File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/610c01b70edb7a61daf9a47b1a317e/.command.out
Size
32.8 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (aih-tih-sc-d45d48-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: 1528
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1528
=> 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:1528
  => 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: 
AC103810.3--TK1	HAVANA	gene	4278	10300	.	+	.	FI_gene_label "TK1^ENSG00000167900.12"  ; ID "AC103810.3--TK1^TK1^ENSG00000167900.12"  ; ccdsid "CCDS11754.1"  ; exon_id "ENSE00003843293.1"  ; exon_number 1 ; gene_id "AC103810.3--TK1^TK1^ENSG00000167900.12"  ; gene_name TK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150674.6"  ; havana_transcript "OTTHUMT00000319577.3"  ; hgnc_id "HGNC:11830"  ; level 2 ; orig_coord_info "chr17,78186929,78186994,-"  ; protein_id "ENSP00000301634.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC103810.3--TK1^ENST00000301634.12"  ; transcript_name "TK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC103810.3--TK1	HAVANA	mRNA	4278	10300	.	+	.	FI_gene_label "TK1^ENSG00000167900.12"  ; ID "AC103810.3--TK1^ENST00000301634.12"  ; Parent "AC103810.3--TK1^TK1^ENSG00000167900.12"  ; ccdsid "CCDS11754.1"  ; exon_id "ENSE00003843293.1"  ; exon_number 1 ; gene_id "AC103810.3--TK1^TK1^ENSG00000167900.12"  ; gene_name TK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150674.6"  ; havana_transcript "OTTHUMT00000319577.3"  ; hgnc_id "HGNC:11830"  ; level 2 ; orig_coord_info "chr17,78186929,78186994,-"  ; protein_id "ENSP00000301634.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC103810.3--TK1^ENST00000301634.12"  ; transcript_name "TK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP8--FBLN1	HAVANA	gene	23610	44687	.	+	.	FI_gene_label "FBLN1^ENSG00000077942.19"  ; ID "ARHGAP8--FBLN1^FBLN1^ENSG00000077942.19"  ; ccdsid "CCDS14069.1"  ; exon_id "ENSE00001873674.1"  ; exon_number 1 ; gene_id "ARHGAP8--FBLN1^FBLN1^ENSG00000077942.19"  ; gene_name FBLN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151340.4"  ; havana_transcript "OTTHUMT00000322289.1"  ; hgnc_id "HGNC:3600"  ; level 2 ; orig_coord_info "chr22,45502986,45503064,+"  ; protein_id "ENSP00000262722.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "ARHGAP8--FBLN1^ENST00000262722.11"  ; transcript_name "FBLN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGAP8--FBLN1	HAVANA	mRNA	23610	44687	.	+	.	FI_gene_label "FBLN1^ENSG00000077942.19"  ; ID "ARHGAP8--FBLN1^ENST00000262722.11"  ; Parent "ARHGAP8--FBLN1^FBLN1^ENSG00000077942.19"  ; ccdsid "CCDS14069.1"  ; exon_id "ENSE00001873674.1"  ; exon_number 1 ; gene_id "ARHGAP8--FBLN1^FBLN1^ENSG00000077942.19"  ; gene_name FBLN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151340.4"  ; havana_transcript "OTTHUMT00000322289.1"  ; hgnc_id "HGNC:3600"  ; level 2 ; orig_coord_info "chr22,45502986,45503064,+"  ; protein_id "ENSP00000262722.7"  ; tag basic appris_alternative_1 CCDS ; transcript_id "ARHGAP8--FBLN1^ENST00000262722.11"  ; transcript_name "FBLN1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP8--FBLN1	HAVANA	gene	1046	19964	.	