File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/206ed51e46643f7deeb62e7f9293c7/.command.out
Size
36.0 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-33eb27-R1_A23WJ53LT4_1)
Attempt

Content

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

 ------------------------------------------------------------------------------
|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 1617
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1617
=> 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:1617
  => 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: 
AGPAT3--GRM5	HAVANA	gene	1001	31260	.	+	.	FI_gene_label "AGPAT3^ENSG00000160216.21"  ; ID "AGPAT3--GRM5^AGPAT3^ENSG00000160216.21"  ; ccdsid "CCDS13703.1"  ; exon_id "ENSE00001414183.1"  ; exon_number 3 ; gene_id "AGPAT3--GRM5^AGPAT3^ENSG00000160216.21"  ; gene_name AGPAT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086892.16"  ; havana_transcript "OTTHUMT00000195719.2"  ; hgnc_id "HGNC:326"  ; level 2 ; orig_coord_info "chr21,43959682,43959859,+"  ; protein_id "ENSP00000291572.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGPAT3--GRM5^ENST00000291572.13"  ; transcript_name "AGPAT3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AGPAT3--GRM5	HAVANA	mRNA	1001	31260	.	+	.	FI_gene_label "AGPAT3^ENSG00000160216.21"  ; ID "AGPAT3--GRM5^ENST00000291572.13"  ; Parent "AGPAT3--GRM5^AGPAT3^ENSG00000160216.21"  ; ccdsid "CCDS13703.1"  ; exon_id "ENSE00001414183.1"  ; exon_number 3 ; gene_id "AGPAT3--GRM5^AGPAT3^ENSG00000160216.21"  ; gene_name AGPAT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086892.16"  ; havana_transcript "OTTHUMT00000195719.2"  ; hgnc_id "HGNC:326"  ; level 2 ; orig_coord_info "chr21,43959682,43959859,+"  ; protein_id "ENSP00000291572.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AGPAT3--GRM5^ENST00000291572.13"  ; transcript_name "AGPAT3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AGPAT3--GRM5	HAVANA	gene	36649	53683	.	+	.	FI_gene_label "GRM5^ENSG00000168959.14"  ; ID "AGPAT3--GRM5^GRM5^ENSG00000168959.14"  ; ccdsid "CCDS8283.1"  ; exon_id "ENSE00001153874.1"  ; exon_number 1 ; gene_id "AGPAT3--GRM5^GRM5^ENSG00000168959.14"  ; gene_name GRM5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000134306.3"  ; havana_transcript "OTTHUMT00000259222.1"  ; hgnc_id "HGNC:4597"  ; level 2 ; orig_coord_info "chr11,89047212,89047872,-"  ; protein_id "ENSP00000305905.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "AGPAT3--GRM5^ENST00000305432.9"  ; transcript_name "GRM5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AGPAT3--GRM5	HAVANA	mRNA	36649	53683	.	+	.	FI_gene_label "GRM5^ENSG00000168959.14"  ; ID "AGPAT3--GRM5^ENST00000305432.9"  ; Parent "AGPAT3--GRM5^GRM5^ENSG00000168959.14"  ; ccdsid "CCDS8283.1"  ; exon_id "ENSE00001153874.1"  ; exon_number 1 ; gene_id "AGPAT3--GRM5^GRM5^ENSG00000168959.14"  ; gene_name GRM5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000134306.3"  ; havana_transcript "OTTHUMT00000259222.1"  ; hgnc_id "HGNC:4597"  ; level 2 ; orig_coord_info "chr11,89047212,89047872,-"  ; protein_id "ENSP00000305905.5"  ; tag basic appris_alternative_2 CCDS ; transcript_id "AGPAT3--GRM5^ENST00000305432.9"  ; transcript_name "GRM5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AL669831.4--SEPTIN14	HAVANA	gene	8876	22423	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
