.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cfy-T1-TRNA-1_B23WHTKLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/672104bfbbc6f98f5f891326b816b6/.command.log
Size: 33.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (659_cfy-T1-TRNA-1_B23WHTKLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/672104bfbbc6f98f5f891326b816b6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/a80b510e6d9a6da7b5a5074b7bef61/fi_workdir/659_cfy-T1-TRNA-1_B23WHTKLT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/672104bfbbc6f98f5f891326b816b6/.command.run
==> STAGING COMPLETE (3 inputs)

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: 2097
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2097
=> 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:2097
  => 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: 
ACTBP6--ACTB	HAVANA	gene	6203	10583	.	+	.	FI_gene_label "ACTB^ENSG00000075624.17"  ; ID "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; exon_id "ENSE00003542066.1"  ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12"  ; havana_transcript "OTTHUMT00000324028.2"  ; hgnc_id "HGNC:132"  ; level 2 ; orig_coord_info "chr7,5529535,5529657,-"  ; protein_id "ENSP00000401032.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1"  ; transcript_name "ACTB-201"  ; transcript_support_level 4 ; transcript_type protein_coding
ACTBP6--ACTB	HAVANA	mRNA	6203	10583	.	+	.	FI_gene_label "ACTB^ENSG00000075624.17"  ; ID "ACTBP6--ACTB^ENST00000414620.1"  ; Parent "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; exon_id "ENSE00003542066.1"  ; exon_number 3 ; gene_id "ACTBP6--ACTB^ACTB^ENSG00000075624.17"  ; gene_name ACTB ; gene_type protein_coding ; havana_gene "OTTHUMG00000023268.12"  ; havana_transcript "OTTHUMT00000324028.2"  ; hgnc_id "HGNC:132"  ; level 2 ; orig_coord_info "chr7,5529535,5529657,-"  ; protein_id "ENSP00000401032.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF dotter_confirmed ; transcript_id "ACTBP6--ACTB^ENST00000414620.1"  ; transcript_name "ACTB-201"  ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created: 
BCAR3--GLMN	HAVANA	gene	11472	31098	.	+	.	FI_gene_label "BCAR3^ENSG00000137936.18"  ; ID "BCAR3--GLMN^BCAR3^ENSG00000137936.18"  ; ccdsid "CCDS745.1"  ; exon_id "ENSE00001452146.1"  ; exon_number 2 ; gene_id "BCAR3--GLMN^BCAR3^ENSG00000137936.18"  ; gene_name BCAR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010301.5"  ; havana_transcript "OTTHUMT00000028418.2"  ; hgnc_id "HGNC:973"  ; level 2 ; orig_coord_info "chr1,93674614,93674930,-"  ; protein_id "ENSP00000260502.6"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "BCAR3--GLMN^ENST00000260502.11"  ; transcript_name "BCAR3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BCAR3--GLMN	HAVANA	mRNA	11472	31098	.	+	.	FI_gene_label "BCAR3^ENSG00000137936.18"  ; ID "BCAR3--GLMN^ENST00000260502.11"  ; Parent "BCAR3--GLMN^BCAR3^ENSG00000137936.18"  ; ccdsid "CCDS745.1"  ; exon_id "ENSE00001452146.1"  ; exon_number 2 ; gene_id "BCAR3--GLMN^BCAR3^ENSG00000137936.18"  ; gene_name BCAR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000010301.5"  ; havana_transcript "OTTHUMT00000028418.2"  ; hgnc_id "HGNC:973"  ; level 2 ; orig_coord_info "chr1,93674614,93674930,-"  ; protein_id "ENSP00000260502.6"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "BCAR3--GLMN^ENST00000260502.11"  ; transcript_name "BCAR3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
