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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/320185fa9c3a83e9505480d7ed2bfb/.command.log
Size: 35.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_ri-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/163bdf1ef0252749091c7df7e35b7b/fi_workdir/659_ri-T1-TRNA-1_B23MHV2LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/320185fa9c3a83e9505480d7ed2bfb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/320185fa9c3a83e9505480d7ed2bfb/.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: 1871
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1871
=> 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:1871
  => 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: 
AC131094.1--LRMDA	HAVANA	gene	12835	32102	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "AC131094.1--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "AC131094.1--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "AC131094.1--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC131094.1--LRMDA	HAVANA	mRNA	12835	32102	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "AC131094.1--LRMDA^ENST00000372499.5"  ; Parent "AC131094.1--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "AC131094.1--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "AC131094.1--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AL136367.1--LRMDA	HAVANA	gene	8546	27813	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "AL136367.1--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "AL136367.1--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "AL136367.1--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AL136367.1--LRMDA	HAVANA	mRNA	8546	27813	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "AL136367.1--LRMDA^ENST00000372499.5"  ; Parent "AL136367.1--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "AL136367.1--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "AL136367.1--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AL353752.1--LRMDA	HAVANA	gene	8670	27937	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "AL353752.1--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "AL353752.1--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "AL353752.1--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AL353752.1--LRMDA	HAVANA	mRNA	8670	27937	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "AL353752.1--LRMDA^ENST00000372499.5"  ; Parent "AL353752.1--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "AL353752.1--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "AL353752.1--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FGFR3--TACC3	HAVANA	gene	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7"  ; havana_transcript "OTTHUMT00000495785.1"  ; hgnc_id "HGNC:3690"  ; level 2 ; orig_coord_info "chr4,1793935,1794043,+"  ; protein_id "ENSP00000260795.3"  ; transcript_id "FGFR3--TACC3^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--TACC3	HAVANA	mRNA	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--TACC3^ENST00000260795.8"  ; Parent "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20"  ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7"  ; havana_transcript "OTTHUMT00000495785.1"  ; hgnc_id "HGNC:3690"  ; level 2 ; orig_coord_info "chr4,1793935,1794043,+"  ; protein_id "ENSP00000260795.3"  ; transcript_id "FGFR3--TACC3^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