AL669831.4--SEPTIN14	HAVANA	mRNA	8876	22423	.	+	.	FI_gene_label "SEPTIN14^ENSG00000154997.9"  ; ID "AL669831.4--SEPTIN14^ENST00000388975.4"  ; Parent "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; ccdsid "CCDS5519.2"  ; exon_id "ENSE00003671928.1"  ; exon_number 2 ; gene_id "AL669831.4--SEPTIN14^SEPTIN14^ENSG00000154997.9"  ; gene_name SEPTIN14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129341.4"  ; havana_transcript "OTTHUMT00000251489.3"  ; hgnc_id "HGNC:33280"  ; level 2 ; orig_coord_info "chr7,55861943,55861996,-"  ; protein_id "ENSP00000373627.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AL669831.4--SEPTIN14^ENST00000388975.4"  ; transcript_name "SEPTIN14-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ANKH--HNRNPKP5	HAVANA	gene	1001	25417	.	+	.	FI_gene_label "ANKH^ENSG00000154122.14"  ; ID "ANKH--HNRNPKP5^ANKH^ENSG00000154122.14"  ; ccdsid "CCDS3885.1"  ; exon_id "ENSE00001262580.8"  ; exon_number 1 ; gene_id "ANKH--HNRNPKP5^ANKH^ENSG00000154122.14"  ; gene_name ANKH ; gene_type protein_coding ; havana_gene "OTTHUMG00000090539.5"  ; havana_transcript "OTTHUMT00000207063.4"  ; hgnc_id "HGNC:15492"  ; level 2 ; orig_coord_info "chr5,14871352,14871447,-"  ; protein_id "ENSP00000284268.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANKH--HNRNPKP5^ENST00000284268.8"  ; transcript_name "ANKH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ANKH--HNRNPKP5	HAVANA	mRNA	1001	25417	.	+	.	FI_gene_label "ANKH^ENSG00000154122.14"  ; ID "ANKH--HNRNPKP5^ENST00000284268.8"  ; Parent "ANKH--HNRNPKP5^ANKH^ENSG00000154122.14"  ; ccdsid "CCDS3885.1"  ; exon_id "ENSE00001262580.8"  ; exon_number 1 ; gene_id "ANKH--HNRNPKP5^ANKH^ENSG00000154122.14"  ; gene_name ANKH ; gene_type protein_coding ; havana_gene "OTTHUMG00000090539.5"  ; havana_transcript "OTTHUMT00000207063.4"  ; hgnc_id "HGNC:15492"  ; level 2 ; orig_coord_info "chr5,14871352,14871447,-"  ; protein_id "ENSP00000284268.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ANKH--HNRNPKP5^ENST00000284268.8"  ; transcript_name "ANKH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KCNN4--LYPD5	HAVANA	gene	18128	23361	.	+	.	FI_gene_label "LYPD5^ENSG00000159871.15"  ; ID "KCNN4--LYPD5^LYPD5^ENSG00000159871.15"  ; ccdsid "CCDS46096.1"  ; exon_id "ENSE00002224542.2"  ; exon_number 1 ; gene_id "KCNN4--LYPD5^LYPD5^ENSG00000159871.15"  ; gene_name LYPD5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182781.5"  ; havana_transcript "OTTHUMT00000463611.2"  ; hgnc_id "HGNC:26397"  ; level 2 ; orig_coord_info "chr19,43802317,43802380,-"  ; protein_id "ENSP00000367185.2"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "KCNN4--LYPD5^ENST00000377950.8"  ; transcript_name "LYPD5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KCNN4--LYPD5	HAVANA	mRNA	18128	23361	.	+	.	FI_gene_label "LYPD5^ENSG00000159871.15"  ; ID "KCNN4--LYPD5^ENST00000377950.8"  ; Parent "KCNN4--LYPD5^LYPD5^ENSG00000159871.15"  ; ccdsid "CCDS46096.1"  ; exon_id "ENSE00002224542.2"  ; exon_number 1 ; gene_id "KCNN4--LYPD5^LYPD5^ENSG00000159871.15"  ; gene_name LYPD5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182781.5"  ; havana_transcript "OTTHUMT00000463611.2"  ; hgnc_id "HGNC:26397"  ; level 2 ; orig_coord_info "chr19,43802317,43802380,-"  ; protein_id "ENSP00000367185.2"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "KCNN4--LYPD5^ENST00000377950.8"  ; transcript_name "LYPD5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KCNN4--LYPD5	HAVANA	gene	6814	9800	.	+	.	FI_gene_label "KCNN4^ENSG00000104783.14"  ; ID "KCNN4--LYPD5^KCNN4^ENSG00000104783.14"  ; exon_id "ENSE00003168052.1"  ; exon_number 1 ; gene_id "KCNN4--LYPD5^KCNN4^ENSG00000104783.14"  ; gene_name KCNN4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182779.6"  ; havana_transcript "OTTHUMT00000463599.1"  ; hgnc_id "HGNC:6293"  ; level 2 ; orig_coord_info "chr19,43769719,43769827,-"  ; protein_id "ENSP00000471900.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "KCNN4--LYPD5^ENST00000598836.1"  ; transcript_name "KCNN4-202"  ; transcript_support_level 5 ; transcript_type protein_coding
