.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (BVT_FFPE_TRNA_bld_02_A23WKFTLT4_3)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/40d94ffb4eda1bbaf6c693a1490aa4/.command.out
Size: 27.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (BVT_FFPE_TRNA_bld_02_A23WKFTLT4_3)
Attempt
Content

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 986
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 986
=> 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:986
  => 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: 
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: 
IL9R--WASH4P	HAVANA	gene	1001	10010	.	+	.	FI_gene_label "IL9R^ENSG00000124334.17"  ; ID "IL9R--WASH4P^IL9R^ENSG00000124334.17"  ; ccdsid "CCDS14771.4"  ; exon_id "ENSE00003693591.1"  ; exon_number 1 ; gene_id "IL9R--WASH4P^IL9R^ENSG00000124334.17"  ; gene_name IL9R ; gene_type protein_coding ; havana_gene "OTTHUMG00000022720.1"  ; havana_transcript "OTTHUMT00000058981.1"  ; hgnc_id "HGNC:6030"  ; level 2 ; orig_coord_info "chrX,155997760,155997787,+"  ; protein_id "ENSP00000244174.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "IL9R--WASH4P^ENST00000244174.10"  ; transcript_name "IL9R-201"  ; transcript_support_level 1 ; transcript_type protein_coding
IL9R--WASH4P	HAVANA	mRNA	1001	10010	.	+	.	FI_gene_label "IL9R^ENSG00000124334.17"  ; ID "IL9R--WASH4P^ENST00000244174.10"  ; Parent "IL9R--WASH4P^IL9R^ENSG00000124334.17"  ; ccdsid "CCDS14771.4"  ; exon_id "ENSE00003693591.1"  ; exon_number 1 ; gene_id "IL9R--WASH4P^IL9R^ENSG00000124334.17"  ; gene_name IL9R ; gene_type protein_coding ; havana_gene "OTTHUMG00000022720.1"  ; havana_transcript "OTTHUMT00000058981.1"  ; hgnc_id "HGNC:6030"  ; level 2 ; orig_coord_info "chrX,155997760,155997787,+"  ; protein_id "ENSP00000244174.5"  ; tag basic appris_principal_1 CCDS ; transcript_id "IL9R--WASH4P^ENST00000244174.10"  ; transcript_name "IL9R-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
MSI2--SETP3	HAVANA	gene	1673	54046	.	+	.	FI_gene_label "MSI2^ENSG00000153944.12"  ; ID "MSI2--SETP3^MSI2^ENSG00000153944.12"  ; ccdsid "CCDS11596.1"  ; exon_id "ENSE00002219180.3"  ; exon_number 1 ; gene_id "MSI2--SETP3^MSI2^ENSG00000153944.12"  ; gene_name MSI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178398.4"  ; havana_transcript "OTTHUMT00000441813.2"  ; hgnc_id "HGNC:18585"  ; level 2 ; orig_coord_info "chr17,57256743,57256804,+"  ; protein_id "ENSP00000284073.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--SETP3^ENST00000284073.7"  ; transcript_name "MSI2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
MSI2--SETP3	HAVANA	mRNA	1673	54046	.	+	.	FI_gene_label "MSI2^ENSG00000153944.12"  ; ID "MSI2--SETP3^ENST00000284073.7"  ; Parent "MSI2--SETP3^MSI2^ENSG00000153944.12"  ; ccdsid "CCDS11596.1"  ; exon_id "ENSE00002219180.3"  ; exon_number 1 ; gene_id "MSI2--SETP3^MSI2^ENSG00000153944.12"  ; gene_name MSI2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000178398.4"  ; havana_transcript "OTTHUMT00000441813.2"  ; hgnc_id "HGNC:18585"  ; level 2 ; orig_coord_info "chr17,57256743,57256804,+"  ; protein_id "ENSP00000284073.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "MSI2--SETP3^ENST00000284073.7"  ; transcript_name "MSI2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	HAVANA	gene	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHA13	HAVANA	mRNA	14666	23106	.	+	.	FI_gene_label "PCDHA13^ENSG00000239389.8"  ; ID "PCDHA4--PCDHA13^ENST00000289272.3"  ; Parent "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; ccdsid "CCDS4240.1"  ; exon_id "ENSE00001038419.2"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA13^ENSG00000239389.8"  ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4"  ; havana_transcript "OTTHUMT00000335000.2"  ; hgnc_id "HGNC:8667"  ; level 2 ; orig_coord_info "chr5,140882269,140884662,+"  ; protein_id "ENSP00000289272.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHA13^ENST00000289272.3"  ; transcript_name "PCDHA13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHA13	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHA13	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHA13^ENST00000378125.4"  ; Parent "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHA13^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHA13^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	HAVANA	gene	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC1	HAVANA	mRNA	14666	24681	.	+	.	