBIN--ARHGAP26^ARHGAP26^ENSG00000145819.18"  ; ccdsid "CCDS4277.1"  ; exon_id "ENSE00001921830.2"  ; exon_number 1 ; gene_id "ERBIN--ARHGAP26^ARHGAP26^ENSG00000145819.18"  ; gene_name ARHGAP26 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059705.15"  ; havana_transcript "OTTHUMT00000496686.1"  ; hgnc_id "HGNC:17073"  ; level 2 ; orig_coord_info "chr5,142770762,142770915,+"  ; protein_id "ENSP00000274498.4"  ; tag CAGE_supported_TSS basic appris_alternative_1 CCDS ; transcript_id "ERBIN--ARHGAP26^ENST00000274498.9"  ; transcript_name "ARHGAP26-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ERBIN--ARHGAP26	HAVANA	mRNA	38475	91117	.	+	.	FI_gene_label "ARHGAP26^ENSG00000145819.18"  ; ID "ERBIN--ARHGAP26^ENST00000274498.9"  ; Parent "ERBIN--ARHGAP26^ARHGAP26^ENSG00000145819.18"  ; ccdsid "CCDS4277.1"  ; exon_id "ENSE00001921830.2"  ; exon_number 1 ; gene_id "ERBIN--ARHGAP26^ARHGAP26^ENSG00000145819.18"  ; gene_name ARHGAP26 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059705.15"  ; havana_transcript "OTTHUMT00000496686.1"  ; hgnc_id "HGNC:17073"  ; level 2 ; orig_coord_info "chr5,142770762,142770915,+"  ; protein_id "ENSP00000274498.4"  ; tag CAGE_supported_TSS basic appris_alternative_1 CCDS ; transcript_id "ERBIN--ARHGAP26^ENST00000274498.9"  ; transcript_name "ARHGAP26-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ERBIN--ARHGAP26	HAVANA	gene	1020	35474	.	+	.	FI_gene_label "ERBIN^ENSG00000112851.15"  ; ID "ERBIN--ARHGAP26^ERBIN^ENSG00000112851.15"  ; ccdsid "CCDS58953.1"  ; exon_id "ENSE00000912221.1"  ; exon_number 3 ; gene_id "ERBIN--ARHGAP26^ERBIN^ENSG00000112851.15"  ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3"  ; havana_transcript "OTTHUMT00000215070.1"  ; hgnc_id "HGNC:15842"  ; level 2 ; orig_coord_info "chr5,65992719,65992907,+"  ; protein_id "ENSP00000284037.4"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--ARHGAP26^ENST00000284037.10"  ; transcript_name "ERBIN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ERBIN--ARHGAP26	HAVANA	mRNA	1020	35474	.	+	.	FI_gene_label "ERBIN^ENSG00000112851.15"  ; ID "ERBIN--ARHGAP26^ENST00000284037.10"  ; Parent "ERBIN--ARHGAP26^ERBIN^ENSG00000112851.15"  ; ccdsid "CCDS58953.1"  ; exon_id "ENSE00000912221.1"  ; exon_number 3 ; gene_id "ERBIN--ARHGAP26^ERBIN^ENSG00000112851.15"  ; gene_name ERBIN ; gene_type protein_coding ; havana_gene "OTTHUMG00000097808.3"  ; havana_transcript "OTTHUMT00000215070.1"  ; hgnc_id "HGNC:15842"  ; level 2 ; orig_coord_info "chr5,65992719,65992907,+"  ; protein_id "ENSP00000284037.4"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "ERBIN--ARHGAP26^ENST00000284037.10"  ; transcript_name "ERBIN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NTRK1--NUP210L	ENSEMBL	gene	22273	61957	.	+	.	FI_gene_label "NUP210L^ENSG00000143552.9"  ; ID "NTRK1--NUP210L^NUP210L^ENSG00000143552.9"  ; ccdsid "CCDS53370.1"  ; exon_id "ENSE00002224107.1"  ; exon_number 1 ; gene_id "NTRK1--NUP210L^NUP210L^ENSG00000143552.9"  ; gene_name NUP210L ; gene_type protein_coding ; havana_gene "OTTHUMG00000035852.3"  ; hgnc_id "HGNC:29915"  ; level 3 ; orig_coord_info "chr1,154154842,154155044,-"  ; protein_id "ENSP00000271854.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NTRK1--NUP210L^ENST00000271854.3"  ; transcript_name "NUP210L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
