.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00586_B23MVV7LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/b6cf7de97788dbfc181203d103dd97/.command.log
Size: 40.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:AGAT_CONVERTSPGFF2TSV (tih_rna_sample_00586_B23MVV7LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/619cfc7072d5071743af0e040e44e6/fi_workdir/tih_rna_sample_00586_B23MVV7LT4_1.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/b6cf7de97788dbfc181203d103dd97/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/b6cf7de97788dbfc181203d103dd97/.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: 2208
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2208
=> 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:2208
  => 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: 
AC015911.9--SLFN12L	HAVANA	gene	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
AC015911.9--SLFN12L	HAVANA	mRNA	4692	11059	.	+	.	FI_gene_label "SLFN12L^ENSG00000205045.11"  ; ID "AC015911.9--SLFN12L^ENST00000260908.12"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; exon_id "ENSE00003850559.1"  ; exon_number 2 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000205045.11"  ; gene_name SLFN12L ; gene_type protein_coding ; havana_gene "OTTHUMG00000193506.1"  ; havana_transcript "OTTHUMT00000395748.3"  ; hgnc_id "HGNC:33920"  ; level 2 ; orig_coord_info "chr17,35479117,35480155,-"  ; protein_id "ENSP00000437635.2"  ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AC015911.9--SLFN12L^ENST00000260908.12"  ; transcript_name "SLFN12L-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
AC091057.6--CHRFAM7A	HAVANA	gene	9985	23442	.	+	.	FI_gene_label "CHRFAM7A^ENSG00000166664.14"  ; ID "AC091057.6--CHRFAM7A^CHRFAM7A^ENSG00000166664.14"  ; ccdsid "CCDS32184.1"  ; exon_id "ENSE00003561724.1"  ; exon_number 3 ; gene_id "AC091057.6--CHRFAM7A^CHRFAM7A^ENSG00000166664.14"  ; gene_name CHRFAM7A ; gene_type protein_coding ; havana_gene "OTTHUMG00000175645.4"  ; havana_transcript "OTTHUMT00000430700.2"  ; hgnc_id "HGNC:15781"  ; level 2 ; orig_coord_info "chr15,30383319,30383351,-"  ; protein_id "ENSP00000299847.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC091057.6--CHRFAM7A^ENST00000299847.7"  ; transcript_name "CHRFAM7A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
AC091057.6--CHRFAM7A	HAVANA	mRNA	9985	23442	.	+	.	FI_gene_label "CHRFAM7A^ENSG00000166664.14"  ; ID "AC091057.6--CHRFAM7A^ENST00000299847.7"  ; Parent "AC091057.6--CHRFAM7A^CHRFAM7A^ENSG00000166664.14"  ; ccdsid "CCDS32184.1"  ; exon_id "ENSE00003561724.1"  ; exon_number 3 ; gene_id "AC091057.6--CHRFAM7A^CHRFAM7A^ENSG00000166664.14"  ; gene_name CHRFAM7A ; gene_type protein_coding ; havana_gene "OTTHUMG00000175645.4"  ; havana_transcript "OTTHUMT00000430700.2"  ; hgnc_id "HGNC:15781"  ; level 2 ; orig_coord_info "chr15,30383319,30383351,-"  ; protein_id "ENSP00000299847.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC091057.6--CHRFAM7A^ENST00000299847.7"  ; transcript_name "CHRFAM7A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
AC091057.6--ULK4	HAVANA	gene	9703	54725	.	+	.	FI_gene_label "ULK4^ENSG00000168038.11"  ; ID "AC091057.6--ULK4^ULK4^ENSG00000168038.11"  ; ccdsid "CCDS43071.1"  ; exon_id "ENSE00003538346.1"  ; exon_number 2 ; gene_id "AC091057.6--ULK4^ULK4^ENSG00000168038.11"  ; gene_name ULK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156210.4"  ; havana_transcript "OTTHUMT00000343490.2"  ; hgnc_id "HGNC:15784"  ; level 2 ; orig_coord_info "chr3,41954622,41954759,-"  ; protein_id "ENSP00000301831.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC091057.6--ULK4^ENST00000301831.9"  ; transcript_name "ULK4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