+	.	FI_gene_label "ARHGAP8^ENSG00000241484.10"  ; ID "ARHGAP8--FBLN1^ARHGAP8^ENSG00000241484.10"  ; ccdsid "CCDS56233.1"  ; exon_id "ENSE00003685792.1"  ; exon_number 2 ; gene_id "ARHGAP8--FBLN1^ARHGAP8^ENSG00000241484.10"  ; gene_name ARHGAP8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000030234.13"  ; havana_transcript "OTTHUMT00000157074.2"  ; hgnc_id "HGNC:677"  ; level 1 ; orig_coord_info "chr22,44786528,44786606,+"  ; protein_id "ENSP00000337287.4"  ; tag basic exp_conf CCDS ; transcript_id "ARHGAP8--FBLN1^ENST00000336963.8"  ; transcript_name "ARHGAP8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGAP8--FBLN1	HAVANA	mRNA	1046	19964	.	+	.	FI_gene_label "ARHGAP8^ENSG00000241484.10"  ; ID "ARHGAP8--FBLN1^ENST00000336963.8"  ; Parent "ARHGAP8--FBLN1^ARHGAP8^ENSG00000241484.10"  ; ccdsid "CCDS56233.1"  ; exon_id "ENSE00003685792.1"  ; exon_number 2 ; gene_id "ARHGAP8--FBLN1^ARHGAP8^ENSG00000241484.10"  ; gene_name ARHGAP8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000030234.13"  ; havana_transcript "OTTHUMT00000157074.2"  ; hgnc_id "HGNC:677"  ; level 1 ; orig_coord_info "chr22,44786528,44786606,+"  ; protein_id "ENSP00000337287.4"  ; tag basic exp_conf CCDS ; transcript_id "ARHGAP8--FBLN1^ENST00000336963.8"  ; transcript_name "ARHGAP8-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BPTFP1--TK1	HAVANA	gene	4981	11003	.	+	.	FI_gene_label "TK1^ENSG00000167900.12"  ; ID "BPTFP1--TK1^TK1^ENSG00000167900.12"  ; ccdsid "CCDS11754.1"  ; exon_id "ENSE00003843293.1"  ; exon_number 1 ; gene_id "BPTFP1--TK1^TK1^ENSG00000167900.12"  ; gene_name TK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150674.6"  ; havana_transcript "OTTHUMT00000319577.3"  ; hgnc_id "HGNC:11830"  ; level 2 ; orig_coord_info "chr17,78186929,78186994,-"  ; protein_id "ENSP00000301634.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BPTFP1--TK1^ENST00000301634.12"  ; transcript_name "TK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BPTFP1--TK1	HAVANA	mRNA	4981	11003	.	+	.	FI_gene_label "TK1^ENSG00000167900.12"  ; ID "BPTFP1--TK1^ENST00000301634.12"  ; Parent "BPTFP1--TK1^TK1^ENSG00000167900.12"  ; ccdsid "CCDS11754.1"  ; exon_id "ENSE00003843293.1"  ; exon_number 1 ; gene_id "BPTFP1--TK1^TK1^ENSG00000167900.12"  ; gene_name TK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150674.6"  ; havana_transcript "OTTHUMT00000319577.3"  ; hgnc_id "HGNC:11830"  ; level 2 ; orig_coord_info "chr17,78186929,78186994,-"  ; protein_id "ENSP00000301634.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BPTFP1--TK1^ENST00000301634.12"  ; transcript_name "TK1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DSC2--CCDC68	HAVANA	gene	1102	26354	.	+	.	FI_gene_label "DSC2^ENSG00000134755.17"  ; ID "DSC2--CCDC68^DSC2^ENSG00000134755.17"  ; ccdsid "CCDS11893.1"  ; exon_id "ENSE00003889875.1"  ; exon_number 1 ; gene_id "DSC2--CCDC68^DSC2^ENSG00000134755.17"  ; gene_name DSC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131981.8"  ; havana_transcript "OTTHUMT00000254944.3"  ; hgnc_id "HGNC:3036"  ; level 2 ; orig_coord_info "chr18,31101903,31101971,-"  ; protein_id "ENSP00000251081.6"  ; tag basic CCDS ; transcript_id "DSC2--CCDC68^ENST00000251081.8"  ; transcript_name "DSC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DSC2--CCDC68	HAVANA	mRNA	1102	26354	.	