BCAR3--GLMN	HAVANA	gene	34099	50823	.	+	.	FI_gene_label "GLMN^ENSG00000174842.17"  ; ID "BCAR3--GLMN^GLMN^ENSG00000174842.17"  ; ccdsid "CCDS738.1"  ; exon_id "ENSE00002159430.1"  ; exon_number 2 ; gene_id "BCAR3--GLMN^GLMN^ENSG00000174842.17"  ; gene_name GLMN ; gene_type protein_coding ; havana_gene "OTTHUMG00000010283.9"  ; havana_transcript "OTTHUMT00000028358.2"  ; hgnc_id "HGNC:14373"  ; level 2 ; orig_coord_info "chr1,92297961,92297999,-"  ; protein_id "ENSP00000359385.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCAR3--GLMN^ENST00000370360.8"  ; transcript_name "GLMN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
BCAR3--GLMN	HAVANA	mRNA	34099	50823	.	+	.	FI_gene_label "GLMN^ENSG00000174842.17"  ; ID "BCAR3--GLMN^ENST00000370360.8"  ; Parent "BCAR3--GLMN^GLMN^ENSG00000174842.17"  ; ccdsid "CCDS738.1"  ; exon_id "ENSE00002159430.1"  ; exon_number 2 ; gene_id "BCAR3--GLMN^GLMN^ENSG00000174842.17"  ; gene_name GLMN ; gene_type protein_coding ; havana_gene "OTTHUMG00000010283.9"  ; havana_transcript "OTTHUMT00000028358.2"  ; hgnc_id "HGNC:14373"  ; level 2 ; orig_coord_info "chr1,92297961,92297999,-"  ; protein_id "ENSP00000359385.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCAR3--GLMN^ENST00000370360.8"  ; transcript_name "GLMN-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
DYRK1A--LINC02756	HAVANA	gene	2985	36922	.	+	.	FI_gene_label "DYRK1A^ENSG00000157540.22"  ; ID "DYRK1A--LINC02756^DYRK1A^ENSG00000157540.22"  ; ccdsid "CCDS42926.1"  ; exon_id "ENSE00003829613.1"  ; exon_number 3 ; gene_id "DYRK1A--LINC02756^DYRK1A^ENSG00000157540.22"  ; gene_name DYRK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000086657.9"  ; havana_transcript "OTTHUMT00000194799.2"  ; hgnc_id "HGNC:3091"  ; level 2 ; orig_coord_info "chr21,37420375,37420384,+"  ; protein_id "ENSP00000342690.3"  ; tag basic CCDS ; transcript_id "DYRK1A--LINC02756^ENST00000338785.8"  ; transcript_name "DYRK1A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
DYRK1A--LINC02756	HAVANA	mRNA	2985	36922	.	+	.	FI_gene_label "DYRK1A^ENSG00000157540.22"  ; ID "DYRK1A--LINC02756^ENST00000338785.8"  ; Parent "DYRK1A--LINC02756^DYRK1A^ENSG00000157540.22"  ; ccdsid "CCDS42926.1"  ; exon_id "ENSE00003829613.1"  ; exon_number 3 ; gene_id "DYRK1A--LINC02756^DYRK1A^ENSG00000157540.22"  ; gene_name DYRK1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000086657.9"  ; havana_transcript "OTTHUMT00000194799.2"  ; hgnc_id "HGNC:3091"  ; level 2 ; orig_coord_info "chr21,37420375,37420384,+"  ; protein_id "ENSP00000342690.3"  ; tag basic CCDS ; transcript_id "DYRK1A--LINC02756^ENST00000338785.8"  ; transcript_name "DYRK1A-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: 
