.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00117_23H5VFLT4_s37)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/3612f2ee92050b0705791b6e5d0b14/.command.log
Size: 51.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00117_23H5VFLT4_s37)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/3612f2ee92050b0705791b6e5d0b14/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/40d2cb9a35bc8c1babce70a0a6d66b/fi_workdir/tih_rna_sample_00117_23H5VFLT4_s37.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/3612f2ee92050b0705791b6e5d0b14/.command.run
==> STAGING COMPLETE (3 inputs)

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 578
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 578
=> 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:578
  => 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: 
COL1A1--SLC45A4	HAVANA	gene	25435	34927	.	+	.	FI_gene_label "SLC45A4^ENSG00000022567.10"  ; ID "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; ccdsid "CCDS34948.1"  ; exon_id "ENSE00001475008.1"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; gene_name SLC45A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164393.4"  ; havana_transcript "OTTHUMT00000378571.3"  ; hgnc_id "HGNC:29196"  ; level 2 ; orig_coord_info "chr8,141228179,141228266,-"  ; protein_id "ENSP00000024061.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000024061.7"  ; transcript_name "SLC45A4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COL1A1--SLC45A4	HAVANA	mRNA	25435	34927	.	+	.	FI_gene_label "SLC45A4^ENSG00000022567.10"  ; ID "COL1A1--SLC45A4^ENST00000024061.7"  ; Parent "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; ccdsid "CCDS34948.1"  ; exon_id "ENSE00001475008.1"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^SLC45A4^ENSG00000022567.10"  ; gene_name SLC45A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164393.4"  ; havana_transcript "OTTHUMT00000378571.3"  ; hgnc_id "HGNC:29196"  ; level 2 ; orig_coord_info "chr8,141228179,141228266,-"  ; protein_id "ENSP00000024061.3"  ; tag basic appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000024061.7"  ; transcript_name "SLC45A4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
COL1A1--SLC45A4	HAVANA	gene	1002	18313	.	+	.	FI_gene_label "COL1A1^ENSG00000108821.14"  ; ID "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; ccdsid "CCDS11561.1"  ; exon_id "ENSE00003500023.2"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; gene_name COL1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148674.9"  ; havana_transcript "OTTHUMT00000309036.3"  ; hgnc_id "HGNC:2197"  ; level 2 ; orig_coord_info "chr17,50201411,50201513,-"  ; protein_id "ENSP00000225964.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000225964.10"  ; transcript_name "COL1A1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
COL1A1--SLC45A4	HAVANA	mRNA	1002	18313	.	+	.	FI_gene_label "COL1A1^ENSG00000108821.14"  ; ID "COL1A1--SLC45A4^ENST00000225964.10"  ; Parent "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; ccdsid "CCDS11561.1"  ; exon_id "ENSE00003500023.2"  ; exon_number 1 ; gene_id "COL1A1--SLC45A4^COL1A1^ENSG00000108821.14"  ; gene_name COL1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000148674.9"  ; havana_transcript "OTTHUMT00000309036.3"  ; hgnc_id "HGNC:2197"  ; level 2 ; orig_coord_info "chr17,50201411,50201513,-"  ; protein_id "ENSP00000225964.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "COL1A1--SLC45A4^ENST00000225964.10"  ; transcript_name "COL1A1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FSIP1--AC013652.1	HAVANA	gene	1001	15962	.	+	.	FI_gene_label "FSIP1^ENSG00000150667.8"  ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; ccdsid "CCDS10050.1"  ; exon_id "ENSE00003574039.1"  ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3"  ; havana_transcript "OTTHUMT00000252118.4"  ; hgnc_id "HGNC:21674"  ; level 2 ; orig_coord_info "chr15,39776399,39776524,-"  ; protein_id "ENSP00000280236.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4"  ; transcript_name "FSIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1	HAVANA	mRNA	1001	15962	.	+	.	FI_gene_label "FSIP1^ENSG00000150667.8"  ; ID "FSIP1--AC013652.1^ENST00000350221.4"  ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; ccdsid "CCDS10050.1"  ; exon_id "ENSE00003574039.1"  ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8"  ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3"  ; havana_transcript "OTTHUMT00000252118.4"  ; hgnc_id "HGNC:21674"  ; level 2 ; orig_coord_info "chr15,39776399,39776524,-"  ; protein_id "ENSP00000280236.