+	.	FI_gene_label "DSC2^ENSG00000134755.17"  ; ID "DSC2--CCDC68^ENST00000251081.8"  ; Parent "DSC2--CCDC68^DSC2^ENSG00000134755.17"  ; ccdsid "CCDS11893.1"  ; exon_id "ENSE00003889875.1"  ; exon_number 1 ; gene_id "DSC2--CCDC68^DSC2^ENSG00000134755.17"  ; gene_name DSC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131981.8"  ; havana_transcript "OTTHUMT00000254944.3"  ; hgnc_id "HGNC:3036"  ; level 2 ; orig_coord_info "chr18,31101903,31101971,-"  ; protein_id "ENSP00000251081.6"  ; tag basic CCDS ; transcript_id "DSC2--CCDC68^ENST00000251081.8"  ; transcript_name "DSC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DSC2--CCDC68	HAVANA	gene	30634	43239	.	+	.	FI_gene_label "CCDC68^ENSG00000166510.14"  ; ID "DSC2--CCDC68^CCDC68^ENSG00000166510.14"  ; ccdsid "CCDS11959.1"  ; exon_id "ENSE00002840834.1"  ; exon_number 3 ; gene_id "DSC2--CCDC68^CCDC68^ENSG00000166510.14"  ; gene_name CCDC68 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132708.4"  ; havana_transcript "OTTHUMT00000448364.1"  ; hgnc_id "HGNC:24350"  ; level 2 ; orig_coord_info "chr18,54942675,54942791,-"  ; protein_id "ENSP00000337209.3"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "DSC2--CCDC68^ENST00000337363.8"  ; transcript_name "CCDC68-201"  ; transcript_support_level 2 ; transcript_type protein_coding
DSC2--CCDC68	HAVANA	mRNA	30634	43239	.	+	.	FI_gene_label "CCDC68^ENSG00000166510.14"  ; ID "DSC2--CCDC68^ENST00000337363.8"  ; Parent "DSC2--CCDC68^CCDC68^ENSG00000166510.14"  ; ccdsid "CCDS11959.1"  ; exon_id "ENSE00002840834.1"  ; exon_number 3 ; gene_id "DSC2--CCDC68^CCDC68^ENSG00000166510.14"  ; gene_name CCDC68 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132708.4"  ; havana_transcript "OTTHUMT00000448364.1"  ; hgnc_id "HGNC:24350"  ; level 2 ; orig_coord_info "chr18,54942675,54942791,-"  ; protein_id "ENSP00000337209.3"  ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "DSC2--CCDC68^ENST00000337363.8"  ; transcript_name "CCDC68-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
DSC2--LINC01929	HAVANA	gene	1102	26354	.	+	.	FI_gene_label "DSC2^ENSG00000134755.17"  ; ID "DSC2--LINC01929^DSC2^ENSG00000134755.17"  ; ccdsid "CCDS11893.1"  ; exon_id "ENSE00003889875.1"  ; exon_number 1 ; gene_id "DSC2--LINC01929^DSC2^ENSG00000134755.17"  ; gene_name DSC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131981.8"  ; havana_transcript "OTTHUMT00000254944.3"  ; hgnc_id "HGNC:3036"  ; level 2 ; orig_coord_info "chr18,31101903,31101971,-"  ; protein_id "ENSP00000251081.6"  ; tag basic CCDS ; transcript_id "DSC2--LINC01929^ENST00000251081.8"  ; transcript_name "DSC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DSC2--LINC01929	HAVANA	mRNA	1102	26354	.	+	.	