MTAP--DMRTA1	HAVANA	gene	29696	36281	.	+	.	FI_gene_label "DMRTA1^ENSG00000176399.4"  ; ID "MTAP--DMRTA1^DMRTA1^ENSG00000176399.4"  ; ccdsid "CCDS6514.1"  ; exon_id "ENSE00001268100.3"  ; exon_number 1 ; gene_id "MTAP--DMRTA1^DMRTA1^ENSG00000176399.4"  ; gene_name DMRTA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019693.3"  ; havana_transcript "OTTHUMT00000051935.3"  ; hgnc_id "HGNC:13826"  ; level 2 ; orig_coord_info "chr9,22447066,22447732,+"  ; protein_id "ENSP00000319651.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MTAP--DMRTA1^ENST00000325870.3"  ; transcript_name "DMRTA1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MTAP--DMRTA1	HAVANA	mRNA	29696	36281	.	+	.	FI_gene_label "DMRTA1^ENSG00000176399.4"  ; ID "MTAP--DMRTA1^ENST00000325870.3"  ; Parent "MTAP--DMRTA1^DMRTA1^ENSG00000176399.4"  ; ccdsid "CCDS6514.1"  ; exon_id "ENSE00001268100.3"  ; exon_number 1 ; gene_id "MTAP--DMRTA1^DMRTA1^ENSG00000176399.4"  ; gene_name DMRTA1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019693.3"  ; havana_transcript "OTTHUMT00000051935.3"  ; hgnc_id "HGNC:13826"  ; level 2 ; orig_coord_info "chr9,22447066,22447732,+"  ; protein_id "ENSP00000319651.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MTAP--DMRTA1^ENST00000325870.3"  ; transcript_name "DMRTA1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MTAP--DMRTA1	HAVANA	gene	1022	14638	.	+	.	FI_gene_label "MTAP^ENSG00000099810.21"  ; ID "MTAP--DMRTA1^MTAP^ENSG00000099810.21"  ; exon_id "ENSE00001547793.2"  ; exon_number 1 ; gene_id "MTAP--DMRTA1^MTAP^ENSG00000099810.21"  ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10"  ; havana_transcript "OTTHUMT00000334287.1"  ; hgnc_id "HGNC:7413"  ; level 2 ; orig_coord_info "chr9,21802749,21802781,+"  ; protein_id "ENSP00000393507.1"  ; tag not_organism_supported ; transcript_id "MTAP--DMRTA1^ENST00000419385.5"  ; transcript_name "MTAP-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
MTAP--DMRTA1	HAVANA	mRNA	1022	14638	.	+	.	FI_gene_label "MTAP^ENSG00000099810.21"  ; ID "MTAP--DMRTA1^ENST00000419385.5"  ; Parent "MTAP--DMRTA1^MTAP^ENSG00000099810.21"  ; exon_id "ENSE00001547793.2"  ; exon_number 1 ; gene_id "MTAP--DMRTA1^MTAP^ENSG00000099810.21"  ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10"  ; havana_transcript "OTTHUMT00000334287.1"  ; hgnc_id "HGNC:7413"  ; level 2 ; orig_coord_info "chr9,21802749,21802781,+"  ; protein_id "ENSP00000393507.1"  ; tag not_organism_supported ; transcript_id "MTAP--DMRTA1^ENST00000419385.5"  ; transcript_name "MTAP-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
MTAP--LINC01239	HAVANA	gene	1022	14638	.	+	.	FI_gene_label "MTAP^ENSG00000099810.21"  ; ID "MTAP--LINC01239^MTAP^ENSG00000099810.21"  ; exon_id "ENSE00001547793.2"  ; exon_number 1 ; gene_id "MTAP--LINC01239^MTAP^ENSG00000099810.21"  ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10"  ; havana_transcript "OTTHUMT00000334287.1"  ; hgnc_id "HGNC:7413"  ; level 2 ; orig_coord_info "chr9,21802749,21802781,+"  ; protein_id "ENSP00000393507.1"  ; tag not_organism_supported ; transcript_id "MTAP--LINC01239^ENST00000419385.5"  ; transcript_name "MTAP-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