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4"  ; transcript_name "FSIP1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHA13	HAVANA	gene	7268	15708	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHA13	HAVANA	mRNA	7268	15708	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA6--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHA13	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHA13	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHA13^ENST00000378126.4"  ; Parent "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHA13^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHA13^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC1	HAVANA	gene	7268	17283	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC1	HAVANA	mRNA	7268	17283	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA6--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC1	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC1	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC1^ENST00000378126.4"  ; Parent "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC1^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC1^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC2	HAVANA	gene	7274	18009	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA6--PCDHAC2	HAVANA	mRNA	7274	18009	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA6--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA6--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA6--PCDHAC2	HAVANA	gene	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHA6--PCDHAC2	HAVANA	mRNA	1001	4267	.	+	.	FI_gene_label "PCDHA6^ENSG00000081842.18"  ; ID "PCDHA6--PCDHAC2^ENST00000378126.4"  ; Parent "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; exon_id "ENSE00001476364.4"  ; exon_number 1 ; gene_id "PCDHA6--PCDHAC2^PCDHA6^ENSG00000081842.18"  ; gene_name PCDHA6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163353.5"  ; havana_transcript "OTTHUMT00000477550.1"  ; hgnc_id "HGNC:8672"  ; level 2 ; orig_coord_info "chr5,140828092,140830500,+"  ; protein_id "ENSP00000367366.4"  ; tag upstream_ATG RNA_Seq_supported_partial basic ; transcript_id "PCDHA6--PCDHAC2^ENST00000378126.4"  ; transcript_name "PCDHA6-201"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA10	HAVANA	gene	6881	16334	.	+	.	FI_gene_label "PCDHGA10^ENSG00000253846.2"  ; ID "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2"  ; ccdsid "CCDS47292.1"  ; exon_id "ENSE00001792208.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2"  ; gene_name PCDHGA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163688.2"  ; havana_transcript "OTTHUMT00000374747.1"  ; hgnc_id "HGNC:8697"  ; level 2 ; orig_coord_info "chr5,141413176,141415611,+"  ; protein_id "ENSP00000381611.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000398610.2"  ; transcript_name "PCDHGA10-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA10	HAVANA	mRNA	6881	16334	.	+	.	FI_gene_label "PCDHGA10^ENSG00000253846.2"  ; ID "PCDHGA4--PCDHGA10^ENST00000398610.2"  ; Parent "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2"  ; ccdsid "CCDS47292.1"  ; exon_id "ENSE00001792208.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA10^ENSG00000253846.2"  ; gene_name PCDHGA10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163688.2"  ; havana_transcript "OTTHUMT00000374747.1"  ; hgnc_id "HGNC:8697"  ; level 2 ; orig_coord_info "chr5,141413176,141415611,+"  ; protein_id "ENSP00000381611.2"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000398610.2"  ; transcript_name "PCDHGA10-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA10	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA10	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA10^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA10^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA10^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA11	HAVANA	gene	6696	15501	.	+	.	FI_gene_label "PCDHGA11^ENSG00000253873.6"  ; ID "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6"  ; ccdsid "CCDS47294.1"  ; exon_id "ENSE00001533810.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6"  ; gene_name PCDHGA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164055.3"  ; havana_transcript "OTTHUMT00000376974.3"  ; hgnc_id "HGNC:8698"  ; level 2 ; orig_coord_info "chr5,141421228,141423660,+"  ; protein_id "ENSP00000381589.