NTRK1--NUP210L	ENSEMBL	mRNA	22273	61957	.	+	.	FI_gene_label "NUP210L^ENSG00000143552.9"  ; ID "NTRK1--NUP210L^ENST00000271854.3"  ; Parent "NTRK1--NUP210L^NUP210L^ENSG00000143552.9"  ; ccdsid "CCDS53370.1"  ; exon_id "ENSE00002224107.1"  ; exon_number 1 ; gene_id "NTRK1--NUP210L^NUP210L^ENSG00000143552.9"  ; gene_name NUP210L ; gene_type protein_coding ; havana_gene "OTTHUMG00000035852.3"  ; hgnc_id "HGNC:29915"  ; level 3 ; orig_coord_info "chr1,154154842,154155044,-"  ; protein_id "ENSP00000271854.3"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NTRK1--NUP210L^ENST00000271854.3"  ; transcript_name "NUP210L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
NTRK1--NUP210L	HAVANA	gene	5049	19133	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "NTRK1--NUP210L^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "NTRK1--NUP210L^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "NTRK1--NUP210L^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
NTRK1--NUP210L	HAVANA	mRNA	5049	19133	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "NTRK1--NUP210L^ENST00000358660.3"  ; Parent "NTRK1--NUP210L^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "NTRK1--NUP210L^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "NTRK1--NUP210L^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
RARS1--WWC1	HAVANA	gene	1021	17148	.	+	.	FI_gene_label "RARS1^ENSG00000113643.9"  ; ID "RARS1--WWC1^RARS1^ENSG00000113643.9"  ; ccdsid "CCDS4367.1"  ; exon_id "ENSE00001148323.6"  ; exon_number 1 ; gene_id "RARS1--WWC1^RARS1^ENSG00000113643.9"  ; gene_name RARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130411.4"  ; havana_transcript "OTTHUMT00000252794.3"  ; hgnc_id "HGNC:9870"  ; level 2 ; orig_coord_info "chr5,168486499,168486543,+"  ; protein_id "ENSP00000231572.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RARS1--WWC1^ENST00000231572.8"  ; transcript_name "RARS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RARS1--WWC1	HAVANA	mRNA	1021	17148	.	+	.	FI_gene_label "RARS1^ENSG00000113643.9"  ; ID "RARS1--WWC1^ENST00000231572.8"  ; Parent "RARS1--WWC1^RARS1^ENSG00000113643.9"  ; ccdsid "CCDS4367.1"  ; exon_id "ENSE00001148323.6"  ; exon_number 1 ; gene_id "RARS1--WWC1^RARS1^ENSG00000113643.9"  ; gene_name RARS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130411.4"  ; havana_transcript "OTTHUMT00000252794.3"  ; hgnc_id "HGNC:9870"  ; level 2 ; orig_coord_info "chr5,168486499,168486543,+"  ; protein_id "ENSP00000231572.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RARS1--WWC1^ENST00000231572.8"  ; transcript_name "RARS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RARS1--WWC1	HAVANA	gene	20149	54097	.	+	.	FI_gene_label "WWC1^ENSG00000113645.15"  ; ID "RARS1--WWC1^WWC1^ENSG00000113645.15"  ; ccdsid "CCDS4366.1"  ; exon_id "ENSE00001869765.3"  ; exon_number 1 ; gene_id "RARS1--WWC1^WWC1^ENSG00000113645.15"  ; gene_name WWC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130408.4"  ; havana_transcript "OTTHUMT00000252791.2"  ; hgnc_id "HGNC:29435"  ; level 2 ; orig_coord_info "chr5,168292153,168292271,+"  ; protein_id "ENSP00000265293.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RARS1--WWC1^ENST00000265293.9"  ; transcript_name "WWC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RARS1--WWC1	HAVANA	mRNA	20149	54097	.	+	.	