MTAP--LINC01239	HAVANA	mRNA	1022	14638	.	+	.	FI_gene_label "MTAP^ENSG00000099810.21"  ; ID "MTAP--LINC01239^ENST00000419385.5"  ; Parent "MTAP--LINC01239^MTAP^ENSG00000099810.21"  ; exon_id "ENSE00001547793.2"  ; exon_number 1 ; gene_id "MTAP--LINC01239^MTAP^ENSG00000099810.21"  ; gene_name MTAP ; gene_type protein_coding ; havana_gene "OTTHUMG00000019690.10"  ; havana_transcript "OTTHUMT00000334287.1"  ; hgnc_id "HGNC:7413"  ; level 2 ; orig_coord_info "chr9,21802749,21802781,+"  ; protein_id "ENSP00000393507.1"  ; tag not_organism_supported ; transcript_id "MTAP--LINC01239^ENST00000419385.5"  ; transcript_name "MTAP-201"  ; transcript_support_level 5 ; transcript_type nonsense_mediated_decay
L1 and L2 created: 
NUS1--AC114501.3	HAVANA	gene	1001	9659	.	+	.	FI_gene_label "NUS1^ENSG00000153989.8"  ; ID "NUS1--AC114501.3^NUS1^ENSG00000153989.8"  ; ccdsid "CCDS5118.1"  ; exon_id "ENSE00001447272.4"  ; exon_number 1 ; gene_id "NUS1--AC114501.3^NUS1^ENSG00000153989.8"  ; gene_name NUS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015458.2"  ; havana_transcript "OTTHUMT00000041989.2"  ; hgnc_id "HGNC:21042"  ; level 2 ; orig_coord_info "chr6,117675671,117676085,+"  ; protein_id "ENSP00000357480.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NUS1--AC114501.3^ENST00000368494.4"  ; transcript_name "NUS1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NUS1--AC114501.3	HAVANA	mRNA	1001	9659	.	+	.	FI_gene_label "NUS1^ENSG00000153989.8"  ; ID "NUS1--AC114501.3^ENST00000368494.4"  ; Parent "NUS1--AC114501.3^NUS1^ENSG00000153989.8"  ; ccdsid "CCDS5118.1"  ; exon_id "ENSE00001447272.4"  ; exon_number 1 ; gene_id "NUS1--AC114501.3^NUS1^ENSG00000153989.8"  ; gene_name NUS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015458.2"  ; havana_transcript "OTTHUMT00000041989.2"  ; hgnc_id "HGNC:21042"  ; level 2 ; orig_coord_info "chr6,117675671,117676085,+"  ; protein_id "ENSP00000357480.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NUS1--AC114501.3^ENST00000368494.4"  ; transcript_name "NUS1-201"  ; 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: 
UBR5--BAALC-AS1	HAVANA	gene	1071	53320	.	+	.	FI_gene_label "UBR5^ENSG00000104517.13"  ; ID "UBR5--BAALC-AS1^UBR5^ENSG00000104517.13"  ; ccdsid "CCDS64946.1"  ; exon_id "ENSE00001162016.4"  ; exon_number 1 ; gene_id "UBR5--BAALC-AS1^UBR5^ENSG00000104517.13"  ; gene_name UBR5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164755.5"  ; havana_transcript "OTTHUMT00000380196.1"  ; hgnc_id "HGNC:16806"  ; level 2 ; orig_coord_info "chr8,102412173,102412234,-"  ; protein_id "ENSP00000220959.4"  ; tag basic appris_alternative_1 CCDS ; transcript_id "UBR5--BAALC-AS1^ENST00000220959.8"  ; transcript_name "UBR5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