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000398587.7"  ; transcript_name "PCDHGA11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA11	HAVANA	mRNA	6696	15501	.	+	.	FI_gene_label "PCDHGA11^ENSG00000253873.6"  ; ID "PCDHGA4--PCDHGA11^ENST00000398587.7"  ; Parent "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6"  ; ccdsid "CCDS47294.1"  ; exon_id "ENSE00001533810.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA11^ENSG00000253873.6"  ; gene_name PCDHGA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164055.3"  ; havana_transcript "OTTHUMT00000376974.3"  ; hgnc_id "HGNC:8698"  ; level 2 ; orig_coord_info "chr5,141421228,141423660,+"  ; protein_id "ENSP00000381589.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000398587.7"  ; transcript_name "PCDHGA11-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA11	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA11	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA11^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA11^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA11^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA12	HAVANA	gene	6692	14584	.	+	.	FI_gene_label "PCDHGA12^ENSG00000253159.3"  ; ID "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3"  ; ccdsid "CCDS4260.1"  ; exon_id "ENSE00000814269.5"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3"  ; gene_name PCDHGA12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129611.6"  ; havana_transcript "OTTHUMT00000251806.3"  ; hgnc_id "HGNC:8699"  ; level 2 ; orig_coord_info "chr5,141430760,141433183,+"  ; protein_id "ENSP00000252085.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000252085.4"  ; transcript_name "PCDHGA12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA12	HAVANA	mRNA	6692	14584	.	+	.	FI_gene_label "PCDHGA12^ENSG00000253159.3"  ; ID "PCDHGA4--PCDHGA12^ENST00000252085.4"  ; Parent "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3"  ; ccdsid "CCDS4260.1"  ; exon_id "ENSE00000814269.5"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA12^ENSG00000253159.3"  ; gene_name PCDHGA12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129611.6"  ; havana_transcript "OTTHUMT00000251806.3"  ; hgnc_id "HGNC:8699"  ; level 2 ; orig_coord_info "chr5,141430760,141433183,+"  ; protein_id "ENSP00000252085.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000252085.4"  ; transcript_name "PCDHGA12-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA12	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA12	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA12^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA12^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA12^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA8	HAVANA	gene	9168	18348	.	+	.	FI_gene_label "PCDHGA8^ENSG00000253767.3"  ; ID "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3"  ; ccdsid "CCDS47291.1"  ; exon_id "ENSE00001533882.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3"  ; gene_name PCDHGA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164053.2"  ; havana_transcript "OTTHUMT00000376972.1"  ; hgnc_id "HGNC:8706"  ; level 2 ; orig_coord_info "chr5,141392814,141395237,+"  ; protein_id "ENSP00000381605.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000398604.3"  ; transcript_name "PCDHGA8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA8	HAVANA	mRNA	9168	18348	.	+	.	FI_gene_label "PCDHGA8^ENSG00000253767.3"  ; ID "PCDHGA4--PCDHGA8^ENST00000398604.3"  ; Parent "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3"  ; ccdsid "CCDS47291.1"  ; exon_id "ENSE00001533882.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA8^ENSG00000253767.3"  ; gene_name PCDHGA8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164053.2"  ; havana_transcript "OTTHUMT00000376972.1"  ; hgnc_id "HGNC:8706"  ; level 2 ; orig_coord_info "chr5,141392814,141395237,+"  ; protein_id "ENSP00000381605.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000398604.3"  ; transcript_name "PCDHGA8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA8	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA8	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA8^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA8^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA8^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA9	HAVANA	gene	6713	14440	.	+	.	FI_gene_label "PCDHGA9^ENSG00000261934.2"  ; ID "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2"  ; ccdsid "CCDS58981.1"  ; exon_id "ENSE00002639131.