FI_gene_label "WWC1^ENSG00000113645.15"  ; ID "RARS1--WWC1^ENST00000265293.9"  ; Parent "RARS1--WWC1^WWC1^ENSG00000113645.15"  ; ccdsid "CCDS4366.1"  ; exon_id "ENSE00001869765.3"  ; exon_number 1 ; gene_id "RARS1--WWC1^WWC1^ENSG00000113645.15"  ; gene_name WWC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130408.4"  ; havana_transcript "OTTHUMT00000252791.2"  ; hgnc_id "HGNC:29435"  ; level 2 ; orig_coord_info "chr5,168292153,168292271,+"  ; protein_id "ENSP00000265293.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RARS1--WWC1^ENST00000265293.9"  ; transcript_name "WWC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TPM3--NTRK1	HAVANA	gene	2360	24514	.	+	.	FI_gene_label "TPM3^ENSG00000143549.21"  ; ID "TPM3--NTRK1^TPM3^ENSG00000143549.21"  ; exon_id "ENSE00002024480.1"  ; exon_number 1 ; gene_id "TPM3--NTRK1^TPM3^ENSG00000143549.21"  ; gene_name TPM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035853.12"  ; havana_transcript "OTTHUMT00000360295.1"  ; hgnc_id "HGNC:12012"  ; level 2 ; orig_coord_info "chr1,154191902,154192018,-"  ; protein_id "ENSP00000271850.7"  ; tag not_organism_supported basic ; transcript_id "TPM3--NTRK1^ENST00000271850.11"  ; transcript_name "TPM3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TPM3--NTRK1	HAVANA	mRNA	2360	24514	.	+	.	FI_gene_label "TPM3^ENSG00000143549.21"  ; ID "TPM3--NTRK1^ENST00000271850.11"  ; Parent "TPM3--NTRK1^TPM3^ENSG00000143549.21"  ; exon_id "ENSE00002024480.1"  ; exon_number 1 ; gene_id "TPM3--NTRK1^TPM3^ENSG00000143549.21"  ; gene_name TPM3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000035853.12"  ; havana_transcript "OTTHUMT00000360295.1"  ; hgnc_id "HGNC:12012"  ; level 2 ; orig_coord_info "chr1,154191902,154192018,-"  ; protein_id "ENSP00000271850.7"  ; tag not_organism_supported basic ; transcript_id "TPM3--NTRK1^ENST00000271850.11"  ; transcript_name "TPM3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
TPM3--NTRK1	HAVANA	gene	33577	47661	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "TPM3--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "TPM3--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "TPM3--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TPM3--NTRK1	HAVANA	mRNA	33577	47661	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "TPM3--NTRK1^ENST00000358660.3"  ; Parent "TPM3--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "TPM3--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "TPM3--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
TPM4--NTRK1	HAVANA	gene	3909	21814	.	+	.	FI_gene_label "TPM4^ENSG00000167460.17"  ; ID "TPM4--NTRK1^TPM4^ENSG00000167460.17"  ; exon_id "ENSE00003879509.1"  ; exon_number 1 ; gene_id "TPM4--NTRK1^TPM4^ENSG00000167460.17"  ; gene_name TPM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182134.12"  ; havana_transcript "OTTHUMT00000505346.1"  ; hgnc_id "HGNC:12013"  ; level 2 ; orig_coord_info "chr19,16076645,16076697,+"  ; protein_id "ENSP00000300933.4"  ; tag mRNA_start_NF cds_start_NF RNA_Seq_supported_only ; transcript_id "TPM4--NTRK1^ENST00000300933.9"  ; transcript_name "TPM4-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
TPM4--NTRK1	HAVANA	mRNA	3909	21814	.	+	.	FI_gene_label "TPM4^ENSG00000167460.17"  ; ID "TPM4--NTRK1^ENST00000300933.9"  ; Parent "TPM4--NTRK1^TPM4^ENSG00000167460.17"  ; exon_id "ENSE00003879509.1"  ; exon_number 1 ; gene_id "TPM4--NTRK1^TPM4^ENSG00000167460.17"  ; gene_name TPM4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182134.12"  ; havana_transcript "OTTHUMT00000505346.1"  ; hgnc_id "HGNC:12013"  ; level 2 ; orig_coord_info "chr19,16076645,16076697,+"  ; protein_id "ENSP00000300933.4"  ; tag mRNA_start_NF cds_start_NF RNA_Seq_supported_only ; transcript_id "TPM4--NTRK1^ENST00000300933.9"  ; transcript_name "TPM4-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