KCNN4--LYPD5	HAVANA	mRNA	6814	9800	.	+	.	FI_gene_label "KCNN4^ENSG00000104783.14"  ; ID "KCNN4--LYPD5^ENST00000598836.1"  ; Parent "KCNN4--LYPD5^KCNN4^ENSG00000104783.14"  ; exon_id "ENSE00003168052.1"  ; exon_number 1 ; gene_id "KCNN4--LYPD5^KCNN4^ENSG00000104783.14"  ; gene_name KCNN4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182779.6"  ; havana_transcript "OTTHUMT00000463599.1"  ; hgnc_id "HGNC:6293"  ; level 2 ; orig_coord_info "chr19,43769719,43769827,-"  ; protein_id "ENSP00000471900.1"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "KCNN4--LYPD5^ENST00000598836.1"  ; transcript_name "KCNN4-202"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
RIPK4--KCNJ6	HAVANA	gene	1038	11618	.	+	.	FI_gene_label "RIPK4^ENSG00000183421.12"  ; ID "RIPK4--KCNJ6^RIPK4^ENSG00000183421.12"  ; ccdsid "CCDS13675.1"  ; exon_id "ENSE00002730798.2"  ; exon_number 1 ; gene_id "RIPK4--KCNJ6^RIPK4^ENSG00000183421.12"  ; gene_name RIPK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086770.2"  ; havana_transcript "OTTHUMT00000195204.2"  ; hgnc_id "HGNC:496"  ; level 2 ; orig_coord_info "chr21,41766860,41767041,-"  ; protein_id "ENSP00000332454.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RIPK4--KCNJ6^ENST00000332512.8"  ; transcript_name "RIPK4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RIPK4--KCNJ6	HAVANA	mRNA	1038	11618	.	+	.	FI_gene_label "RIPK4^ENSG00000183421.12"  ; ID "RIPK4--KCNJ6^ENST00000332512.8"  ; Parent "RIPK4--KCNJ6^RIPK4^ENSG00000183421.12"  ; ccdsid "CCDS13675.1"  ; exon_id "ENSE00002730798.2"  ; exon_number 1 ; gene_id "RIPK4--KCNJ6^RIPK4^ENSG00000183421.12"  ; gene_name RIPK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086770.2"  ; havana_transcript "OTTHUMT00000195204.2"  ; hgnc_id "HGNC:496"  ; level 2 ; orig_coord_info "chr21,41766860,41767041,-"  ; protein_id "ENSP00000332454.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "RIPK4--KCNJ6^ENST00000332512.8"  ; transcript_name "RIPK4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
RIPK4--KCNJ6	HAVANA	gene	16662	39320	.	+	.	FI_gene_label "KCNJ6^ENSG00000157542.11"  ; ID "RIPK4--KCNJ6^KCNJ6^ENSG00000157542.11"  ; ccdsid "CCDS42927.1"  ; exon_id "ENSE00001543115.1"  ; exon_number 2 ; gene_id "RIPK4--KCNJ6^KCNJ6^ENSG00000157542.11"  ; gene_name KCNJ6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086667.5"  ; havana_transcript "OTTHUMT00000194828.4"  ; hgnc_id "HGNC:6267"  ; level 2 ; orig_coord_info "chr21,37840658,37840682,-"  ; protein_id "ENSP00000477437.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RIPK4--KCNJ6^ENST00000609713.2"  ; transcript_name "KCNJ6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
RIPK4--KCNJ6	HAVANA	mRNA	16662	39320	.	+	.	FI_gene_label "KCNJ6^ENSG00000157542.11"  ; ID "RIPK4--KCNJ6^ENST00000609713.2"  ; Parent "RIPK4--KCNJ6^KCNJ6^ENSG00000157542.11"  ; ccdsid "CCDS42927.1"  ; exon_id "ENSE00001543115.1"  ; exon_number 2 ; gene_id "RIPK4--KCNJ6^KCNJ6^ENSG00000157542.11"  ; gene_name KCNJ6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086667.5"  ; havana_transcript "OTTHUMT00000194828.4"  ; hgnc_id "HGNC:6267"  ; level 2 ; orig_coord_info "chr21,37840658,37840682,-"  ; protein_id "ENSP00000477437.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RIPK4--KCNJ6^ENST00000609713.2"  ; transcript_name "KCNJ6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TCF7L2--AL158212.1	HAVANA	gene	15542	23732	.	