FGFR3--TACC3	HAVANA	gene	16535	31742	.	+	.	FI_gene_label "TACC3^ENSG00000013810.20"  ; ID "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; ccdsid "CCDS3352.1"  ; exon_id "ENSE00003597099.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25"  ; havana_transcript "OTTHUMT00000203730.4"  ; hgnc_id "HGNC:11524"  ; level 2 ; orig_coord_info "chr4,1723422,1723583,+"  ; protein_id "ENSP00000326550.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9"  ; transcript_name "TACC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--TACC3	HAVANA	mRNA	16535	31742	.	+	.	FI_gene_label "TACC3^ENSG00000013810.20"  ; ID "FGFR3--TACC3^ENST00000313288.9"  ; Parent "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; ccdsid "CCDS3352.1"  ; exon_id "ENSE00003597099.1"  ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20"  ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25"  ; havana_transcript "OTTHUMT00000203730.4"  ; hgnc_id "HGNC:11524"  ; level 2 ; orig_coord_info "chr4,1723422,1723583,+"  ; protein_id "ENSP00000326550.4"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9"  ; transcript_name "TACC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
GUCY1B2--NKAIN2	HAVANA	gene	24657	32303	.	+	.	FI_gene_label "NKAIN2^ENSG00000188580.15"  ; ID "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15"  ; exon_id "ENSE00003552753.1"  ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15"  ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3"  ; havana_transcript "OTTHUMT00000042056.1"  ; hgnc_id "HGNC:16443"  ; level 2 ; orig_coord_info "chr6,123804201,123804254,+"  ; protein_id "ENSP00000357401.1"  ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5"  ; transcript_name "NKAIN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
GUCY1B2--NKAIN2	HAVANA	mRNA	24657	32303	.	+	.	FI_gene_label "NKAIN2^ENSG00000188580.15"  ; ID "GUCY1B2--NKAIN2^ENST00000368416.5"  ; Parent "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15"  ; exon_id "ENSE00003552753.1"  ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15"  ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3"  ; havana_transcript "OTTHUMT00000042056.1"  ; hgnc_id "HGNC:16443"  ; level 2 ; orig_coord_info "chr6,123804201,123804254,+"  ; protein_id "ENSP00000357401.1"  ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5"  ; transcript_name "NKAIN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LINC-ROR--LRMDA	HAVANA	gene	18026	37293	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "LINC-ROR--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "LINC-ROR--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "LINC-ROR--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LINC-ROR--LRMDA	HAVANA	mRNA	18026	37293	.	+	.	FI_gene_label "LRMDA^ENSG00000148655.15"  ; ID "LINC-ROR--LRMDA^ENST00000372499.5"  ; Parent "LINC-ROR--LRMDA^LRMDA^ENSG00000148655.15"  ; ccdsid "CCDS7351.1"  ; exon_id "ENSE00001457957.1"  ; exon_number 1 ; gene_id "LINC-ROR--LRMDA^LRMDA^ENSG00000148655.15"  ; gene_name LRMDA ; gene_type protein_coding ; havana_gene "OTTHUMG00000018532.5"  ; havana_transcript "OTTHUMT00000048839.1"  ; hgnc_id "HGNC:23405"  ; level 2 ; orig_coord_info "chr10,75782976,75783022,+"  ; protein_id "ENSP00000361577.1"  ; tag basic CCDS ; transcript_id "LINC-ROR--LRMDA^ENST00000372499.5"  ; transcript_name "LRMDA-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LINC00381--NKAIN2	HAVANA	gene	10218	17864	.	+	.	FI_gene_label "NKAIN2^ENSG00000188580.15"  ; ID "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15"  ; exon_id "ENSE00003552753.1"  ; exon_number 1 ; gene_id "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15"  ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3"  ; havana_transcript "OTTHUMT00000042056.1"  ; hgnc_id "HGNC:16443"  ; level 2 ; orig_coord_info "chr6,123804201,123804254,+"  ; protein_id "ENSP00000357401.1"  ; tag basic ; transcript_id "LINC00381--NKAIN2^ENST00000368416.5"  ; transcript_name "NKAIN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
