.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (V4_0001_RNA_0005_23H5VFLT4_s07)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/4647a28962ed8c5012ac5ee25b790e/.command.log
Size: 33.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (V4_0001_RNA_0005_23H5VFLT4_s07)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/b45fa5320c154c7d9c50552f22b756/fi_workdir/V4_0001_RNA_0005_23H5VFLT4_s07.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/4647a28962ed8c5012ac5ee25b790e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/4647a28962ed8c5012ac5ee25b790e/.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         |
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                          ------ 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: 3162
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3162
=> 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:3162
  => 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 2 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: 
CCDC6--RET	HAVANA	gene	1001	16128	.	+	.	FI_gene_label "CCDC6^ENSG00000108091.11"  ; ID "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; ccdsid "CCDS7257.1"  ; exon_id "ENSE00001950758.3"  ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3"  ; havana_transcript "OTTHUMT00000048176.3"  ; hgnc_id "HGNC:18782"  ; level 2 ; orig_coord_info "chr10,59906122,59906424,-"  ; protein_id "ENSP00000263102.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7"  ; transcript_name "CCDC6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET	HAVANA	mRNA	1001	16128	.	+	.	FI_gene_label "CCDC6^ENSG00000108091.11"  ; ID "CCDC6--RET^ENST00000263102.7"  ; Parent "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; ccdsid "CCDS7257.1"  ; exon_id "ENSE00001950758.3"  ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11"  ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3"  ; havana_transcript "OTTHUMT00000048176.3"  ; hgnc_id "HGNC:18782"  ; level 2 ; orig_coord_info "chr10,59906122,59906424,-"  ; protein_id "ENSP00000263102.6"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7"  ; transcript_name "CCDC6-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
CCDC6--RET	HAVANA	gene	19134	39754	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "CCDC6--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET	HAVANA	mRNA	19134	39754	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "CCDC6--RET^ENST00000340058.6"  ; Parent "CCDC6--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FGFR3--BAIAP2L1	HAVANA	gene	14817	31823	.	+	.	FI_gene_label "BAIAP2L1^ENSG00000006453.14"  ; ID "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14"  ; ccdsid "CCDS34687.1"  ; exon_id "ENSE00003618813.2"  ; exon_number 1 ; gene_id "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14"  ; gene_name BAIAP2L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165117.2"  ; havana_transcript "OTTHUMT00000334681.2"  ; hgnc_id "HGNC:21649"  ; level 2 ; orig_coord_info "chr7,98400802,98400852,-"  ; protein_id "ENSP00000005260.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FGFR3--BAIAP2L1^ENST00000005260.9"  ; transcript_name "BAIAP2L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--BAIAP2L1	HAVANA	mRNA	14817	31823	.	+	.	FI_gene_label "BAIAP2L1^ENSG00000006453.14"  ; ID "FGFR3--BAIAP2L1^ENST00000005260.9"  ; Parent "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14"  ; ccdsid "CCDS34687.1"  ; exon_id "ENSE00003618813.2"  ; exon_number 1 ; gene_id "FGFR3--BAIAP2L1^BAIAP2L1^ENSG00000006453.14"  ; gene_name BAIAP2L1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165117.2"  ; havana_transcript "OTTHUMT00000334681.2"  ; hgnc_id "HGNC:21649"  ; level 2 ; orig_coord_info "chr7,98400802,98400852,-"  ; protein_id "ENSP00000005260.8"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FGFR3--BAIAP2L1^ENST00000005260.9"  ; transcript_name "BAIAP2L1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
FGFR3--BAIAP2L1	HAVANA	gene	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--BAIAP2L1^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--BAIAP2L1^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--BAIAP2L1	HAVANA	mRNA	1020	10219	.	+	.	FI_gene_label "FGFR3^ENSG00000068078.20"  ; ID "FGFR3--BAIAP2L1^ENST00000260795.8"  ; Parent "FGFR3--BAIAP2L1^FGFR3^ENSG00000068078.20"  ; exon_id "ENSE00001596390.1"  ; exon_number 2 ; gene_id "FGFR3--BAIAP2L1^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--BAIAP2L1^ENST00000260795.8"  ; transcript_name "FGFR3-201"  ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