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2"  ; gene_name PCDHGA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177473.2"  ; havana_transcript "OTTHUMT00000437105.1"  ; hgnc_id "HGNC:8707"  ; level 2 ; orig_coord_info "chr5,141402953,141405376,+"  ; protein_id "ENSP00000460274.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000573521.1"  ; transcript_name "PCDHGA9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGA9	HAVANA	mRNA	6713	14440	.	+	.	FI_gene_label "PCDHGA9^ENSG00000261934.2"  ; ID "PCDHGA4--PCDHGA9^ENST00000573521.1"  ; Parent "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2"  ; ccdsid "CCDS58981.1"  ; exon_id "ENSE00002639131.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA9^ENSG00000261934.2"  ; gene_name PCDHGA9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177473.2"  ; havana_transcript "OTTHUMT00000437105.1"  ; hgnc_id "HGNC:8707"  ; level 2 ; orig_coord_info "chr5,141402953,141405376,+"  ; protein_id "ENSP00000460274.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000573521.1"  ; transcript_name "PCDHGA9-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGA9	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGA9	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGA9^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGA9^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGA9^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGB6	HAVANA	gene	6874	16473	.	+	.	FI_gene_label "PCDHGB6^ENSG00000253305.2"  ; ID "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2"  ; ccdsid "CCDS54929.1"  ; exon_id "ENSE00002122685.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2"  ; gene_name PCDHGB6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163687.2"  ; havana_transcript "OTTHUMT00000374746.1"  ; hgnc_id "HGNC:8713"  ; level 2 ; orig_coord_info "chr5,141408203,141410620,+"  ; protein_id "ENSP00000428603.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000520790.1"  ; transcript_name "PCDHGB6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGB6	HAVANA	mRNA	6874	16473	.	+	.	FI_gene_label "PCDHGB6^ENSG00000253305.2"  ; ID "PCDHGA4--PCDHGB6^ENST00000520790.1"  ; Parent "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2"  ; ccdsid "CCDS54929.1"  ; exon_id "ENSE00002122685.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGB6^ENSG00000253305.2"  ; gene_name PCDHGB6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163687.2"  ; havana_transcript "OTTHUMT00000374746.1"  ; hgnc_id "HGNC:8713"  ; level 2 ; orig_coord_info "chr5,141408203,141410620,+"  ; protein_id "ENSP00000428603.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000520790.1"  ; transcript_name "PCDHGB6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGB6	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGB6	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGB6^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB6^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB6^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGB7	HAVANA	gene	6724	14653	.	+	.	FI_gene_label "PCDHGB7^ENSG00000254122.3"  ; ID "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3"  ; ccdsid "CCDS47293.1"  ; exon_id "ENSE00001533845.4"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3"  ; gene_name PCDHGB7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164054.2"  ; havana_transcript "OTTHUMT00000376973.2"  ; hgnc_id "HGNC:8714"  ; level 2 ; orig_coord_info "chr5,141417860,141420274,+"  ; protein_id "ENSP00000381594.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000398594.4"  ; transcript_name "PCDHGB7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGB7	HAVANA	mRNA	6724	14653	.	+	.	FI_gene_label "PCDHGB7^ENSG00000254122.3"  ; ID "PCDHGA4--PCDHGB7^ENST00000398594.4"  ; Parent "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3"  ; ccdsid "CCDS47293.1"  ; exon_id "ENSE00001533845.4"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGB7^ENSG00000254122.3"  ; gene_name PCDHGB7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164054.2"  ; havana_transcript "OTTHUMT00000376973.2"  ; hgnc_id "HGNC:8714"  ; level 2 ; orig_coord_info "chr5,141417860,141420274,+"  ; protein_id "ENSP00000381594.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000398594.4"  ; transcript_name "PCDHGB7-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGB7	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGB7	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGB7^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGB7^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGB7^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC3	HAVANA	gene	6711	16897	.	