TPM4--NTRK1	HAVANA	gene	28913	42997	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "TPM4--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "TPM4--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "TPM4--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
TPM4--NTRK1	HAVANA	mRNA	28913	42997	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "TPM4--NTRK1^ENST00000358660.3"  ; Parent "TPM4--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "TPM4--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "TPM4--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; 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: 
WWC1--ADAMTS2	HAVANA	gene	37950	66763	.	+	.	FI_gene_label "ADAMTS2^ENSG00000087116.16"  ; ID "WWC1--ADAMTS2^ADAMTS2^ENSG00000087116.16"  ; ccdsid "CCDS4444.1"  ; exon_id "ENSE00003847948.1"  ; exon_number 1 ; gene_id "WWC1--ADAMTS2^ADAMTS2^ENSG00000087116.16"  ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7"  ; havana_transcript "OTTHUMT00000253507.2"  ; hgnc_id "HGNC:218"  ; level 2 ; orig_coord_info "chr5,179345190,179345328,-"  ; protein_id "ENSP00000251582.7"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WWC1--ADAMTS2^ENST00000251582.12"  ; transcript_name "ADAMTS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
WWC1--ADAMTS2	HAVANA	mRNA	37950	66763	.	+	.	FI_gene_label "ADAMTS2^ENSG00000087116.16"  ; ID "WWC1--ADAMTS2^ENST00000251582.12"  ; Parent "WWC1--ADAMTS2^ADAMTS2^ENSG00000087116.16"  ; ccdsid "CCDS4444.1"  ; exon_id "ENSE00003847948.1"  ; exon_number 1 ; gene_id "WWC1--ADAMTS2^ADAMTS2^ENSG00000087116.16"  ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7"  ; havana_transcript "OTTHUMT00000253507.2"  ; hgnc_id "HGNC:218"  ; level 2 ; orig_coord_info "chr5,179345190,179345328,-"  ; protein_id "ENSP00000251582.7"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WWC1--ADAMTS2^ENST00000251582.12"  ; transcript_name "ADAMTS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
WWC1--ADAMTS2	HAVANA	gene	1001	34949	.	+	.	FI_gene_label "WWC1^ENSG00000113645.15"  ; ID "WWC1--ADAMTS2^WWC1^ENSG00000113645.15"  ; ccdsid "CCDS4366.1"  ; exon_id "ENSE00001869765.3"  ; exon_number 1 ; gene_id "WWC1--ADAMTS2^WWC1^ENSG00000113645.15"  ; gene_name WWC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130408.4"  ; havana_transcript "OTTHUMT00000252791.2"  ; hgnc_id "HGNC:29435"  ; level 2 ; orig_coord_info "chr5,168292153,168292271,+"  ; protein_id "ENSP00000265293.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WWC1--ADAMTS2^ENST00000265293.9"  ; transcript_name "WWC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
WWC1--ADAMTS2	HAVANA	mRNA	1001	34949	.	+	.	FI_gene_label "WWC1^ENSG00000113645.15"  ; ID "WWC1--ADAMTS2^ENST00000265293.9"  ; Parent "WWC1--ADAMTS2^WWC1^ENSG00000113645.15"  ; ccdsid "CCDS4366.1"  ; exon_id "ENSE00001869765.3"  ; exon_number 1 ; gene_id "WWC1--ADAMTS2^WWC1^ENSG00000113645.15"  ; gene_name WWC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130408.4"  ; havana_transcript "OTTHUMT00000252791.2"  ; hgnc_id "HGNC:29435"  ; level 2 ; orig_coord_info "chr5,168292153,168292271,+"  ; protein_id "ENSP00000265293.4"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "WWC1--ADAMTS2^ENST00000265293.9"  ; transcript_name "WWC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC013268.1--MALL	HAVANA	gene	3129	10448	.	