+	.	FI_gene_label "TCF7L2^ENSG00000148737.17"  ; ID "TCF7L2--AL158212.1^TCF7L2^ENSG00000148737.17"  ; exon_id "ENSE00001738678.1"  ; exon_number 1 ; gene_id "TCF7L2--AL158212.1^TCF7L2^ENSG00000148737.17"  ; gene_name TCF7L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019070.11"  ; havana_transcript "OTTHUMT00000050420.2"  ; hgnc_id "HGNC:11641"  ; level 2 ; orig_coord_info "chr10,113146072,113146097,+"  ; protein_id "ENSP00000277945.7"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "TCF7L2--AL158212.1^ENST00000277945.11"  ; transcript_name "TCF7L2-201"  ; transcript_support_level 5 ; transcript_type protein_coding
TCF7L2--AL158212.1	HAVANA	mRNA	15542	23732	.	+	.	FI_gene_label "TCF7L2^ENSG00000148737.17"  ; ID "TCF7L2--AL158212.1^ENST00000277945.11"  ; Parent "TCF7L2--AL158212.1^TCF7L2^ENSG00000148737.17"  ; exon_id "ENSE00001738678.1"  ; exon_number 1 ; gene_id "TCF7L2--AL158212.1^TCF7L2^ENSG00000148737.17"  ; gene_name TCF7L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019070.11"  ; havana_transcript "OTTHUMT00000050420.2"  ; hgnc_id "HGNC:11641"  ; level 2 ; orig_coord_info "chr10,113146072,113146097,+"  ; protein_id "ENSP00000277945.7"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "TCF7L2--AL158212.1^ENST00000277945.11"  ; transcript_name "TCF7L2-201"  ; transcript_support_level 5 ; 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: 
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: 
WASH3P--IQSEC3	HAVANA	gene	13234	26909	.	+	.	FI_gene_label "IQSEC3^ENSG00000120645.12"  ; ID "WASH3P--IQSEC3^IQSEC3^ENSG00000120645.12"  ; ccdsid "CCDS31725.1"  ; exon_id "ENSE00003622153.1"  ; exon_number 3 ; gene_id "WASH3P--IQSEC3^IQSEC3^ENSG00000120645.12"  ; gene_name IQSEC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167975.5"  ; havana_transcript "OTTHUMT00000397383.2"  ; hgnc_id "HGNC:29193"  ; level 2 ; orig_coord_info "chr12,138273,139354,+"  ; protein_id "ENSP00000372292.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "WASH3P--IQSEC3^ENST00000382841.2"  ; transcript_name "IQSEC3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
WASH3P--IQSEC3	HAVANA	mRNA	13234	26909	.	+	.	FI_gene_label "IQSEC3^ENSG00000120645.12"  ; ID "WASH3P--IQSEC3^ENST00000382841.2"  ; Parent "WASH3P--IQSEC3^IQSEC3^ENSG00000120645.12"  ; ccdsid "CCDS31725.1"  ; exon_id "ENSE00003622153.1"  ; exon_number 3 ; gene_id "WASH3P--IQSEC3^IQSEC3^ENSG00000120645.12"  ; gene_name IQSEC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167975.5"  ; havana_transcript "OTTHUMT00000397383.2"  ; hgnc_id "HGNC:29193"  ; level 2 ; orig_coord_info "chr12,138273,139354,+"  ; protein_id "ENSP00000372292.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "WASH3P--IQSEC3^ENST00000382841.2"  ; transcript_name "IQSEC3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
WASHC1--IQSEC3	HAVANA	gene	15424	29099	.	+	.	FI_gene_label "IQSEC3^ENSG00000120645.12"  ; ID "WASHC1--IQSEC3^IQSEC3^ENSG00000120645.12"  ; ccdsid "CCDS31725.1"  ; exon_id "ENSE00003622153.1"  ; exon_number 3 ; gene_id "WASHC1--IQSEC3^IQSEC3^ENSG00000120645.12"  ; gene_name IQSEC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167975.5"  ; havana_transcript "OTTHUMT00000397383.2"  ; hgnc_id "HGNC:29193"  ; level 2 ; orig_coord_info "chr12,138273,139354,+"  ; protein_id "ENSP00000372292.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "WASHC1--IQSEC3^ENST00000382841.2"  ; transcript_name "IQSEC3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