+	.	FI_gene_label "PCDHGC3^ENSG00000240184.7"  ; ID "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7"  ; ccdsid "CCDS4261.1"  ; exon_id "ENSE00001199459.7"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7"  ; gene_name PCDHGC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129613.8"  ; havana_transcript "OTTHUMT00000251808.5"  ; hgnc_id "HGNC:8716"  ; level 2 ; orig_coord_info "chr5,141476117,141478546,+"  ; protein_id "ENSP00000312070.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000308177.5"  ; transcript_name "PCDHGC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC3	HAVANA	mRNA	6711	16897	.	+	.	FI_gene_label "PCDHGC3^ENSG00000240184.7"  ; ID "PCDHGA4--PCDHGC3^ENST00000308177.5"  ; Parent "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7"  ; ccdsid "CCDS4261.1"  ; exon_id "ENSE00001199459.7"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGC3^ENSG00000240184.7"  ; gene_name PCDHGC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129613.8"  ; havana_transcript "OTTHUMT00000251808.5"  ; hgnc_id "HGNC:8716"  ; level 2 ; orig_coord_info "chr5,141476117,141478546,+"  ; protein_id "ENSP00000312070.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000308177.5"  ; transcript_name "PCDHGC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC3	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC3	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC3^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC3^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC3^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC4	HAVANA	gene	6869	14665	.	+	.	FI_gene_label "PCDHGC4^ENSG00000242419.5"  ; ID "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5"  ; ccdsid "CCDS4262.1"  ; exon_id "ENSE00001162305.2"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5"  ; gene_name PCDHGC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129625.4"  ; havana_transcript "OTTHUMT00000251820.2"  ; hgnc_id "HGNC:8717"  ; level 2 ; orig_coord_info "chr5,141485174,141487615,+"  ; protein_id "ENSP00000306918.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000306593.1"  ; transcript_name "PCDHGC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC4	HAVANA	mRNA	6869	14665	.	+	.	FI_gene_label "PCDHGC4^ENSG00000242419.5"  ; ID "PCDHGA4--PCDHGC4^ENST00000306593.1"  ; Parent "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5"  ; ccdsid "CCDS4262.1"  ; exon_id "ENSE00001162305.2"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGC4^ENSG00000242419.5"  ; gene_name PCDHGC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129625.4"  ; havana_transcript "OTTHUMT00000251820.2"  ; hgnc_id "HGNC:8717"  ; level 2 ; orig_coord_info "chr5,141485174,141487615,+"  ; protein_id "ENSP00000306918.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000306593.1"  ; transcript_name "PCDHGC4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC4	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC4	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC4^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC4^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC4^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC5	HAVANA	gene	6692	14717	.	+	.	FI_gene_label "PCDHGC5^ENSG00000240764.4"  ; ID "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4"  ; ccdsid "CCDS4263.1"  ; exon_id "ENSE00000766474.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4"  ; gene_name PCDHGC5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129624.2"  ; havana_transcript "OTTHUMT00000251819.2"  ; hgnc_id "HGNC:8718"  ; level 2 ; orig_coord_info "chr5,141489241,141491700,+"  ; protein_id "ENSP00000252087.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000252087.3"  ; transcript_name "PCDHGC5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHGA4--PCDHGC5	HAVANA	mRNA	6692	14717	.	+	.	FI_gene_label "PCDHGC5^ENSG00000240764.4"  ; ID "PCDHGA4--PCDHGC5^ENST00000252087.3"  ; Parent "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4"  ; ccdsid "CCDS4263.1"  ; exon_id "ENSE00000766474.3"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGC5^ENSG00000240764.4"  ; gene_name PCDHGC5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129624.2"  ; havana_transcript "OTTHUMT00000251819.2"  ; hgnc_id "HGNC:8718"  ; level 2 ; orig_coord_info "chr5,141489241,141491700,+"  ; protein_id "ENSP00000252087.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000252087.3"  ; transcript_name "PCDHGC5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHGA4--PCDHGC5	HAVANA	gene	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