UBR5--BAALC-AS1	HAVANA	mRNA	1071	53320	.	+	.	FI_gene_label "UBR5^ENSG00000104517.13"  ; ID "UBR5--BAALC-AS1^ENST00000220959.8"  ; Parent "UBR5--BAALC-AS1^UBR5^ENSG00000104517.13"  ; ccdsid "CCDS64946.1"  ; exon_id "ENSE00001162016.4"  ; exon_number 1 ; gene_id "UBR5--BAALC-AS1^UBR5^ENSG00000104517.13"  ; gene_name UBR5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000164755.5"  ; havana_transcript "OTTHUMT00000380196.1"  ; hgnc_id "HGNC:16806"  ; level 2 ; orig_coord_info "chr8,102412173,102412234,-"  ; protein_id "ENSP00000220959.4"  ; tag basic appris_alternative_1 CCDS ; transcript_id "UBR5--BAALC-AS1^ENST00000220959.8"  ; transcript_name "UBR5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ZNF431--RPSAP58	HAVANA	gene	1017	22132	.	+	.	FI_gene_label "ZNF431^ENSG00000196705.8"  ; ID "ZNF431--RPSAP58^ZNF431^ENSG00000196705.8"  ; ccdsid "CCDS32979.1"  ; exon_id "ENSE00003141770.1"  ; exon_number 1 ; gene_id "ZNF431--RPSAP58^ZNF431^ENSG00000196705.8"  ; gene_name ZNF431 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182835.3"  ; havana_transcript "OTTHUMT00000463943.2"  ; hgnc_id "HGNC:20809"  ; level 2 ; orig_coord_info "chr19,21142184,21142186,+"  ; protein_id "ENSP00000308578.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF431--RPSAP58^ENST00000311048.11"  ; transcript_name "ZNF431-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ZNF431--RPSAP58	HAVANA	mRNA	1017	22132	.	+	.	FI_gene_label "ZNF431^ENSG00000196705.8"  ; ID "ZNF431--RPSAP58^ENST00000311048.11"  ; Parent "ZNF431--RPSAP58^ZNF431^ENSG00000196705.8"  ; ccdsid "CCDS32979.1"  ; exon_id "ENSE00003141770.1"  ; exon_number 1 ; gene_id "ZNF431--RPSAP58^ZNF431^ENSG00000196705.8"  ; gene_name ZNF431 ; gene_type protein_coding ; havana_gene "OTTHUMG00000182835.3"  ; havana_transcript "OTTHUMT00000463943.2"  ; hgnc_id "HGNC:20809"  ; level 2 ; orig_coord_info "chr19,21142184,21142186,+"  ; protein_id "ENSP00000308578.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZNF431--RPSAP58^ENST00000311048.11"  ; transcript_name "ZNF431-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ACTBP6--ACTB	HAVANA	gene	1001	2090	.	+	.	FI_gene_label "ACTBP6^ENSG00000203413.3"  ; ID "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; exon_id "ENSE00002116857.1"  ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2"  ; havana_transcript "OTTHUMT00000379462.2"  ; hgnc_id "HGNC:139"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,84948585,84949674,+"  ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1"  ; transcript_name "ACTBP6-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
ACTBP6--ACTB	HAVANA	RNA	1001	2090	.	+	.	FI_gene_label "ACTBP6^ENSG00000203413.3"  ; ID "ACTBP6--ACTB^ENST00000520036.1"  ; Parent "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; exon_id "ENSE00002116857.1"  ; exon_number 1 ; gene_id "ACTBP6--ACTB^ACTBP6^ENSG00000203413.3"  ; gene_name ACTBP6 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000164632.2"  ; havana_transcript "OTTHUMT00000379462.2"  ; hgnc_id "HGNC:139"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr8,84948585,84949674,+"  ; tag pseudo_consens basic ; transcript_id "ACTBP6--ACTB^ENST00000520036.1"  ; transcript_name "ACTBP6-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