FI_gene_label "DSC2^ENSG00000134755.17"  ; ID "DSC2--LINC01929^ENST00000251081.8"  ; Parent "DSC2--LINC01929^DSC2^ENSG00000134755.17"  ; ccdsid "CCDS11893.1"  ; exon_id "ENSE00003889875.1"  ; exon_number 1 ; gene_id "DSC2--LINC01929^DSC2^ENSG00000134755.17"  ; gene_name DSC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131981.8"  ; havana_transcript "OTTHUMT00000254944.3"  ; hgnc_id "HGNC:3036"  ; level 2 ; orig_coord_info "chr18,31101903,31101971,-"  ; protein_id "ENSP00000251081.6"  ; tag basic CCDS ; transcript_id "DSC2--LINC01929^ENST00000251081.8"  ; transcript_name "DSC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
INO80D--PLA2R1	HAVANA	gene	27803	67861	.	+	.	FI_gene_label "PLA2R1^ENSG00000153246.13"  ; ID "INO80D--PLA2R1^PLA2R1^ENSG00000153246.13"  ; ccdsid "CCDS33309.1"  ; exon_id "ENSE00003850718.1"  ; exon_number 1 ; gene_id "INO80D--PLA2R1^PLA2R1^ENSG00000153246.13"  ; gene_name PLA2R1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154087.4"  ; havana_transcript "OTTHUMT00000333820.3"  ; hgnc_id "HGNC:9042"  ; level 2 ; orig_coord_info "chr2,160062295,160062403,-"  ; protein_id "ENSP00000283243.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "INO80D--PLA2R1^ENST00000283243.13"  ; transcript_name "PLA2R1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
INO80D--PLA2R1	HAVANA	mRNA	27803	67861	.	+	.	FI_gene_label "PLA2R1^ENSG00000153246.13"  ; ID "INO80D--PLA2R1^ENST00000283243.13"  ; Parent "INO80D--PLA2R1^PLA2R1^ENSG00000153246.13"  ; ccdsid "CCDS33309.1"  ; exon_id "ENSE00003850718.1"  ; exon_number 1 ; gene_id "INO80D--PLA2R1^PLA2R1^ENSG00000153246.13"  ; gene_name PLA2R1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154087.4"  ; havana_transcript "OTTHUMT00000333820.3"  ; hgnc_id "HGNC:9042"  ; level 2 ; orig_coord_info "chr2,160062295,160062403,-"  ; protein_id "ENSP00000283243.7"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "INO80D--PLA2R1^ENST00000283243.13"  ; transcript_name "PLA2R1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
INO80D--PLA2R1	HAVANA	gene	1130	24802	.	+	.	FI_gene_label "INO80D^ENSG00000114933.16"  ; ID "INO80D--PLA2R1^INO80D^ENSG00000114933.16"  ; ccdsid "CCDS46500.1"  ; exon_id "ENSE00001621693.1"  ; exon_number 3 ; gene_id "INO80D--PLA2R1^INO80D^ENSG00000114933.16"  ; gene_name INO80D ; gene_type protein_coding ; havana_gene "OTTHUMG00000154649.4"  ; havana_transcript "OTTHUMT00000336459.2"  ; hgnc_id "HGNC:25997"  ; level 2 ; orig_coord_info "chr2,206062799,206063016,-"  ; protein_id "ENSP00000384198.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "INO80D--PLA2R1^ENST00000403263.6"  ; transcript_name "INO80D-201"  ; transcript_support_level 5 ; transcript_type protein_coding
INO80D--PLA2R1	HAVANA	mRNA	1130	24802	.	+	.	FI_gene_label "INO80D^ENSG00000114933.16"  ; ID "INO80D--PLA2R1^ENST00000403263.6"  ; Parent "INO80D--PLA2R1^INO80D^ENSG00000114933.16"  ; ccdsid "CCDS46500.1"  ; exon_id "ENSE00001621693.1"  ; exon_number 3 ; gene_id "INO80D--PLA2R1^INO80D^ENSG00000114933.16"  ; gene_name INO80D ; gene_type protein_coding ; havana_gene "OTTHUMG00000154649.4"  ; havana_transcript "OTTHUMT00000336459.2"  ; hgnc_id "HGNC:25997"  ; level 2 ; orig_coord_info "chr2,206062799,206063016,-"  ; protein_id "ENSP00000384198.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "INO80D--PLA2R1^ENST00000403263.6"  ; transcript_name "INO80D-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