PCDHGA4--PCDHGC5	HAVANA	mRNA	1001	3691	.	+	.	FI_gene_label "PCDHGA4^ENSG00000262576.3"  ; ID "PCDHGA4--PCDHGC5^ENST00000612927.1"  ; Parent "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3"  ; ccdsid "CCDS75331.1"  ; exon_id "ENSE00003715198.1"  ; exon_number 1 ; gene_id "PCDHGA4--PCDHGC5^PCDHGA4^ENSG00000262576.3"  ; gene_name PCDHGA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000177593.4"  ; havana_transcript "OTTHUMT00000476684.1"  ; hgnc_id "HGNC:8702"  ; level 2 ; orig_coord_info "chr5,141355108,141357660,+"  ; protein_id "ENSP00000477894.1"  ; tag basic CCDS ; transcript_id "PCDHGA4--PCDHGC5^ENST00000612927.1"  ; transcript_name "PCDHGA4-202"  ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created: 
RBM14--RBM4B	HAVANA	gene	15007	22557	.	+	.	FI_gene_label "RBM4B^ENSG00000173914.12"  ; ID "RBM14--RBM4B^RBM4B^ENSG00000173914.12"  ; ccdsid "CCDS8149.1"  ; exon_id "ENSE00002463386.1"  ; exon_number 2 ; gene_id "RBM14--RBM4B^RBM4B^ENSG00000173914.12"  ; gene_name RBM4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167243.4"  ; havana_transcript "OTTHUMT00000393852.2"  ; hgnc_id "HGNC:28842"  ; level 2 ; orig_coord_info "chr11,66676668,66677079,-"  ; protein_id "ENSP00000310471.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4B^ENST00000310046.9"  ; transcript_name "RBM4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4B	HAVANA	mRNA	15007	22557	.	+	.	FI_gene_label "RBM4B^ENSG00000173914.12"  ; ID "RBM14--RBM4B^ENST00000310046.9"  ; Parent "RBM14--RBM4B^RBM4B^ENSG00000173914.12"  ; ccdsid "CCDS8149.1"  ; exon_id "ENSE00002463386.1"  ; exon_number 2 ; gene_id "RBM14--RBM4B^RBM4B^ENSG00000173914.12"  ; gene_name RBM4B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167243.4"  ; havana_transcript "OTTHUMT00000393852.2"  ; hgnc_id "HGNC:28842"  ; level 2 ; orig_coord_info "chr11,66676668,66677079,-"  ; protein_id "ENSP00000310471.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBM14--RBM4B^ENST00000310046.9"  ; transcript_name "RBM4B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RBM14--RBM4B	HAVANA	gene	1005	12006	.	+	.	FI_gene_label "RBM14^ENSG00000239306.5"  ; ID "RBM14--RBM4B^RBM14^ENSG00000239306.5"  ; ccdsid "CCDS8147.1"  ; exon_id "ENSE00003902856.1"  ; exon_number 1 ; gene_id "RBM14--RBM4B^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--RBM4B^ENST00000310137.5"  ; transcript_name "RBM14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RBM14--RBM4B	HAVANA	mRNA	1005	12006	.	+	.	FI_gene_label "RBM14^ENSG00000239306.5"  ; ID "RBM14--RBM4B^ENST00000310137.5"  ; Parent "RBM14--RBM4B^RBM14^ENSG00000239306.5"  ; ccdsid "CCDS8147.1"  ; exon_id "ENSE00003902856.1"  ; exon_number 1 ; gene_id "RBM14--RBM4B^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--RBM4B^ENST00000310137.5"  ; transcript_name "RBM14-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FSIP1--AC013652.1	HAVANA	gene	21835	37275	.	+	.	FI_gene_label "AC013652.1^ENSG00000259345.7"  ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; exon_id "ENSE00002558629.1"  ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; gene_name "AC013652.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4"  ; havana_transcript "OTTHUMT00000418683.1"  ; level 2 ; orig_coord_info "chr15,39427098,39427195,-"  ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1"  ; transcript_name "AC013652.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1	HAVANA	RNA	21835	37275	.	+	.	FI_gene_label "AC013652.1^ENSG00000259345.7"  ; ID "FSIP1--AC013652.1^ENST00000558209.1"  ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; exon_id "ENSE00002558629.1"  ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7"  ; gene_name "AC013652.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4"  ; havana_transcript "OTTHUMT00000418683.1"  ; level 2 ; orig_coord_info "chr15,39427098,39427195,-"  ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1"  ; transcript_name "AC013652.1-205"  ; transcript_support_level 3 ; transcript_type lncRNA
102 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 ------------------------------
141 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 14 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