.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/d307a292968a48c9ac2cf7cf76d1d8/.command.log
Size: 25.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/6ae1b7a15d34f62dce429a4639b223/fi_workdir/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/d307a292968a48c9ac2cf7cf76d1d8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/d307a292968a48c9ac2cf7cf76d1d8/.command.run
==> STAGING COMPLETE (3 inputs)

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

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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------
                                        
                                       
                          ------ Start parsing ------                           
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
	* locus_tag
	* gene_id
=> merge_loci option deactivated
=> Machine information:
	This script is being run by perl v5.32.1
	Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
	Operating system being used: linux 
=> Accessing Ontology
	No ontology accessible from the gff file header!
	We use the SOFA ontology distributed with AGAT:
		/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
	Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
		4 root terms, and 2596 total terms, and 1516 leaf terms
	Filtering ontology:
		We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 1567
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1567
=> Number of feature type (3rd column): 2
	* Level1: 0 => 
	* level2: 0 => 
	* level3: 2 => CDS exon
	* unknown: 0 => 
=>Check because only level3 features:
 * Number of feature with Parent attribute:0
 * Number of feature with a common attribute:1567
  => 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: 
B4GALT5--WFDC3	HAVANA	gene	16271	24892	.	+	.	FI_gene_label "WFDC3^ENSG00000124116.19"  ; ID "B4GALT5--WFDC3^WFDC3^ENSG00000124116.19"  ; ccdsid "CCDS33478.1"  ; exon_id "ENSE00001693288.1"  ; exon_number 2 ; gene_id "B4GALT5--WFDC3^WFDC3^ENSG00000124116.19"  ; gene_name WFDC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032614.5"  ; havana_transcript "OTTHUMT00000316858.2"  ; hgnc_id "HGNC:15957"  ; level 2 ; orig_coord_info "chr20,45789894,45789975,-"  ; protein_id "ENSP00000243938.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "B4GALT5--WFDC3^ENST00000243938.9"  ; transcript_name "WFDC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
B4GALT5--WFDC3	HAVANA	mRNA	16271	24892	.	+	.	FI_gene_label "WFDC3^ENSG00000124116.19"  ; ID "B4GALT5--WFDC3^ENST00000243938.9"  ; Parent "B4GALT5--WFDC3^WFDC3^ENSG00000124116.19"  ; ccdsid "CCDS33478.1"  ; exon_id "ENSE00001693288.1"  ; exon_number 2 ; gene_id "B4GALT5--WFDC3^WFDC3^ENSG00000124116.19"  ; gene_name WFDC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032614.5"  ; havana_transcript "OTTHUMT00000316858.2"  ; hgnc_id "HGNC:15957"  ; level 2 ; orig_coord_info "chr20,45789894,45789975,-"  ; protein_id "ENSP00000243938.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "B4GALT5--WFDC3^ENST00000243938.9"  ; transcript_name "WFDC3-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
B4GALT5--WFDC3	HAVANA	gene	1001	13221	.	+	.	FI_gene_label "B4GALT5^ENSG00000158470.5"  ; ID "B4GALT5--WFDC3^B4GALT5^ENSG00000158470.5"  ; ccdsid "CCDS13420.1"  ; exon_id "ENSE00001455930.4"  ; exon_number 1 ; gene_id "B4GALT5--WFDC3^B4GALT5^ENSG00000158470.5"  ; gene_name B4GALT5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033086.3"  ; havana_transcript "OTTHUMT00000080543.3"  ; hgnc_id "HGNC:928"  ; level 2 ; orig_coord_info "chr20,49713576,49713690,-"  ; protein_id "ENSP00000360776.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "B4GALT5--WFDC3^ENST00000371711.4"  ; transcript_name "B4GALT5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