WASHC1--IQSEC3	HAVANA	mRNA	15424	29099	.	+	.	FI_gene_label "IQSEC3^ENSG00000120645.12"  ; ID "WASHC1--IQSEC3^ENST00000382841.2"  ; Parent "WASHC1--IQSEC3^IQSEC3^ENSG00000120645.12"  ; ccdsid "CCDS31725.1"  ; exon_id "ENSE00003622153.1"  ; exon_number 3 ; gene_id "WASHC1--IQSEC3^IQSEC3^ENSG00000120645.12"  ; gene_name IQSEC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167975.5"  ; havana_transcript "OTTHUMT00000397383.2"  ; hgnc_id "HGNC:29193"  ; level 2 ; orig_coord_info "chr12,138273,139354,+"  ; protein_id "ENSP00000372292.2"  ; tag basic appris_alternative_2 CCDS ; transcript_id "WASHC1--IQSEC3^ENST00000382841.2"  ; transcript_name "IQSEC3-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
WASHC1--IQSEC3	HAVANA	gene	4444	10753	.	+	.	FI_gene_label "WASHC1^ENSG00000181404.17"  ; ID "WASHC1--IQSEC3^WASHC1^ENSG00000181404.17"  ; ccdsid "CCDS78375.1"  ; exon_id "ENSE00001724555.1"  ; exon_number 2 ; gene_id "WASHC1--IQSEC3^WASHC1^ENSG00000181404.17"  ; gene_name WASHC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019420.5"  ; havana_transcript "OTTHUMT00000051448.4"  ; hgnc_id "HGNC:24361"  ; level 2 ; orig_coord_info "chr9,24851,24999,-"  ; protein_id "ENSP00000485627.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "WASHC1--IQSEC3^ENST00000442898.5"  ; transcript_name "WASHC1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
WASHC1--IQSEC3	HAVANA	mRNA	4444	10753	.	+	.	FI_gene_label "WASHC1^ENSG00000181404.17"  ; ID "WASHC1--IQSEC3^ENST00000442898.5"  ; Parent "WASHC1--IQSEC3^WASHC1^ENSG00000181404.17"  ; ccdsid "CCDS78375.1"  ; exon_id "ENSE00001724555.1"  ; exon_number 2 ; gene_id "WASHC1--IQSEC3^WASHC1^ENSG00000181404.17"  ; gene_name WASHC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019420.5"  ; havana_transcript "OTTHUMT00000051448.4"  ; hgnc_id "HGNC:24361"  ; level 2 ; orig_coord_info "chr9,24851,24999,-"  ; protein_id "ENSP00000485627.1"  ; tag basic appris_principal_1 CCDS ; transcript_id "WASHC1--IQSEC3^ENST00000442898.5"  ; transcript_name "WASHC1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
AL669831.4--SEPTIN14	HAVANA	gene	1001	5872	.	+	.	FI_gene_label "AL669831.4^ENSG00000230092.7"  ; ID "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; exon_id "ENSE00001746491.1"  ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; gene_name "AL669831.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3"  ; havana_transcript "OTTHUMT00000448550.2"  ; level 2 ; orig_coord_info "chr1,817373,817712,-"  ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4"  ; transcript_name "AL669831.4-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
AL669831.4--SEPTIN14	HAVANA	RNA	1001	5872	.	+	.	FI_gene_label "AL669831.4^ENSG00000230092.7"  ; ID "AL669831.4--SEPTIN14^ENST00000447500.4"  ; Parent "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; exon_id "ENSE00001746491.1"  ; exon_number 1 ; gene_id "AL669831.4--SEPTIN14^AL669831.4^ENSG00000230092.7"  ; gene_name "AL669831.4"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000002403.3"  ; havana_transcript "OTTHUMT00000448550.2"  ; level 2 ; orig_coord_info "chr1,817373,817712,-"  ; tag basic ; transcript_id "AL669831.4--SEPTIN14^ENST00000447500.4"  ; transcript_name "AL669831.4-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
ANKH--HNRNPKP5	HAVANA	gene	28418	28670	.	+	.	FI_gene_label "HNRNPKP5^ENSG00000250662.1"  ; ID "ANKH--HNRNPKP5^HNRNPKP5^ENSG00000250662.1"  ; exon_id "ENSE00002052678.1"  ; exon_number 1 ; gene_id "ANKH--HNRNPKP5^HNRNPKP5^ENSG00000250662.1"  ; gene_name HNRNPKP5 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000161816.1"  ; havana_transcript "OTTHUMT00000366151.1"  ; hgnc_id "HGNC:42378"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr5,14877667,14877919,-"  ; tag pseudo_consens basic ; transcript_id "ANKH--HNRNPKP5^ENST00000515300.1"  ; transcript_name "HNRNPKP5-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