LINC00381--NKAIN2	HAVANA	mRNA	10218	17864	.	+	.	FI_gene_label "NKAIN2^ENSG00000188580.15"  ; ID "LINC00381--NKAIN2^ENST00000368416.5"  ; Parent "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15"  ; exon_id "ENSE00003552753.1"  ; exon_number 1 ; gene_id "LINC00381--NKAIN2^NKAIN2^ENSG00000188580.15"  ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3"  ; havana_transcript "OTTHUMT00000042056.1"  ; hgnc_id "HGNC:16443"  ; level 2 ; orig_coord_info "chr6,123804201,123804254,+"  ; protein_id "ENSP00000357401.1"  ; tag basic ; transcript_id "LINC00381--NKAIN2^ENST00000368416.5"  ; transcript_name "NKAIN2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MZT1--HSPH1	HAVANA	gene	8716	28022	.	+	.	FI_gene_label "HSPH1^ENSG00000120694.20"  ; ID "MZT1--HSPH1^HSPH1^ENSG00000120694.20"  ; ccdsid "CCDS9340.1"  ; exon_id "ENSE00003896099.1"  ; exon_number 1 ; gene_id "MZT1--HSPH1^HSPH1^ENSG00000120694.20"  ; gene_name HSPH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016685.6"  ; havana_transcript "OTTHUMT00000044384.3"  ; hgnc_id "HGNC:16969"  ; level 2 ; orig_coord_info "chr13,31161476,31161582,-"  ; protein_id "ENSP00000318687.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MZT1--HSPH1^ENST00000320027.10"  ; transcript_name "HSPH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MZT1--HSPH1	HAVANA	mRNA	8716	28022	.	+	.	FI_gene_label "HSPH1^ENSG00000120694.20"  ; ID "MZT1--HSPH1^ENST00000320027.10"  ; Parent "MZT1--HSPH1^HSPH1^ENSG00000120694.20"  ; ccdsid "CCDS9340.1"  ; exon_id "ENSE00003896099.1"  ; exon_number 1 ; gene_id "MZT1--HSPH1^HSPH1^ENSG00000120694.20"  ; gene_name HSPH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016685.6"  ; havana_transcript "OTTHUMT00000044384.3"  ; hgnc_id "HGNC:16969"  ; level 2 ; orig_coord_info "chr13,31161476,31161582,-"  ; protein_id "ENSP00000318687.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MZT1--HSPH1^ENST00000320027.10"  ; transcript_name "HSPH1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MZT1--HSPH1	HAVANA	gene	1001	5231	.	+	.	FI_gene_label "MZT1^ENSG00000204899.6"  ; ID "MZT1--HSPH1^MZT1^ENSG00000204899.6"  ; ccdsid "CCDS31990.1"  ; exon_id "ENSE00001829898.2"  ; exon_number 1 ; gene_id "MZT1--HSPH1^MZT1^ENSG00000204899.6"  ; gene_name MZT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017069.2"  ; havana_transcript "OTTHUMT00000045249.2"  ; hgnc_id "HGNC:33830"  ; level 2 ; orig_coord_info "chr13,72727524,72727602,-"  ; protein_id "ENSP00000367049.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MZT1--HSPH1^ENST00000377818.4"  ; transcript_name "MZT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MZT1--HSPH1	HAVANA	mRNA	1001	5231	.	+	.	FI_gene_label "MZT1^ENSG00000204899.6"  ; ID "MZT1--HSPH1^ENST00000377818.4"  ; Parent "MZT1--HSPH1^MZT1^ENSG00000204899.6"  ; ccdsid "CCDS31990.1"  ; exon_id "ENSE00001829898.2"  ; exon_number 1 ; gene_id "MZT1--HSPH1^MZT1^ENSG00000204899.6"  ; gene_name MZT1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017069.2"  ; havana_transcript "OTTHUMT00000045249.2"  ; hgnc_id "HGNC:33830"  ; level 2 ; orig_coord_info "chr13,72727524,72727602,-"  ; protein_id "ENSP00000367049.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MZT1--HSPH1^ENST00000377818.4"  ; transcript_name "MZT1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PPP6R2--GRAP2	HAVANA	gene	2300	24449	.	+	.	FI_gene_label "PPP6R2^ENSG00000100239.16"  ; ID "PPP6R2--GRAP2^PPP6R2^ENSG00000100239.16"  ; exon_id "ENSE00003893516.1"  ; exon_number 4 ; gene_id "PPP6R2--GRAP2^PPP6R2^ENSG00000100239.16"  ; gene_name PPP6R2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150199.6"  ; havana_transcript "OTTHUMT00000316809.1"  ; hgnc_id "HGNC:19253"  ; level 2 ; orig_coord_info "chr22,50393909,50394135,+"  ; protein_id "ENSP00000216061.5"  ; tag basic appris_alternative_2 ; transcript_id "PPP6R2--GRAP2^ENST00000216061.9"  ; transcript_name "PPP6R2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PPP6R2--GRAP2	HAVANA	mRNA	2300	24449	.	+	.	FI_gene_label "PPP6R2^ENSG00000100239.16"  ; ID "PPP6R2--GRAP2^ENST00000216061.9"  ; Parent "PPP6R2--GRAP2^PPP6R2^ENSG00000100239.16"  ; exon_id "ENSE00003893516.1"  ; exon_number 4 ; gene_id "PPP6R2--GRAP2^PPP6R2^ENSG00000100239.16"  ; gene_name PPP6R2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150199.6"  ; havana_transcript "OTTHUMT00000316809.1"  ; hgnc_id "HGNC:19253"  ; level 2 ; orig_coord_info "chr22,50393909,50394135,+"  ; protein_id "ENSP00000216061.5"  ; tag basic appris_alternative_2 ; transcript_id "PPP6R2--GRAP2^ENST00000216061.9"  ; transcript_name "PPP6R2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PPP6R2--GRAP2	HAVANA	gene	28149	42014	.	