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: 
KIF5B--RET	HAVANA	gene	1001	24630	.	+	.	FI_gene_label "KIF5B^ENSG00000170759.11"  ; ID "KIF5B--RET^KIF5B^ENSG00000170759.11"  ; ccdsid "CCDS7171.1"  ; exon_id "ENSE00001551533.4"  ; exon_number 1 ; gene_id "KIF5B--RET^KIF5B^ENSG00000170759.11"  ; gene_name KIF5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017913.2"  ; havana_transcript "OTTHUMT00000047467.2"  ; hgnc_id "HGNC:6324"  ; level 2 ; orig_coord_info "chr10,32055848,32055973,-"  ; protein_id "ENSP00000307078.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KIF5B--RET^ENST00000302418.5"  ; transcript_name "KIF5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KIF5B--RET	HAVANA	mRNA	1001	24630	.	+	.	FI_gene_label "KIF5B^ENSG00000170759.11"  ; ID "KIF5B--RET^ENST00000302418.5"  ; Parent "KIF5B--RET^KIF5B^ENSG00000170759.11"  ; ccdsid "CCDS7171.1"  ; exon_id "ENSE00001551533.4"  ; exon_number 1 ; gene_id "KIF5B--RET^KIF5B^ENSG00000170759.11"  ; gene_name KIF5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000017913.2"  ; havana_transcript "OTTHUMT00000047467.2"  ; hgnc_id "HGNC:6324"  ; level 2 ; orig_coord_info "chr10,32055848,32055973,-"  ; protein_id "ENSP00000307078.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KIF5B--RET^ENST00000302418.5"  ; transcript_name "KIF5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
KIF5B--RET	HAVANA	gene	27636	48256	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "KIF5B--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "KIF5B--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "KIF5B--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
KIF5B--RET	HAVANA	mRNA	27636	48256	.	+	.	FI_gene_label "RET^ENSG00000165731.20"  ; ID "KIF5B--RET^ENST00000340058.6"  ; Parent "KIF5B--RET^RET^ENSG00000165731.20"  ; ccdsid "CCDS53525.1"  ; exon_id "ENSE00003744437.1"  ; exon_number 1 ; gene_id "KIF5B--RET^RET^ENSG00000165731.20"  ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7"  ; havana_transcript "OTTHUMT00000358138.3"  ; hgnc_id "HGNC:9967"  ; level 2 ; orig_coord_info "chr10,43077259,43077331,+"  ; protein_id "ENSP00000344798.4"  ; tag basic CCDS ; transcript_id "KIF5B--RET^ENST00000340058.6"  ; transcript_name "RET-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
LMNA--NTRK1	HAVANA	gene	31461	45545	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "LMNA--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "LMNA--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "LMNA--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
LMNA--NTRK1	HAVANA	mRNA	31461	45545	.	+	.	FI_gene_label "NTRK1^ENSG00000198400.13"  ; ID "LMNA--NTRK1^ENST00000358660.3"  ; Parent "LMNA--NTRK1^NTRK1^ENSG00000198400.13"  ; exon_id "ENSE00001378279.3"  ; exon_number 1 ; gene_id "LMNA--NTRK1^NTRK1^ENSG00000198400.13"  ; gene_name NTRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000041304.3"  ; havana_transcript "OTTHUMT00000392280.1"  ; hgnc_id "HGNC:8031"  ; level 2 ; orig_coord_info "chr1,156860935,156861146,+"  ; protein_id "ENSP00000351486.3"  ; tag basic appris_alternative_2 ; transcript_id "LMNA--NTRK1^ENST00000358660.3"  ; transcript_name "NTRK1-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
LMNA--NTRK1	HAVANA	gene	11719	23624	.	+	.	FI_gene_label "LMNA^ENSG00000160789.23"  ; ID "LMNA--NTRK1^LMNA^ENSG00000160789.23"  ; ccdsid "CCDS1129.1"  ; exon_id "ENSE00001554780.1"  ; exon_number 2 ; gene_id "LMNA--NTRK1^LMNA^ENSG00000160789.23"  ; gene_name LMNA ; gene_type protein_coding ; havana_gene "OTTHUMG00000013961.6"  ; hgnc_id "HGNC:6636"  ; level 2 ; orig_coord_info "chr1,156114919,156115274,+"  ; protein_id "ENSP00000355292.6"  ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "LMNA--NTRK1^ENST00000361308.9"  ; transcript_name "LMNA-201"  ; transcript_support_level 5 ; transcript_type protein_coding