NCBP1--AL391117.1	HAVANA	gene	19092	21437	.	+	.	FI_gene_label "NCBP1^ENSG00000136937.13"  ; ID "NCBP1--AL391117.1^NCBP1^ENSG00000136937.13"  ; exon_id "ENSE00001728703.1"  ; exon_number 1 ; gene_id "NCBP1--AL391117.1^NCBP1^ENSG00000136937.13"  ; gene_name NCBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020332.5"  ; havana_transcript "OTTHUMT00000053340.2"  ; hgnc_id "HGNC:7658"  ; level 2 ; orig_coord_info "chr9,97666763,97666877,+"  ; protein_id "ENSP00000364272.2"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "NCBP1--AL391117.1^ENST00000375130.2"  ; transcript_name "NCBP1-201"  ; transcript_support_level 3 ; transcript_type protein_coding
NCBP1--AL391117.1	HAVANA	mRNA	19092	21437	.	+	.	FI_gene_label "NCBP1^ENSG00000136937.13"  ; ID "NCBP1--AL391117.1^ENST00000375130.2"  ; Parent "NCBP1--AL391117.1^NCBP1^ENSG00000136937.13"  ; exon_id "ENSE00001728703.1"  ; exon_number 1 ; gene_id "NCBP1--AL391117.1^NCBP1^ENSG00000136937.13"  ; gene_name NCBP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020332.5"  ; havana_transcript "OTTHUMT00000053340.2"  ; hgnc_id "HGNC:7658"  ; level 2 ; orig_coord_info "chr9,97666763,97666877,+"  ; protein_id "ENSP00000364272.2"  ; tag mRNA_start_NF cds_start_NF ; transcript_id "NCBP1--AL391117.1^ENST00000375130.2"  ; transcript_name "NCBP1-201"  ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created: 
PPA1--AC048352.1	HAVANA	gene	1575	8612	.	+	.	FI_gene_label "PPA1^ENSG00000180817.12"  ; ID "PPA1--AC048352.1^PPA1^ENSG00000180817.12"  ; exon_id "ENSE00001552651.2"  ; exon_number 1 ; gene_id "PPA1--AC048352.1^PPA1^ENSG00000180817.12"  ; gene_name PPA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018399.3"  ; havana_transcript "OTTHUMT00000048493.2"  ; hgnc_id "HGNC:9226"  ; level 2 ; orig_coord_info "chr10,70233264,70233327,-"  ; protein_id "ENSP00000362327.4"  ; transcript_id "PPA1--AC048352.1^ENST00000373230.7"  ; transcript_name "PPA1-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
PPA1--AC048352.1	HAVANA	mRNA	1575	8612	.	+	.	FI_gene_label "PPA1^ENSG00000180817.12"  ; ID "PPA1--AC048352.1^ENST00000373230.7"  ; Parent "PPA1--AC048352.1^PPA1^ENSG00000180817.12"  ; exon_id "ENSE00001552651.2"  ; exon_number 1 ; gene_id "PPA1--AC048352.1^PPA1^ENSG00000180817.12"  ; gene_name PPA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018399.3"  ; havana_transcript "OTTHUMT00000048493.2"  ; hgnc_id "HGNC:9226"  ; level 2 ; orig_coord_info "chr10,70233264,70233327,-"  ; protein_id "ENSP00000362327.4"  ; transcript_id "PPA1--AC048352.1^ENST00000373230.7"  ; transcript_name "PPA1-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
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: 