B4GALT5--WFDC3	HAVANA	mRNA	1001	13221	.	+	.	FI_gene_label "B4GALT5^ENSG00000158470.5"  ; ID "B4GALT5--WFDC3^ENST00000371711.4"  ; Parent "B4GALT5--WFDC3^B4GALT5^ENSG00000158470.5"  ; ccdsid "CCDS13420.1"  ; exon_id "ENSE00001455930.4"  ; exon_number 1 ; gene_id "B4GALT5--WFDC3^B4GALT5^ENSG00000158470.5"  ; gene_name B4GALT5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033086.3"  ; havana_transcript "OTTHUMT00000080543.3"  ; hgnc_id "HGNC:928"  ; level 2 ; orig_coord_info "chr20,49713576,49713690,-"  ; protein_id "ENSP00000360776.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "B4GALT5--WFDC3^ENST00000371711.4"  ; transcript_name "B4GALT5-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
HEATR5B--AC142381.4	HAVANA	gene	1001	40979	.	+	.	FI_gene_label "HEATR5B^ENSG00000008869.12"  ; ID "HEATR5B--AC142381.4^HEATR5B^ENSG00000008869.12"  ; ccdsid "CCDS33181.1"  ; exon_id "ENSE00001796147.1"  ; exon_number 2 ; gene_id "HEATR5B--AC142381.4^HEATR5B^ENSG00000008869.12"  ; gene_name HEATR5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000152158.2"  ; havana_transcript "OTTHUMT00000325492.2"  ; hgnc_id "HGNC:29273"  ; level 2 ; orig_coord_info "chr2,37083289,37083414,-"  ; protein_id "ENSP00000233099.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HEATR5B--AC142381.4^ENST00000233099.6"  ; transcript_name "HEATR5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
HEATR5B--AC142381.4	HAVANA	mRNA	1001	40979	.	+	.	FI_gene_label "HEATR5B^ENSG00000008869.12"  ; ID "HEATR5B--AC142381.4^ENST00000233099.6"  ; Parent "HEATR5B--AC142381.4^HEATR5B^ENSG00000008869.12"  ; ccdsid "CCDS33181.1"  ; exon_id "ENSE00001796147.1"  ; exon_number 2 ; gene_id "HEATR5B--AC142381.4^HEATR5B^ENSG00000008869.12"  ; gene_name HEATR5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000152158.2"  ; havana_transcript "OTTHUMT00000325492.2"  ; hgnc_id "HGNC:29273"  ; level 2 ; orig_coord_info "chr2,37083289,37083414,-"  ; protein_id "ENSP00000233099.5"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "HEATR5B--AC142381.4^ENST00000233099.6"  ; transcript_name "HEATR5B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
INPP5A--AL596223.1	HAVANA	gene	2397	15201	.	+	.	FI_gene_label "INPP5A^ENSG00000068383.19"  ; ID "INPP5A--AL596223.1^INPP5A^ENSG00000068383.19"  ; exon_id "ENSE00001635546.1"  ; exon_number 1 ; gene_id "INPP5A--AL596223.1^INPP5A^ENSG00000068383.19"  ; gene_name INPP5A ; gene_type protein_coding ; havana_gene "OTTHUMG00000019293.6"  ; havana_transcript "OTTHUMT00000051087.2"  ; hgnc_id "HGNC:6076"  ; level 2 ; orig_coord_info "chr10,132607926,132607956,+"  ; protein_id "ENSP00000340707.6"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "INPP5A--AL596223.1^ENST00000342652.6"  ; transcript_name "INPP5A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
INPP5A--AL596223.1	HAVANA	mRNA	2397	15201	.	+	.	FI_gene_label "INPP5A^ENSG00000068383.19"  ; ID "INPP5A--AL596223.1^ENST00000342652.6"  ; Parent "INPP5A--AL596223.1^INPP5A^ENSG00000068383.19"  ; exon_id "ENSE00001635546.1"  ; exon_number 1 ; gene_id "INPP5A--AL596223.1^INPP5A^ENSG00000068383.19"  ; gene_name INPP5A ; gene_type protein_coding ; havana_gene "OTTHUMG00000019293.6"  ; havana_transcript "OTTHUMT00000051087.2"  ; hgnc_id "HGNC:6076"  ; level 2 ; orig_coord_info "chr10,132607926,132607956,+"  ; protein_id "ENSP00000340707.6"  ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "INPP5A--AL596223.1^ENST00000342652.6"  ; transcript_name "INPP5A-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