FI_gene_label "PCDHAC1^ENSG00000248383.5"  ; ID "PCDHA4--PCDHAC1^ENST00000253807.3"  ; Parent "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; ccdsid "CCDS4241.1"  ; exon_id "ENSE00001085780.5"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHAC1^ENSG00000248383.5"  ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3"  ; havana_transcript "OTTHUMT00000251798.1"  ; hgnc_id "HGNC:8676"  ; level 2 ; orig_coord_info "chr5,140926893,140929325,+"  ; protein_id "ENSP00000253807.2"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC1^ENST00000253807.3"  ; transcript_name "PCDHAC1-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC1	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC1	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC1^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC1^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC1^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	HAVANA	gene	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA4--PCDHAC2	HAVANA	mRNA	14672	25407	.	+	.	FI_gene_label "PCDHAC2^ENSG00000243232.6"  ; ID "PCDHA4--PCDHAC2^ENST00000289269.7"  ; Parent "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; ccdsid "CCDS4242.1"  ; exon_id "ENSE00001038414.4"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHAC2^ENSG00000243232.6"  ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7"  ; havana_transcript "OTTHUMT00000251802.4"  ; hgnc_id "HGNC:8677"  ; level 2 ; orig_coord_info "chr5,140966767,140969331,+"  ; protein_id "ENSP00000289269.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA4--PCDHAC2^ENST00000289269.7"  ; transcript_name "PCDHAC2-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PCDHA4--PCDHAC2	ENSEMBL	gene	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PCDHA4--PCDHAC2	ENSEMBL	mRNA	1001	3590	.	+	.	FI_gene_label "PCDHA4^ENSG00000204967.12"  ; ID "PCDHA4--PCDHAC2^ENST00000378125.4"  ; Parent "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; exon_id "ENSE00003735925.1"  ; exon_number 1 ; gene_id "PCDHA4--PCDHAC2^PCDHA4^ENSG00000204967.12"  ; gene_name PCDHA4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163360.5"  ; hgnc_id "HGNC:8670"  ; level 3 ; orig_coord_info "chr5,140806929,140806945,+"  ; protein_id "ENSP00000367365.4"  ; tag basic ; transcript_id "PCDHA4--PCDHAC2^ENST00000378125.4"  ; transcript_name "PCDHA4-201"  ; transcript_support_level 5 ; 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: 
IL9R--WASH4P	HAVANA	gene	13220	16907	.	+	.	FI_gene_label "WASH4P^ENSG00000234769.7"  ; ID "IL9R--WASH4P^WASH4P^ENSG00000234769.7"  ; exon_id "ENSE00001656805.1"  ; exon_number 1 ; gene_id "IL9R--WASH4P^WASH4P^ENSG00000234769.7"  ; gene_name WASH4P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000059914.6"  ; havana_transcript "OTTHUMT00000133175.3"  ; hgnc_id "HGNC:14126"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr16,17957,18068,-"  ; tag basic ; transcript_id "IL9R--WASH4P^ENST00000564273.4"  ; transcript_name "WASH4P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
IL9R--WASH4P	HAVANA	RNA	13220	16907	.	+	.	FI_gene_label "WASH4P^ENSG00000234769.7"  ; ID "IL9R--WASH4P^ENST00000564273.4"  ; Parent "IL9R--WASH4P^WASH4P^ENSG00000234769.7"  ; exon_id "ENSE00001656805.1"  ; exon_number 1 ; gene_id "IL9R--WASH4P^WASH4P^ENSG00000234769.7"  ; gene_name WASH4P ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000059914.6"  ; havana_transcript "OTTHUMT00000133175.3"  ; hgnc_id "HGNC:14126"  ; level 2 ; ont "PGO:0000005"  ; orig_coord_info "chr16,17957,18068,-"  ; tag basic ; transcript_id "IL9R--WASH4P^ENST00000564273.4"  ; transcript_name "WASH4P-201"  ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created: 
MSI2--SETP3	HAVANA	gene	57047	57859	.	+	.	FI_gene_label "SETP3^ENSG00000266648.1"  ; ID "MSI2--SETP3^SETP3^ENSG00000266648.1"  ; exon_id "ENSE00002726807.1"  ; exon_number 1 ; gene_id "MSI2--SETP3^SETP3^ENSG00000266648.1"  ; gene_name SETP3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000179241.1"  ; havana_transcript "OTTHUMT00000445410.1"  ; hgnc_id "HGNC:31115"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,58476138,58476950,-"  ; tag pseudo_consens basic ; transcript_id "MSI2--SETP3^ENST00000581726.1"  ; transcript_name "SETP3-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
MSI2--SETP3	HAVANA	RNA	57047	57859	.	+	.	FI_gene_label "SETP3^ENSG00000266648.1"  ; ID "MSI2--SETP3^ENST00000581726.1"  ; Parent "MSI2--SETP3^SETP3^ENSG00000266648.1"  ; exon_id "ENSE00002726807.1"  ; exon_number 1 ; gene_id "MSI2--SETP3^SETP3^ENSG00000266648.1"  ; gene_name SETP3 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000179241.1"  ; havana_transcript "OTTHUMT00000445410.1"  ; hgnc_id "HGNC:31115"  ; level 1 ; ont "PGO:0000004"  ; orig_coord_info "chr17,58476138,58476950,-"  ; tag pseudo_consens basic ; transcript_id "MSI2--SETP3^ENST00000581726.1"  ; transcript_name "SETP3-201"  ; transcript_support_level NA ; transcript_type processed_pseudogene
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
98 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 ------------------------------
160 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 10 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