ANKH--HNRNPKP5	HAVANA	RNA	28418	28670	.	+	.	FI_gene_label "HNRNPKP5^ENSG00000250662.1"  ; ID "ANKH--HNRNPKP5^ENST00000515300.1"  ; Parent "ANKH--HNRNPKP5^HNRNPKP5^ENSG00000250662.1"  ; exon_id "ENSE00002052678.1"  ; exon_number 1 ; gene_id "ANKH--HNRNPKP5^HNRNPKP5^ENSG00000250662.1"  ; gene_name HNRNPKP5 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000161816.1"  ; havana_transcript "OTTHUMT00000366151.1"  ; hgnc_id "HGNC:42378"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr5,14877667,14877919,-"  ; tag pseudo_consens basic ; transcript_id "ANKH--HNRNPKP5^ENST00000515300.1"  ; transcript_name "HNRNPKP5-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TCF7L2--AL158212.1	HAVANA	gene	28779	31093	.	+	.	FI_gene_label "AL158212.1^ENSG00000225292.2"  ; ID "TCF7L2--AL158212.1^AL158212.1^ENSG00000225292.2"  ; exon_id "ENSE00001736417.2"  ; exon_number 1 ; gene_id "TCF7L2--AL158212.1^AL158212.1^ENSG00000225292.2"  ; gene_name "AL158212.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000019067.2"  ; havana_transcript "OTTHUMT00000050408.2"  ; level 2 ; orig_coord_info "chr10,112888735,112888807,+"  ; tag basic ; transcript_id "TCF7L2--AL158212.1^ENST00000428766.2"  ; transcript_name "AL158212.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TCF7L2--AL158212.1	HAVANA	RNA	28779	31093	.	+	.	FI_gene_label "AL158212.1^ENSG00000225292.2"  ; ID "TCF7L2--AL158212.1^ENST00000428766.2"  ; Parent "TCF7L2--AL158212.1^AL158212.1^ENSG00000225292.2"  ; exon_id "ENSE00001736417.2"  ; exon_number 1 ; gene_id "TCF7L2--AL158212.1^AL158212.1^ENSG00000225292.2"  ; gene_name "AL158212.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000019067.2"  ; havana_transcript "OTTHUMT00000050408.2"  ; level 2 ; orig_coord_info "chr10,112888735,112888807,+"  ; tag basic ; transcript_id "TCF7L2--AL158212.1^ENST00000428766.2"  ; transcript_name "AL158212.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
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
L1 and L2 created: 
WASH3P--IQSEC3	HAVANA	gene	1016	5959	.	+	.	FI_gene_label "WASH3P^ENSG00000185596.16"  ; ID "WASH3P--IQSEC3^WASH3P^ENSG00000185596.16"  ; exon_id "ENSE00002534869.1"  ; exon_number 1 ; gene_id "WASH3P--IQSEC3^WASH3P^ENSG00000185596.16"  ; gene_name WASH3P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000172275.2"  ; havana_transcript "OTTHUMT00000417607.1"  ; hgnc_id "HGNC:24362"  ; level 2 ; orig_coord_info "chr15,101961618,101961641,+"  ; transcript_id "WASH3P--IQSEC3^ENST00000354296.9"  ; transcript_name "WASH3P-201"  ; transcript_support_level 2 ; transcript_type processed_transcript
WASH3P--IQSEC3	HAVANA	RNA	1016	5959	.	+	.	FI_gene_label "WASH3P^ENSG00000185596.16"  ; ID "WASH3P--IQSEC3^ENST00000354296.9"  ; Parent "WASH3P--IQSEC3^WASH3P^ENSG00000185596.16"  ; exon_id "ENSE00002534869.1"  ; exon_number 1 ; gene_id "WASH3P--IQSEC3^WASH3P^ENSG00000185596.16"  ; gene_name WASH3P ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000172275.2"  ; havana_transcript "OTTHUMT00000417607.1"  ; hgnc_id "HGNC:24362"  ; level 2 ; orig_coord_info "chr15,101961618,101961641,+"  ; transcript_id "WASH3P--IQSEC3^ENST00000354296.9"  ; transcript_name "WASH3P-201"  ; transcript_support_level 2 ; transcript_type processed_transcript
145 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 ------------------------------
229 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