ITCH--PHF20	HAVANA	gene	1072	35781	.	+	.	FI_gene_label "ITCH^ENSG00000078747.16"  ; ID "ITCH--PHF20^ITCH^ENSG00000078747.16"  ; ccdsid "CCDS58768.1"  ; exon_id "ENSE00003669122.1"  ; exon_number 3 ; gene_id "ITCH--PHF20^ITCH^ENSG00000078747.16"  ; gene_name ITCH ; gene_type protein_coding ; havana_gene "OTTHUMG00000032300.6"  ; havana_transcript "OTTHUMT00000078783.2"  ; hgnc_id "HGNC:13890"  ; level 2 ; orig_coord_info "chr20,34393812,34393881,+"  ; protein_id "ENSP00000262650.5"  ; tag basic CCDS ; transcript_id "ITCH--PHF20^ENST00000262650.10"  ; transcript_name "ITCH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ITCH--PHF20	HAVANA	mRNA	1072	35781	.	+	.	FI_gene_label "ITCH^ENSG00000078747.16"  ; ID "ITCH--PHF20^ENST00000262650.10"  ; Parent "ITCH--PHF20^ITCH^ENSG00000078747.16"  ; ccdsid "CCDS58768.1"  ; exon_id "ENSE00003669122.1"  ; exon_number 3 ; gene_id "ITCH--PHF20^ITCH^ENSG00000078747.16"  ; gene_name ITCH ; gene_type protein_coding ; havana_gene "OTTHUMG00000032300.6"  ; havana_transcript "OTTHUMT00000078783.2"  ; hgnc_id "HGNC:13890"  ; level 2 ; orig_coord_info "chr20,34393812,34393881,+"  ; protein_id "ENSP00000262650.5"  ; tag basic CCDS ; transcript_id "ITCH--PHF20^ENST00000262650.10"  ; transcript_name "ITCH-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ITCH--PHF20	HAVANA	gene	45984	67184	.	+	.	FI_gene_label "PHF20^ENSG00000025293.17"  ; ID "ITCH--PHF20^PHF20^ENSG00000025293.17"  ; exon_id "ENSE00003477874.1"  ; exon_number 3 ; gene_id "ITCH--PHF20^PHF20^ENSG00000025293.17"  ; gene_name PHF20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032367.8"  ; havana_transcript "OTTHUMT00000078947.3"  ; hgnc_id "HGNC:16098"  ; level 2 ; orig_coord_info "chr20,35801523,35801605,+"  ; protein_id "ENSP00000341900.6"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "ITCH--PHF20^ENST00000339089.10"  ; transcript_name "PHF20-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ITCH--PHF20	HAVANA	mRNA	45984	67184	.	+	.	FI_gene_label "PHF20^ENSG00000025293.17"  ; ID "ITCH--PHF20^ENST00000339089.10"  ; Parent "ITCH--PHF20^PHF20^ENSG00000025293.17"  ; exon_id "ENSE00003477874.1"  ; exon_number 3 ; gene_id "ITCH--PHF20^PHF20^ENSG00000025293.17"  ; gene_name PHF20 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032367.8"  ; havana_transcript "OTTHUMT00000078947.3"  ; hgnc_id "HGNC:16098"  ; level 2 ; orig_coord_info "chr20,35801523,35801605,+"  ; protein_id "ENSP00000341900.6"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "ITCH--PHF20^ENST00000339089.10"  ; transcript_name "PHF20-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
PAN3--POLR1D	HAVANA	gene	28431	29988	.	+	.	FI_gene_label "POLR1D^ENSG00000186184.19"  ; ID "PAN3--POLR1D^POLR1D^ENSG00000186184.19"  ; ccdsid "CCDS9325.1"  ; exon_id "ENSE00003899880.1"  ; exon_number 1 ; gene_id "PAN3--POLR1D^POLR1D^ENSG00000186184.19"  ; gene_name POLR1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000016635.10"  ; havana_transcript "OTTHUMT00000044305.2"  ; hgnc_id "HGNC:20422"  ; level 2 ; orig_coord_info "chr13,27621984,27622009,+"  ; protein_id "ENSP00000302478.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PAN3--POLR1D^ENST00000302979.5"  ; transcript_name "POLR1D-201"  ; transcript_support_level 1 ; transcript_type protein_coding