+	.	FI_gene_label "GRAP2^ENSG00000100351.17"  ; ID "PPP6R2--GRAP2^GRAP2^ENSG00000100351.17"  ; ccdsid "CCDS13999.1"  ; exon_id "ENSE00003491090.1"  ; exon_number 2 ; gene_id "PPP6R2--GRAP2^GRAP2^ENSG00000100351.17"  ; gene_name GRAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151097.3"  ; havana_transcript "OTTHUMT00000321295.2"  ; hgnc_id "HGNC:4563"  ; level 2 ; orig_coord_info "chr22,39947107,39947184,+"  ; protein_id "ENSP00000339186.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPP6R2--GRAP2^ENST00000344138.9"  ; transcript_name "GRAP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PPP6R2--GRAP2	HAVANA	mRNA	28149	42014	.	+	.	FI_gene_label "GRAP2^ENSG00000100351.17"  ; ID "PPP6R2--GRAP2^ENST00000344138.9"  ; Parent "PPP6R2--GRAP2^GRAP2^ENSG00000100351.17"  ; ccdsid "CCDS13999.1"  ; exon_id "ENSE00003491090.1"  ; exon_number 2 ; gene_id "PPP6R2--GRAP2^GRAP2^ENSG00000100351.17"  ; gene_name GRAP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151097.3"  ; havana_transcript "OTTHUMT00000321295.2"  ; hgnc_id "HGNC:4563"  ; level 2 ; orig_coord_info "chr22,39947107,39947184,+"  ; protein_id "ENSP00000339186.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPP6R2--GRAP2^ENST00000344138.9"  ; transcript_name "GRAP2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SCAF4--FTCD	HAVANA	gene	1001	20248	.	+	.	FI_gene_label "SCAF4^ENSG00000156304.15"  ; ID "SCAF4--FTCD^SCAF4^ENSG00000156304.15"  ; ccdsid "CCDS33537.1"  ; exon_id "ENSE00003892481.1"  ; exon_number 1 ; gene_id "SCAF4--FTCD^SCAF4^ENSG00000156304.15"  ; gene_name SCAF4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000084903.6"  ; havana_transcript "OTTHUMT00000192659.2"  ; hgnc_id "HGNC:19304"  ; level 2 ; orig_coord_info "chr21,31731663,31731692,-"  ; protein_id "ENSP00000286835.7"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "SCAF4--FTCD^ENST00000286835.12"  ; transcript_name "SCAF4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SCAF4--FTCD	HAVANA	mRNA	1001	20248	.	+	.	FI_gene_label "SCAF4^ENSG00000156304.15"  ; ID "SCAF4--FTCD^ENST00000286835.12"  ; Parent "SCAF4--FTCD^SCAF4^ENSG00000156304.15"  ; ccdsid "CCDS33537.1"  ; exon_id "ENSE00003892481.1"  ; exon_number 1 ; gene_id "SCAF4--FTCD^SCAF4^ENSG00000156304.15"  ; gene_name SCAF4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000084903.6"  ; havana_transcript "OTTHUMT00000192659.2"  ; hgnc_id "HGNC:19304"  ; level 2 ; orig_coord_info "chr21,31731663,31731692,-"  ; protein_id "ENSP00000286835.7"  ; tag basic MANE_Select appris_principal_3 CCDS ; transcript_id "SCAF4--FTCD^ENST00000286835.12"  ; transcript_name "SCAF4-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
SCAF4--FTCD	HAVANA	gene	23261	36188	.	+	.	FI_gene_label "FTCD^ENSG00000160282.14"  ; ID "SCAF4--FTCD^FTCD^ENSG00000160282.14"  ; ccdsid "CCDS13731.1"  ; exon_id "ENSE00003615828.1"  ; exon_number 1 ; gene_id "SCAF4--FTCD^FTCD^ENSG00000160282.14"  ; gene_name FTCD ; gene_type protein_coding ; havana_gene "OTTHUMG00000090488.3"  ; havana_transcript "OTTHUMT00000206962.1"  ; hgnc_id "HGNC:3974"  ; level 2 ; orig_coord_info "chr21,46155470,46155523,-"  ; protein_id "ENSP00000291670.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "SCAF4--FTCD^ENST00000291670.9"  ; transcript_name "FTCD-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SCAF4--FTCD	HAVANA	mRNA	23261	36188	.	+	.	FI_gene_label "FTCD^ENSG00000160282.14"  ; ID "SCAF4--FTCD^ENST00000291670.9"  ; Parent "SCAF4--FTCD^FTCD^ENSG00000160282.14"  ; ccdsid "CCDS13731.1"  ; exon_id "ENSE00003615828.1"  ; exon_number 1 ; gene_id "SCAF4--FTCD^FTCD^ENSG00000160282.14"  ; gene_name FTCD ; gene_type protein_coding ; havana_gene "OTTHUMG00000090488.3"  ; havana_transcript "OTTHUMT00000206962.1"  ; hgnc_id "HGNC:3974"  ; level 2 ; orig_coord_info "chr21,46155470,46155523,-"  ; protein_id "ENSP00000291670.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "SCAF4--FTCD^ENST00000291670.9"  ; transcript_name "FTCD-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: 