AC103810.3--TK1	HAVANA	gene	1001	1096	.	+	.	FI_gene_label "AC103810.3^ENSG00000265982.1"  ; ID "AC103810.3--TK1^AC103810.3^ENSG00000265982.1"  ; exon_id "ENSE00002721172.1"  ; exon_number 1 ; gene_id "AC103810.3--TK1^AC103810.3^ENSG00000265982.1"  ; gene_name "AC103810.3"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000179295.1"  ; havana_transcript "OTTHUMT00000445596.1"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr17,64778842,64778937,-"  ; tag basic ; transcript_id "AC103810.3--TK1^ENST00000583567.1"  ; transcript_name "AC103810.3-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC103810.3--TK1	HAVANA	RNA	1001	1096	.	+	.	FI_gene_label "AC103810.3^ENSG00000265982.1"  ; ID "AC103810.3--TK1^ENST00000583567.1"  ; Parent "AC103810.3--TK1^AC103810.3^ENSG00000265982.1"  ; exon_id "ENSE00002721172.1"  ; exon_number 1 ; gene_id "AC103810.3--TK1^AC103810.3^ENSG00000265982.1"  ; gene_name "AC103810.3"  ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000179295.1"  ; havana_transcript "OTTHUMT00000445596.1"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr17,64778842,64778937,-"  ; tag basic ; transcript_id "AC103810.3--TK1^ENST00000583567.1"  ; transcript_name "AC103810.3-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
BPTFP1--TK1	HAVANA	gene	1001	1799	.	+	.	FI_gene_label "BPTFP1^ENSG00000263647.1"  ; ID "BPTFP1--TK1^BPTFP1^ENSG00000263647.1"  ; exon_id "ENSE00003502189.1"  ; exon_number 1 ; gene_id "BPTFP1--TK1^BPTFP1^ENSG00000263647.1"  ; gene_name BPTFP1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000179294.1"  ; havana_transcript "OTTHUMT00000445595.1"  ; hgnc_id "HGNC:52869"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr17,64762355,64762710,-"  ; tag basic ; transcript_id "BPTFP1--TK1^ENST00000579209.1"  ; transcript_name "BPTFP1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
BPTFP1--TK1	HAVANA	RNA	1001	1799	.	+	.	FI_gene_label "BPTFP1^ENSG00000263647.1"  ; ID "BPTFP1--TK1^ENST00000579209.1"  ; Parent "BPTFP1--TK1^BPTFP1^ENSG00000263647.1"  ; exon_id "ENSE00003502189.1"  ; exon_number 1 ; gene_id "BPTFP1--TK1^BPTFP1^ENSG00000263647.1"  ; gene_name BPTFP1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000179294.1"  ; havana_transcript "OTTHUMT00000445595.1"  ; hgnc_id "HGNC:52869"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr17,64762355,64762710,-"  ; tag basic ; transcript_id "BPTFP1--TK1^ENST00000579209.1"  ; transcript_name "BPTFP1-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
DSC2--LINC01929	HAVANA	gene	29355	35608	.	+	.	FI_gene_label "LINC01929^ENSG00000267013.6"  ; ID "DSC2--LINC01929^LINC01929^ENSG00000267013.6"  ; exon_id "ENSE00002959778.1"  ; exon_number 1 ; gene_id "DSC2--LINC01929^LINC01929^ENSG00000267013.6"  ; gene_name LINC01929 ; gene_type lncRNA ; havana_gene "OTTHUMG00000176191.4"  ; havana_transcript "OTTHUMT00000431614.1"  ; hgnc_id "HGNC:52751"  ; level 2 ; orig_coord_info "chr18,55124120,55124306,-"  ; tag basic ; transcript_id "DSC2--LINC01929^ENST00000589125.5"  ; transcript_name "LINC01929-201"  ; transcript_support_level 2 ; transcript_type lncRNA