LMNA--NTRK1	HAVANA	mRNA	11719	23624	.	+	.	FI_gene_label "LMNA^ENSG00000160789.23"  ; ID "LMNA--NTRK1^ENST00000361308.9"  ; Parent "LMNA--NTRK1^LMNA^ENSG00000160789.23"  ; ccdsid "CCDS1129.1"  ; exon_id "ENSE00001554780.1"  ; exon_number 2 ; gene_id "LMNA--NTRK1^LMNA^ENSG00000160789.23"  ; gene_name LMNA ; gene_type protein_coding ; havana_gene "OTTHUMG00000013961.6"  ; hgnc_id "HGNC:6636"  ; level 2 ; orig_coord_info "chr1,156114919,156115274,+"  ; protein_id "ENSP00000355292.6"  ; tag RNA_Seq_supported_only basic appris_principal_1 CCDS ; transcript_id "LMNA--NTRK1^ENST00000361308.9"  ; transcript_name "LMNA-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SLC34A2--ROS1	HAVANA	gene	21924	69303	.	+	.	FI_gene_label "ROS1^ENSG00000047936.11"  ; ID "SLC34A2--ROS1^ROS1^ENSG00000047936.11"  ; exon_id "ENSE00003906517.1"  ; exon_number 1 ; gene_id "SLC34A2--ROS1^ROS1^ENSG00000047936.11"  ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1"  ; havana_transcript "OTTHUMT00000043465.1"  ; hgnc_id "HGNC:10261"  ; level 2 ; orig_coord_info "chr6,117425534,117425656,-"  ; protein_id "ENSP00000357493.3"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "SLC34A2--ROS1^ENST00000368507.8"  ; transcript_name "ROS1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SLC34A2--ROS1	HAVANA	mRNA	21924	69303	.	+	.	FI_gene_label "ROS1^ENSG00000047936.11"  ; ID "SLC34A2--ROS1^ENST00000368507.8"  ; Parent "SLC34A2--ROS1^ROS1^ENSG00000047936.11"  ; exon_id "ENSE00003906517.1"  ; exon_number 1 ; gene_id "SLC34A2--ROS1^ROS1^ENSG00000047936.11"  ; gene_name ROS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016188.1"  ; havana_transcript "OTTHUMT00000043465.1"  ; hgnc_id "HGNC:10261"  ; level 2 ; orig_coord_info "chr6,117425534,117425656,-"  ; protein_id "ENSP00000357493.3"  ; tag basic MANE_Select appris_principal_4 ; transcript_id "SLC34A2--ROS1^ENST00000368507.8"  ; transcript_name "ROS1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SLC34A2--ROS1	HAVANA	gene	2897	18923	.	+	.	FI_gene_label "SLC34A2^ENSG00000157765.13"  ; ID "SLC34A2--ROS1^SLC34A2^ENSG00000157765.13"  ; ccdsid "CCDS3435.1"  ; exon_id "ENSE00001034812.5"  ; exon_number 2 ; gene_id "SLC34A2--ROS1^SLC34A2^ENSG00000157765.13"  ; gene_name SLC34A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097757.6"  ; havana_transcript "OTTHUMT00000214990.2"  ; hgnc_id "HGNC:11020"  ; level 2 ; orig_coord_info "chr4,25662501,25662612,+"  ; protein_id "ENSP00000371483.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "SLC34A2--ROS1^ENST00000382051.8"  ; transcript_name "SLC34A2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SLC34A2--ROS1	HAVANA	mRNA	2897	18923	.	+	.	FI_gene_label "SLC34A2^ENSG00000157765.13"  ; ID "SLC34A2--ROS1^ENST00000382051.8"  ; Parent "SLC34A2--ROS1^SLC34A2^ENSG00000157765.13"  ; ccdsid "CCDS3435.1"  ; exon_id "ENSE00001034812.5"  ; exon_number 2 ; gene_id "SLC34A2--ROS1^SLC34A2^ENSG00000157765.13"  ; gene_name SLC34A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000097757.6"  ; havana_transcript "OTTHUMT00000214990.2"  ; hgnc_id "HGNC:11020"  ; level 2 ; orig_coord_info "chr4,25662501,25662612,+"  ; protein_id "ENSP00000371483.3"  ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "SLC34A2--ROS1^ENST00000382051.8"  ; transcript_name "SLC34A2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TLK2--AC240565.1	HAVANA	gene	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1	HAVANA	mRNA	4784	35054	.	+	.	FI_gene_label "TLK2^ENSG00000146872.18"  ; ID "TLK2--AC240565.1^ENST00000326270.13"  ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; ccdsid "CCDS62283.1"  ; exon_id "ENSE00003568961.1"  ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18"  ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3"  ; havana_transcript "OTTHUMT00000445140.1"  ; hgnc_id "HGNC:11842"  ; level 2 ; orig_coord_info "chr17,62481126,62481206,+"  ; protein_id "ENSP00000316512.9"  ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13"  ; transcript_name "TLK2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TMPRSS2--ERG	HAVANA	gene	30939	50248	.	+	.	FI_gene_label "ERG^ENSG00000157554.19"  ; ID "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; ccdsid "CCDS13658.1"  ; exon_id "ENSE00001931764.2"  ; exon_number 1 ; gene_id "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; gene_name ERG ; gene_type protein_coding ; havana_gene "OTTHUMG00000090767.4"  ; havana_transcript "OTTHUMT00000207531.2"  ; hgnc_id "HGNC:3446"  ; level 2 ; orig_coord_info "chr21,38498363,38498380,-"  ; protein_id "ENSP00000288319.7"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000288319.12"  ; transcript_name "ERG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMPRSS2--ERG	HAVANA	mRNA	30939	50248	.	