AC131094.1--LRMDA	HAVANA	gene	2373	4862	.	+	.	FI_gene_label "AC131094.1^ENSG00000249945.2"  ; ID "AC131094.1--LRMDA^AC131094.1^ENSG00000249945.2"  ; exon_id "ENSE00002033385.1"  ; exon_number 1 ; gene_id "AC131094.1--LRMDA^AC131094.1^ENSG00000249945.2"  ; gene_name "AC131094.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000160767.2"  ; havana_transcript "OTTHUMT00000362196.1"  ; level 1 ; orig_coord_info "chr4,175466535,175466697,-"  ; tag exp_conf ; transcript_id "AC131094.1--LRMDA^ENST00000506984.1"  ; transcript_name "AC131094.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
AC131094.1--LRMDA	HAVANA	RNA	2373	4862	.	+	.	FI_gene_label "AC131094.1^ENSG00000249945.2"  ; ID "AC131094.1--LRMDA^ENST00000506984.1"  ; Parent "AC131094.1--LRMDA^AC131094.1^ENSG00000249945.2"  ; exon_id "ENSE00002033385.1"  ; exon_number 1 ; gene_id "AC131094.1--LRMDA^AC131094.1^ENSG00000249945.2"  ; gene_name "AC131094.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000160767.2"  ; havana_transcript "OTTHUMT00000362196.1"  ; level 1 ; orig_coord_info "chr4,175466535,175466697,-"  ; tag exp_conf ; transcript_id "AC131094.1--LRMDA^ENST00000506984.1"  ; transcript_name "AC131094.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
AL136367.1--LRMDA	ENSEMBL	gene	1001	1136	.	+	.	FI_gene_label "AL136367.1^ENSG00000212421.1"  ; ID "AL136367.1--LRMDA^AL136367.1^ENSG00000212421.1"  ; exon_id "ENSE00001508903.1"  ; exon_number 1 ; gene_id "AL136367.1--LRMDA^AL136367.1^ENSG00000212421.1"  ; gene_name "AL136367.1"  ; gene_type snoRNA ; level 3 ; orig_coord_info "chr9,87260450,87260585,+"  ; tag basic ; transcript_id "AL136367.1--LRMDA^ENST00000391119.1"  ; transcript_name "AL136367.1-201"  ; transcript_support_level NA ; transcript_type snoRNA
AL136367.1--LRMDA	ENSEMBL	RNA	1001	1136	.	+	.	FI_gene_label "AL136367.1^ENSG00000212421.1"  ; ID "AL136367.1--LRMDA^ENST00000391119.1"  ; Parent "AL136367.1--LRMDA^AL136367.1^ENSG00000212421.1"  ; exon_id "ENSE00001508903.1"  ; exon_number 1 ; gene_id "AL136367.1--LRMDA^AL136367.1^ENSG00000212421.1"  ; gene_name "AL136367.1"  ; gene_type snoRNA ; level 3 ; orig_coord_info "chr9,87260450,87260585,+"  ; tag basic ; transcript_id "AL136367.1--LRMDA^ENST00000391119.1"  ; transcript_name "AL136367.1-201"  ; transcript_support_level NA ; transcript_type snoRNA
L1 and L2 created: 
AL353752.1--LRMDA	HAVANA	gene	1001	1260	.	+	.	FI_gene_label "AL353752.1^ENSG00000228373.2"  ; ID "AL353752.1--LRMDA^AL353752.1^ENSG00000228373.2"  ; exon_id "ENSE00001683183.2"  ; exon_number 1 ; gene_id "AL353752.1--LRMDA^AL353752.1^ENSG00000228373.2"  ; gene_name "AL353752.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000020146.2"  ; havana_transcript "OTTHUMT00000052933.2"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr9,87423634,87423893,+"  ; tag pseudo_consens basic ; transcript_id "AL353752.1--LRMDA^ENST00000454946.2"  ; transcript_name "AL353752.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
AL353752.1--LRMDA	HAVANA	RNA	1001	1260	.	+	.	FI_gene_label "AL353752.1^ENSG00000228373.2"  ; ID "AL353752.1--LRMDA^ENST00000454946.2"  ; Parent "AL353752.1--LRMDA^AL353752.1^ENSG00000228373.2"  ; exon_id "ENSE00001683183.2"  ; exon_number 1 ; gene_id "AL353752.1--LRMDA^AL353752.1^ENSG00000228373.2"  ; gene_name "AL353752.1"  ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000020146.2"  ; havana_transcript "OTTHUMT00000052933.2"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr9,87423634,87423893,+"  ; tag pseudo_consens basic ; transcript_id "AL353752.1--LRMDA^ENST00000454946.2"  ; transcript_name "AL353752.1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