DYRK1A--LINC02756	HAVANA	gene	50943	56986	.	+	.	FI_gene_label "LINC02756^ENSG00000255332.8"  ; ID "DYRK1A--LINC02756^LINC02756^ENSG00000255332.8"  ; exon_id "ENSE00002711875.2"  ; exon_number 1 ; gene_id "DYRK1A--LINC02756^LINC02756^ENSG00000255332.8"  ; gene_name LINC02756 ; gene_type lncRNA ; havana_gene "OTTHUMG00000167330.10"  ; havana_transcript "OTTHUMT00000447347.2"  ; hgnc_id "HGNC:54276"  ; level 1 ; orig_coord_info "chr11,91794358,91794422,+"  ; tag basic TAGENE exp_conf ; transcript_id "DYRK1A--LINC02756^ENST00000525832.3"  ; transcript_name "LINC02756-201"  ; transcript_support_level 3 ; transcript_type lncRNA
DYRK1A--LINC02756	HAVANA	RNA	50943	56986	.	+	.	FI_gene_label "LINC02756^ENSG00000255332.8"  ; ID "DYRK1A--LINC02756^ENST00000525832.3"  ; Parent "DYRK1A--LINC02756^LINC02756^ENSG00000255332.8"  ; exon_id "ENSE00002711875.2"  ; exon_number 1 ; gene_id "DYRK1A--LINC02756^LINC02756^ENSG00000255332.8"  ; gene_name LINC02756 ; gene_type lncRNA ; havana_gene "OTTHUMG00000167330.10"  ; havana_transcript "OTTHUMT00000447347.2"  ; hgnc_id "HGNC:54276"  ; level 1 ; orig_coord_info "chr11,91794358,91794422,+"  ; tag basic TAGENE exp_conf ; transcript_id "DYRK1A--LINC02756^ENST00000525832.3"  ; transcript_name "LINC02756-201"  ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created: 
MTAP--LINC01239	HAVANA	gene	32024	33348	.	+	.	FI_gene_label "LINC01239^ENSG00000234840.2"  ; ID "MTAP--LINC01239^LINC01239^ENSG00000234840.2"  ; exon_id "ENSE00001647776.1"  ; exon_number 1 ; gene_id "MTAP--LINC01239^LINC01239^ENSG00000234840.2"  ; gene_name LINC01239 ; gene_type lncRNA ; havana_gene "OTTHUMG00000019696.2"  ; havana_transcript "OTTHUMT00000051939.1"  ; hgnc_id "HGNC:49796"  ; level 2 ; orig_coord_info "chr9,22682470,22682713,+"  ; transcript_id "MTAP--LINC01239^ENST00000433645.1"  ; transcript_name "LINC01239-201"  ; transcript_support_level 3 ; transcript_type retained_intron
MTAP--LINC01239	HAVANA	RNA	32024	33348	.	+	.	FI_gene_label "LINC01239^ENSG00000234840.2"  ; ID "MTAP--LINC01239^ENST00000433645.1"  ; Parent "MTAP--LINC01239^LINC01239^ENSG00000234840.2"  ; exon_id "ENSE00001647776.1"  ; exon_number 1 ; gene_id "MTAP--LINC01239^LINC01239^ENSG00000234840.2"  ; gene_name LINC01239 ; gene_type lncRNA ; havana_gene "OTTHUMG00000019696.2"  ; havana_transcript "OTTHUMT00000051939.1"  ; hgnc_id "HGNC:49796"  ; level 2 ; orig_coord_info "chr9,22682470,22682713,+"  ; transcript_id "MTAP--LINC01239^ENST00000433645.1"  ; transcript_name "LINC01239-201"  ; transcript_support_level 3 ; transcript_type retained_intron
L1 and L2 created: 
NUS1--AC114501.3	HAVANA	gene	12660	13027	.	+	.	FI_gene_label "AC114501.3^ENSG00000238124.1"  ; ID "NUS1--AC114501.3^AC114501.3^ENSG00000238124.1"  ; exon_id "ENSE00001603093.1"  ; exon_number 1 ; gene_id "NUS1--AC114501.3^AC114501.3^ENSG00000238124.1"  ; gene_name "AC114501.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000156731.1"  ; havana_transcript "OTTHUMT00000345494.1"  ; level 2 ; orig_coord_info "chr7,65463071,65463168,+"  ; tag basic ; transcript_id "NUS1--AC114501.3^ENST00000453648.1"  ; transcript_name "AC114501.3-201"  ; transcript_support_level 5 ; transcript_type lncRNA