+	.	FI_gene_label "ERG^ENSG00000157554.19"  ; ID "TMPRSS2--ERG^ENST00000288319.12"  ; Parent "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; ccdsid "CCDS13658.1"  ; exon_id "ENSE00001931764.2"  ; exon_number 1 ; gene_id "TMPRSS2--ERG^ERG^ENSG00000157554.19"  ; gene_name ERG ; gene_type protein_coding ; havana_gene "OTTHUMG00000090767.4"  ; havana_transcript "OTTHUMT00000207531.2"  ; hgnc_id "HGNC:3446"  ; level 2 ; orig_coord_info "chr21,38498363,38498380,-"  ; protein_id "ENSP00000288319.7"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000288319.12"  ; transcript_name "ERG-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
TMPRSS2--ERG	HAVANA	gene	4575	23486	.	+	.	FI_gene_label "TMPRSS2^ENSG00000184012.14"  ; ID "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; ccdsid "CCDS33564.1"  ; exon_id "ENSE00003502036.1"  ; exon_number 2 ; gene_id "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; gene_name TMPRSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086762.7"  ; havana_transcript "OTTHUMT00000195189.2"  ; hgnc_id "HGNC:11876"  ; level 2 ; orig_coord_info "chr21,41498119,41498133,-"  ; protein_id "ENSP00000330330.5"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000332149.10"  ; transcript_name "TMPRSS2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
TMPRSS2--ERG	HAVANA	mRNA	4575	23486	.	+	.	FI_gene_label "TMPRSS2^ENSG00000184012.14"  ; ID "TMPRSS2--ERG^ENST00000332149.10"  ; Parent "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; ccdsid "CCDS33564.1"  ; exon_id "ENSE00003502036.1"  ; exon_number 2 ; gene_id "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14"  ; gene_name TMPRSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086762.7"  ; havana_transcript "OTTHUMT00000195189.2"  ; hgnc_id "HGNC:11876"  ; level 2 ; orig_coord_info "chr21,41498119,41498133,-"  ; protein_id "ENSP00000330330.5"  ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000332149.10"  ; transcript_name "TMPRSS2-201"  ; 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: 
TLK2--AC240565.1	HAVANA	gene	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1	HAVANA	RNA	40046	48301	.	+	.	FI_gene_label "AC240565.1^ENSG00000280136.2"  ; ID "TLK2--AC240565.1^ENST00000624936.2"  ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; exon_id "ENSE00003756821.1"  ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2"  ; gene_name "AC240565.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2"  ; havana_transcript "OTTHUMT00000479189.2"  ; level 2 ; orig_coord_info "chr17,118383,118578,-"  ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2"  ; transcript_name "AC240565.1-201"  ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1	HAVANA	RNA	1001	4192	.	+	.	FI_gene_label "TLK2P1^ENSG00000226049.3"  ; ID "TLK2P1--AC110079.1^ENST00000530992.1"  ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; exon_id "ENSE00002174619.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3"  ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1"  ; havana_transcript "OTTHUMT00000389700.1"  ; hgnc_id "HGNC:18048"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,34036681,34039872,-"  ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1"  ; transcript_name "TLK2P1-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created: 
TLK2P1--AC110079.1	HAVANA	gene	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1	HAVANA	RNA	7193	19707	.	+	.	FI_gene_label "AC110079.1^ENSG00000260404.3"  ; ID "TLK2P1--AC110079.1^ENST00000567913.2"  ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; exon_id "ENSE00002625896.1"  ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3"  ; gene_name "AC110079.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4"  ; havana_transcript "OTTHUMT00000364170.2"  ; level 2 ; orig_coord_info "chr4,118591773,118591895,+"  ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2"  ; transcript_name "AC110079.1-201"  ; transcript_support_level 5 ; transcript_type processed_transcript
195 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 ------------------------------
508 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 13 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