GUCY1B2--NKAIN2	HAVANA	gene	2157	15439	.	+	.	FI_gene_label "GUCY1B2^ENSG00000123201.14"  ; ID "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14"  ; exon_id "ENSE00001531871.1"  ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14"  ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5"  ; havana_transcript "OTTHUMT00000045017.2"  ; hgnc_id "HGNC:4686"  ; level 2 ; orig_coord_info "chr13,51065951,51066207,-"  ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6"  ; transcript_name "GUCY1B2-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
GUCY1B2--NKAIN2	HAVANA	RNA	2157	15439	.	+	.	FI_gene_label "GUCY1B2^ENSG00000123201.14"  ; ID "GUCY1B2--NKAIN2^ENST00000389600.6"  ; Parent "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14"  ; exon_id "ENSE00001531871.1"  ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14"  ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5"  ; havana_transcript "OTTHUMT00000045017.2"  ; hgnc_id "HGNC:4686"  ; level 2 ; orig_coord_info "chr13,51065951,51066207,-"  ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6"  ; transcript_name "GUCY1B2-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created: 
LINC-ROR--LRMDA	HAVANA	gene	1001	10616	.	+	.	FI_gene_label "LINC-ROR^ENSG00000258609.3"  ; ID "LINC-ROR--LRMDA^LINC-ROR^ENSG00000258609.3"  ; exon_id "ENSE00002471664.1"  ; exon_number 1 ; gene_id "LINC-ROR--LRMDA^LINC-ROR^ENSG00000258609.3"  ; gene_name "LINC-ROR"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000171587.3"  ; havana_transcript "OTTHUMT00000414322.3"  ; hgnc_id "HGNC:43773"  ; level 2 ; orig_coord_info "chr18,57071904,57072119,-"  ; tag basic ; transcript_id "LINC-ROR--LRMDA^ENST00000553704.3"  ; transcript_name "LINC-ROR-201"  ; transcript_support_level 1 ; transcript_type lncRNA
LINC-ROR--LRMDA	HAVANA	RNA	1001	10616	.	+	.	FI_gene_label "LINC-ROR^ENSG00000258609.3"  ; ID "LINC-ROR--LRMDA^ENST00000553704.3"  ; Parent "LINC-ROR--LRMDA^LINC-ROR^ENSG00000258609.3"  ; exon_id "ENSE00002471664.1"  ; exon_number 1 ; gene_id "LINC-ROR--LRMDA^LINC-ROR^ENSG00000258609.3"  ; gene_name "LINC-ROR"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000171587.3"  ; havana_transcript "OTTHUMT00000414322.3"  ; hgnc_id "HGNC:43773"  ; level 2 ; orig_coord_info "chr18,57071904,57072119,-"  ; tag basic ; transcript_id "LINC-ROR--LRMDA^ENST00000553704.3"  ; transcript_name "LINC-ROR-201"  ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created: 
LINC00381--NKAIN2	HAVANA	gene	1016	4365	.	+	.	FI_gene_label "LINC00381^ENSG00000226240.2"  ; ID "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2"  ; exon_id "ENSE00001743371.1"  ; exon_number 1 ; gene_id "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2"  ; gene_name LINC00381 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017081.2"  ; havana_transcript "OTTHUMT00000045275.1"  ; hgnc_id "HGNC:42708"  ; level 2 ; orig_coord_info "chr13,74419173,74419228,+"  ; transcript_id "LINC00381--NKAIN2^ENST00000423629.1"  ; transcript_name "LINC00381-201"  ; transcript_support_level 5 ; transcript_type lncRNA
LINC00381--NKAIN2	HAVANA	RNA	1016	4365	.	+	.	FI_gene_label "LINC00381^ENSG00000226240.2"  ; ID "LINC00381--NKAIN2^ENST00000423629.1"  ; Parent "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2"  ; exon_id "ENSE00001743371.1"  ; exon_number 1 ; gene_id "LINC00381--NKAIN2^LINC00381^ENSG00000226240.2"  ; gene_name LINC00381 ; gene_type lncRNA ; havana_gene "OTTHUMG00000017081.2"  ; havana_transcript "OTTHUMT00000045275.1"  ; hgnc_id "HGNC:42708"  ; level 2 ; orig_coord_info "chr13,74419173,74419228,+"  ; transcript_id "LINC00381--NKAIN2^ENST00000423629.1"  ; transcript_name "LINC00381-201"  ; transcript_support_level 5 ; transcript_type lncRNA
179 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 ------------------------------
200 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 16 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