NUS1--AC114501.3	HAVANA	RNA	12660	13027	.	+	.	FI_gene_label "AC114501.3^ENSG00000238124.1"  ; ID "NUS1--AC114501.3^ENST00000453648.1"  ; Parent "NUS1--AC114501.3^AC114501.3^ENSG00000238124.1"  ; exon_id "ENSE00001603093.1"  ; exon_number 1 ; gene_id "NUS1--AC114501.3^AC114501.3^ENSG00000238124.1"  ; gene_name "AC114501.3"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000156731.1"  ; havana_transcript "OTTHUMT00000345494.1"  ; level 2 ; orig_coord_info "chr7,65463071,65463168,+"  ; tag basic ; transcript_id "NUS1--AC114501.3^ENST00000453648.1"  ; transcript_name "AC114501.3-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
UBR5--BAALC-AS1	HAVANA	gene	59208	75845	.	+	.	FI_gene_label "BAALC-AS1^ENSG00000247081.8"  ; ID "UBR5--BAALC-AS1^BAALC-AS1^ENSG00000247081.8"  ; exon_id "ENSE00001974416.1"  ; exon_number 1 ; gene_id "UBR5--BAALC-AS1^BAALC-AS1^ENSG00000247081.8"  ; gene_name "BAALC-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000164798.6"  ; havana_transcript "OTTHUMT00000380348.1"  ; hgnc_id "HGNC:50461"  ; level 2 ; orig_coord_info "chr8,103285838,103285907,-"  ; tag basic ; transcript_id "UBR5--BAALC-AS1^ENST00000499522.6"  ; transcript_name "BAALC-AS1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
UBR5--BAALC-AS1	HAVANA	RNA	59208	75845	.	+	.	FI_gene_label "BAALC-AS1^ENSG00000247081.8"  ; ID "UBR5--BAALC-AS1^ENST00000499522.6"  ; Parent "UBR5--BAALC-AS1^BAALC-AS1^ENSG00000247081.8"  ; exon_id "ENSE00001974416.1"  ; exon_number 1 ; gene_id "UBR5--BAALC-AS1^BAALC-AS1^ENSG00000247081.8"  ; gene_name "BAALC-AS1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000164798.6"  ; havana_transcript "OTTHUMT00000380348.1"  ; hgnc_id "HGNC:50461"  ; level 2 ; orig_coord_info "chr8,103285838,103285907,-"  ; tag basic ; transcript_id "UBR5--BAALC-AS1^ENST00000499522.6"  ; transcript_name "BAALC-AS1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
ZNF431--RPSAP58	HAVANA	gene	25133	26020	.	+	.	FI_gene_label "RPSAP58^ENSG00000225178.5"  ; ID "ZNF431--RPSAP58^RPSAP58^ENSG00000225178.5"  ; exon_id "ENSE00001619993.3"  ; exon_number 1 ; gene_id "ZNF431--RPSAP58^RPSAP58^ENSG00000225178.5"  ; gene_name RPSAP58 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000158122.3"  ; havana_transcript "OTTHUMT00000350238.3"  ; hgnc_id "HGNC:36809"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr19,23827162,23828049,+"  ; tag pseudo_consens basic ; transcript_id "ZNF431--RPSAP58^ENST00000484897.3"  ; transcript_name "RPSAP58-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
ZNF431--RPSAP58	HAVANA	RNA	25133	26020	.	+	.	FI_gene_label "RPSAP58^ENSG00000225178.5"  ; ID "ZNF431--RPSAP58^ENST00000484897.3"  ; Parent "ZNF431--RPSAP58^RPSAP58^ENSG00000225178.5"  ; exon_id "ENSE00001619993.3"  ; exon_number 1 ; gene_id "ZNF431--RPSAP58^RPSAP58^ENSG00000225178.5"  ; gene_name RPSAP58 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000158122.3"  ; havana_transcript "OTTHUMT00000350238.3"  ; hgnc_id "HGNC:36809"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr19,23827162,23828049,+"  ; tag pseudo_consens basic ; transcript_id "ZNF431--RPSAP58^ENST00000484897.3"  ; transcript_name "RPSAP58-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
180 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 ------------------------------
281 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