DSC2--LINC01929	HAVANA	RNA	29355	35608	.	+	.	FI_gene_label "LINC01929^ENSG00000267013.6"  ; ID "DSC2--LINC01929^ENST00000589125.5"  ; Parent "DSC2--LINC01929^LINC01929^ENSG00000267013.6"  ; exon_id "ENSE00002959778.1"  ; exon_number 1 ; gene_id "DSC2--LINC01929^LINC01929^ENSG00000267013.6"  ; gene_name LINC01929 ; gene_type lncRNA ; havana_gene "OTTHUMG00000176191.4"  ; havana_transcript "OTTHUMT00000431614.1"  ; hgnc_id "HGNC:52751"  ; level 2 ; orig_coord_info "chr18,55124120,55124306,-"  ; tag basic ; transcript_id "DSC2--LINC01929^ENST00000589125.5"  ; transcript_name "LINC01929-201"  ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created: 
NCBP1--AL391117.1	HAVANA	gene	28101	39522	.	+	.	FI_gene_label "AL391117.1^ENSG00000284418.2"  ; ID "NCBP1--AL391117.1^AL391117.1^ENSG00000284418.2"  ; exon_id "ENSE00003811180.1"  ; exon_number 1 ; gene_id "NCBP1--AL391117.1^AL391117.1^ENSG00000284418.2"  ; gene_name "AL391117.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000191913.2"  ; havana_transcript "OTTHUMT00000491114.1"  ; level 2 ; orig_coord_info "chr9,23438562,23438700,-"  ; tag RNA_Seq_supported_only basic ; transcript_id "NCBP1--AL391117.1^ENST00000640003.1"  ; transcript_name "AL391117.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
NCBP1--AL391117.1	HAVANA	RNA	28101	39522	.	+	.	FI_gene_label "AL391117.1^ENSG00000284418.2"  ; ID "NCBP1--AL391117.1^ENST00000640003.1"  ; Parent "NCBP1--AL391117.1^AL391117.1^ENSG00000284418.2"  ; exon_id "ENSE00003811180.1"  ; exon_number 1 ; gene_id "NCBP1--AL391117.1^AL391117.1^ENSG00000284418.2"  ; gene_name "AL391117.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000191913.2"  ; havana_transcript "OTTHUMT00000491114.1"  ; level 2 ; orig_coord_info "chr9,23438562,23438700,-"  ; tag RNA_Seq_supported_only basic ; transcript_id "NCBP1--AL391117.1^ENST00000640003.1"  ; transcript_name "AL391117.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
PPA1--AC048352.1	HAVANA	gene	19612	21844	.	+	.	FI_gene_label "AC048352.1^ENSG00000256389.2"  ; ID "PPA1--AC048352.1^AC048352.1^ENSG00000256389.2"  ; exon_id "ENSE00002321800.1"  ; exon_number 1 ; gene_id "PPA1--AC048352.1^AC048352.1^ENSG00000256389.2"  ; gene_name "AC048352.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000168815.7"  ; havana_transcript "OTTHUMT00000401165.1"  ; level 2 ; orig_coord_info "chr12,17589257,17589383,+"  ; transcript_id "PPA1--AC048352.1^ENST00000539105.1"  ; transcript_name "AC048352.1-201"  ; transcript_support_level 3 ; transcript_type lncRNA
PPA1--AC048352.1	HAVANA	RNA	19612	21844	.	+	.	FI_gene_label "AC048352.1^ENSG00000256389.2"  ; ID "PPA1--AC048352.1^ENST00000539105.1"  ; Parent "PPA1--AC048352.1^AC048352.1^ENSG00000256389.2"  ; exon_id "ENSE00002321800.1"  ; exon_number 1 ; gene_id "PPA1--AC048352.1^AC048352.1^ENSG00000256389.2"  ; gene_name "AC048352.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000168815.7"  ; havana_transcript "OTTHUMT00000401165.1"  ; level 2 ; orig_coord_info "chr12,17589257,17589383,+"  ; transcript_id "PPA1--AC048352.1^ENST00000539105.1"  ; transcript_name "AC048352.1-201"  ; transcript_support_level 3 ; 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
117 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 ------------------------------
207 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