PAN3--POLR1D	HAVANA	mRNA	28431	29988	.	+	.	FI_gene_label "POLR1D^ENSG00000186184.19"  ; ID "PAN3--POLR1D^ENST00000302979.5"  ; Parent "PAN3--POLR1D^POLR1D^ENSG00000186184.19"  ; ccdsid "CCDS9325.1"  ; exon_id "ENSE00003899880.1"  ; exon_number 1 ; gene_id "PAN3--POLR1D^POLR1D^ENSG00000186184.19"  ; gene_name POLR1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000016635.10"  ; havana_transcript "OTTHUMT00000044305.2"  ; hgnc_id "HGNC:20422"  ; level 2 ; orig_coord_info "chr13,27621984,27622009,+"  ; protein_id "ENSP00000302478.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PAN3--POLR1D^ENST00000302979.5"  ; transcript_name "POLR1D-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PAN3--POLR1D	HAVANA	gene	1040	24280	.	+	.	FI_gene_label "PAN3^ENSG00000152520.14"  ; ID "PAN3--POLR1D^PAN3^ENSG00000152520.14"  ; ccdsid "CCDS9329.2"  ; exon_id "ENSE00003572843.2"  ; exon_number 1 ; gene_id "PAN3--POLR1D^PAN3^ENSG00000152520.14"  ; gene_name PAN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016645.6"  ; havana_transcript "OTTHUMT00000044318.5"  ; hgnc_id "HGNC:29991"  ; level 2 ; orig_coord_info "chr13,28138658,28139087,+"  ; protein_id "ENSP00000370345.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PAN3--POLR1D^ENST00000380958.8"  ; transcript_name "PAN3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PAN3--POLR1D	HAVANA	mRNA	1040	24280	.	+	.	FI_gene_label "PAN3^ENSG00000152520.14"  ; ID "PAN3--POLR1D^ENST00000380958.8"  ; Parent "PAN3--POLR1D^PAN3^ENSG00000152520.14"  ; ccdsid "CCDS9329.2"  ; exon_id "ENSE00003572843.2"  ; exon_number 1 ; gene_id "PAN3--POLR1D^PAN3^ENSG00000152520.14"  ; gene_name PAN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016645.6"  ; havana_transcript "OTTHUMT00000044318.5"  ; hgnc_id "HGNC:29991"  ; level 2 ; orig_coord_info "chr13,28138658,28139087,+"  ; protein_id "ENSP00000370345.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PAN3--POLR1D^ENST00000380958.8"  ; transcript_name "PAN3-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SCX--MROH1	ENSEMBL	gene	9017	43278	.	+	.	FI_gene_label "MROH1^ENSG00000179832.17"  ; ID "SCX--MROH1^MROH1^ENSG00000179832.17"  ; ccdsid "CCDS47938.1"  ; exon_id "ENSE00002236754.1"  ; exon_number 1 ; gene_id "SCX--MROH1^MROH1^ENSG00000179832.17"  ; gene_name MROH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165781.1"  ; hgnc_id "HGNC:26958"  ; level 3 ; orig_coord_info "chr8,144163827,144163848,+"  ; protein_id "ENSP00000321737.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "SCX--MROH1^ENST00000326134.9"  ; transcript_name "MROH1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
SCX--MROH1	ENSEMBL	mRNA	9017	43278	.	+	.	FI_gene_label "MROH1^ENSG00000179832.17"  ; ID "SCX--MROH1^ENST00000326134.9"  ; Parent "SCX--MROH1^MROH1^ENSG00000179832.17"  ; ccdsid "CCDS47938.1"  ; exon_id "ENSE00002236754.1"  ; exon_number 1 ; gene_id "SCX--MROH1^MROH1^ENSG00000179832.17"  ; gene_name MROH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165781.1"  ; hgnc_id "HGNC:26958"  ; level 3 ; orig_coord_info "chr8,144163827,144163848,+"  ; protein_id "ENSP00000321737.5"  ; tag basic appris_principal_4 CCDS ; transcript_id "SCX--MROH1^ENST00000326134.9"  ; transcript_name "MROH1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
SCX--MROH1	HAVANA	gene	1001	3029	.	+	.	FI_gene_label "SCX^ENSG00000260428.3"  ; ID "SCX--MROH1^SCX^ENSG00000260428.3"  ; ccdsid "CCDS43779.1"  ; exon_id "ENSE00002607285.3"  ; exon_number 1 ; gene_id "SCX--MROH1^SCX^ENSG00000260428.3"  ; gene_name SCX ; gene_type protein_coding ; havana_gene "OTTHUMG00000175582.3"  ; havana_transcript "OTTHUMT00000430547.3"  ; hgnc_id "HGNC:32322"  ; level 2 ; orig_coord_info "chr8,144266614,144267180,+"  ; protein_id "ENSP00000476384.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCX--MROH1^ENST00000567180.3"  ; transcript_name "SCX-201"  ; transcript_support_level 1 ; transcript_type protein_coding