+	.	FI_gene_label "AC013268.1^ENSG00000186148.13"  ; ID "AC013268.1--MALL^AC013268.1^ENSG00000186148.13"  ; exon_id "ENSE00002526923.1"  ; exon_number 1 ; gene_id "AC013268.1--MALL^AC013268.1^ENSG00000186148.13"  ; gene_name "AC013268.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191773.2"  ; havana_transcript "OTTHUMT00000330194.1"  ; level 2 ; orig_coord_info "chr2,109936342,109938072,+"  ; transcript_id "AC013268.1--MALL^ENST00000417926.5"  ; transcript_name "AC013268.1-202"  ; transcript_support_level 2 ; transcript_type processed_transcript
AC013268.1--MALL	HAVANA	RNA	3129	10448	.	+	.	FI_gene_label "AC013268.1^ENSG00000186148.13"  ; ID "AC013268.1--MALL^ENST00000417926.5"  ; Parent "AC013268.1--MALL^AC013268.1^ENSG00000186148.13"  ; exon_id "ENSE00002526923.1"  ; exon_number 1 ; gene_id "AC013268.1--MALL^AC013268.1^ENSG00000186148.13"  ; gene_name "AC013268.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191773.2"  ; havana_transcript "OTTHUMT00000330194.1"  ; level 2 ; orig_coord_info "chr2,109936342,109938072,+"  ; transcript_id "AC013268.1--MALL^ENST00000417926.5"  ; transcript_name "AC013268.1-202"  ; transcript_support_level 2 ; transcript_type processed_transcript
L1 and L2 created: 
AC092807.3--DDAH1	HAVANA	gene	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1	HAVANA	RNA	1101	8302	.	+	.	FI_gene_label "AC092807.3^ENSG00000282057.1"  ; ID "AC092807.3--DDAH1^ENST00000467530.5"  ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; exon_id "ENSE00001891111.1"  ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1"  ; gene_name "AC092807.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6"  ; havana_transcript "OTTHUMT00000029193.2"  ; level 2 ; orig_coord_info "chr1,85577984,85578150,-"  ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5"  ; transcript_name "AC092807.3-203"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
AVL9--RNU6-1085P	ENSEMBL	gene	33636	33742	.	+	.	FI_gene_label "RNU6-1085P^ENSG00000200446.1"  ; ID "AVL9--RNU6-1085P^RNU6-1085P^ENSG00000200446.1"  ; exon_id "ENSE00001807627.1"  ; exon_number 1 ; gene_id "AVL9--RNU6-1085P^RNU6-1085P^ENSG00000200446.1"  ; gene_name "RNU6-1085P"  ; gene_type snRNA ; hgnc_id "HGNC:48048"  ; level 3 ; orig_coord_info "chr7,35930158,35930264,-"  ; tag basic ; transcript_id "AVL9--RNU6-1085P^ENST00000363576.1"  ; transcript_name "RNU6-1085P-201"  ; transcript_support_level NA ; transcript_type snRNA
AVL9--RNU6-1085P	ENSEMBL	RNA	33636	33742	.	+	.	FI_gene_label "RNU6-1085P^ENSG00000200446.1"  ; ID "AVL9--RNU6-1085P^ENST00000363576.1"  ; Parent "AVL9--RNU6-1085P^RNU6-1085P^ENSG00000200446.1"  ; exon_id "ENSE00001807627.1"  ; exon_number 1 ; gene_id "AVL9--RNU6-1085P^RNU6-1085P^ENSG00000200446.1"  ; gene_name "RNU6-1085P"  ; gene_type snRNA ; hgnc_id "HGNC:48048"  ; level 3 ; orig_coord_info "chr7,35930158,35930264,-"  ; tag basic ; transcript_id "AVL9--RNU6-1085P^ENST00000363576.1"  ; transcript_name "RNU6-1085P-201"  ; transcript_support_level NA ; transcript_type snRNA
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
306 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 ------------------------------
490 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 19 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