SCX--MROH1	HAVANA	mRNA	1001	3029	.	+	.	FI_gene_label "SCX^ENSG00000260428.3"  ; ID "SCX--MROH1^ENST00000567180.3"  ; Parent "SCX--MROH1^SCX^ENSG00000260428.3"  ; ccdsid "CCDS43779.1"  ; exon_id "ENSE00002607285.3"  ; exon_number 1 ; gene_id "SCX--MROH1^SCX^ENSG00000260428.3"  ; gene_name SCX ; gene_type protein_coding ; havana_gene "OTTHUMG00000175582.3"  ; havana_transcript "OTTHUMT00000430547.3"  ; hgnc_id "HGNC:32322"  ; level 2 ; orig_coord_info "chr8,144266614,144267180,+"  ; protein_id "ENSP00000476384.1"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SCX--MROH1^ENST00000567180.3"  ; transcript_name "SCX-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: 
HEATR5B--AC142381.4	HAVANA	gene	45482	45710	.	+	.	FI_gene_label "AC142381.4^ENSG00000261727.2"  ; ID "HEATR5B--AC142381.4^AC142381.4^ENSG00000261727.2"  ; exon_id "ENSE00002612649.1"  ; exon_number 1 ; gene_id "HEATR5B--AC142381.4^AC142381.4^ENSG00000261727.2"  ; gene_name "AC142381.4"  ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000176559.1"  ; havana_transcript "OTTHUMT00000432531.1"  ; level 2 ; ont "PGO:0000004"  "PGO:0000019"  ; orig_coord_info "chr16,32084274,32084502,-"  ; tag basic ; transcript_id "HEATR5B--AC142381.4^ENST00000563973.1"  ; transcript_name "AC142381.4-202"  ; transcript_support_level NA ; transcript_type transcribed_processed_pseudogene
HEATR5B--AC142381.4	HAVANA	RNA	45482	45710	.	+	.	FI_gene_label "AC142381.4^ENSG00000261727.2"  ; ID "HEATR5B--AC142381.4^ENST00000563973.1"  ; Parent "HEATR5B--AC142381.4^AC142381.4^ENSG00000261727.2"  ; exon_id "ENSE00002612649.1"  ; exon_number 1 ; gene_id "HEATR5B--AC142381.4^AC142381.4^ENSG00000261727.2"  ; gene_name "AC142381.4"  ; gene_type transcribed_processed_pseudogene ; havana_gene "OTTHUMG00000176559.1"  ; havana_transcript "OTTHUMT00000432531.1"  ; level 2 ; ont "PGO:0000004"  "PGO:0000019"  ; orig_coord_info "chr16,32084274,32084502,-"  ; tag basic ; transcript_id "HEATR5B--AC142381.4^ENST00000563973.1"  ; transcript_name "AC142381.4-202"  ; transcript_support_level NA ; transcript_type transcribed_processed_pseudogene
L1 and L2 created: 
INPP5A--AL596223.1	HAVANA	gene	21929	27002	.	+	.	FI_gene_label "AL596223.1^ENSG00000229261.1"  ; ID "INPP5A--AL596223.1^AL596223.1^ENSG00000229261.1"  ; exon_id "ENSE00001618677.1"  ; exon_number 1 ; gene_id "INPP5A--AL596223.1^AL596223.1^ENSG00000229261.1"  ; gene_name "AL596223.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000018372.1"  ; havana_transcript "OTTHUMT00000048393.1"  ; level 2 ; orig_coord_info "chr10,69232371,69232490,-"  ; tag basic ; transcript_id "INPP5A--AL596223.1^ENST00000450995.1"  ; transcript_name "AL596223.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
INPP5A--AL596223.1	HAVANA	RNA	21929	27002	.	+	.	FI_gene_label "AL596223.1^ENSG00000229261.1"  ; ID "INPP5A--AL596223.1^ENST00000450995.1"  ; Parent "INPP5A--AL596223.1^AL596223.1^ENSG00000229261.1"  ; exon_id "ENSE00001618677.1"  ; exon_number 1 ; gene_id "INPP5A--AL596223.1^AL596223.1^ENSG00000229261.1"  ; gene_name "AL596223.1"  ; gene_type lncRNA ; havana_gene "OTTHUMG00000018372.1"  ; havana_transcript "OTTHUMT00000048393.1"  ; level 2 ; orig_coord_info "chr10,69232371,69232490,-"  ; tag basic ; transcript_id "INPP5A--AL596223.1^ENST00000450995.1"  ; transcript_name "AL596223.1-201"  ; transcript_support_level 2 ; transcript_type lncRNA
112 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 ------------------------------
189 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 11 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