AC091057.6--ULK4	HAVANA	mRNA	9703	54725	.	+	.	FI_gene_label "ULK4^ENSG00000168038.11"  ; ID "AC091057.6--ULK4^ENST00000301831.9"  ; Parent "AC091057.6--ULK4^ULK4^ENSG00000168038.11"  ; ccdsid "CCDS43071.1"  ; exon_id "ENSE00003538346.1"  ; exon_number 2 ; gene_id "AC091057.6--ULK4^ULK4^ENSG00000168038.11"  ; gene_name ULK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156210.4"  ; havana_transcript "OTTHUMT00000343490.2"  ; hgnc_id "HGNC:15784"  ; level 2 ; orig_coord_info "chr3,41954622,41954759,-"  ; protein_id "ENSP00000301831.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC091057.6--ULK4^ENST00000301831.9"  ; transcript_name "ULK4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP11A--ULK4P2	HAVANA	gene	1361	15827	.	+	.	FI_gene_label "ARHGAP11A^ENSG00000198826.11"  ; ID "ARHGAP11A--ULK4P2^ARHGAP11A^ENSG00000198826.11"  ; ccdsid "CCDS10028.1"  ; exon_id "ENSE00001210960.2"  ; exon_number 1 ; gene_id "ARHGAP11A--ULK4P2^ARHGAP11A^ENSG00000198826.11"  ; gene_name ARHGAP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000129289.4"  ; havana_transcript "OTTHUMT00000251417.2"  ; hgnc_id "HGNC:15783"  ; level 2 ; orig_coord_info "chr15,32616212,32616340,+"  ; protein_id "ENSP00000355090.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ARHGAP11A--ULK4P2^ENST00000361627.8"  ; transcript_name "ARHGAP11A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGAP11A--ULK4P2	HAVANA	mRNA	1361	15827	.	+	.	FI_gene_label "ARHGAP11A^ENSG00000198826.11"  ; ID "ARHGAP11A--ULK4P2^ENST00000361627.8"  ; Parent "ARHGAP11A--ULK4P2^ARHGAP11A^ENSG00000198826.11"  ; ccdsid "CCDS10028.1"  ; exon_id "ENSE00001210960.2"  ; exon_number 1 ; gene_id "ARHGAP11A--ULK4P2^ARHGAP11A^ENSG00000198826.11"  ; gene_name ARHGAP11A ; gene_type protein_coding ; havana_gene "OTTHUMG00000129289.4"  ; havana_transcript "OTTHUMT00000251417.2"  ; hgnc_id "HGNC:15783"  ; level 2 ; orig_coord_info "chr15,32616212,32616340,+"  ; protein_id "ENSP00000355090.3"  ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ARHGAP11A--ULK4P2^ENST00000361627.8"  ; transcript_name "ARHGAP11A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP11B--CHRFAM7A	HAVANA	gene	10052	23509	.	+	.	FI_gene_label "CHRFAM7A^ENSG00000166664.14"  ; ID "ARHGAP11B--CHRFAM7A^CHRFAM7A^ENSG00000166664.14"  ; ccdsid "CCDS32184.1"  ; exon_id "ENSE00003561724.1"  ; exon_number 3 ; gene_id "ARHGAP11B--CHRFAM7A^CHRFAM7A^ENSG00000166664.14"  ; gene_name CHRFAM7A ; gene_type protein_coding ; havana_gene "OTTHUMG00000175645.4"  ; havana_transcript "OTTHUMT00000430700.2"  ; hgnc_id "HGNC:15781"  ; level 2 ; orig_coord_info "chr15,30383319,30383351,-"  ; protein_id "ENSP00000299847.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGAP11B--CHRFAM7A^ENST00000299847.7"  ; transcript_name "CHRFAM7A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
ARHGAP11B--CHRFAM7A	HAVANA	mRNA	10052	23509	.	+	.	FI_gene_label "CHRFAM7A^ENSG00000166664.14"  ; ID "ARHGAP11B--CHRFAM7A^ENST00000299847.7"  ; Parent "ARHGAP11B--CHRFAM7A^CHRFAM7A^ENSG00000166664.14"  ; ccdsid "CCDS32184.1"  ; exon_id "ENSE00003561724.1"  ; exon_number 3 ; gene_id "ARHGAP11B--CHRFAM7A^CHRFAM7A^ENSG00000166664.14"  ; gene_name CHRFAM7A ; gene_type protein_coding ; havana_gene "OTTHUMG00000175645.4"  ; havana_transcript "OTTHUMT00000430700.2"  ; hgnc_id "HGNC:15781"  ; level 2 ; orig_coord_info "chr15,30383319,30383351,-"  ; protein_id "ENSP00000299847.3"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGAP11B--CHRFAM7A^ENST00000299847.7"  ; transcript_name "CHRFAM7A-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
ARHGAP11B--ULK4	HAVANA	gene	9770	54792	.	+	.	FI_gene_label "ULK4^ENSG00000168038.11"  ; ID "ARHGAP11B--ULK4^ULK4^ENSG00000168038.11"  ; ccdsid "CCDS43071.1"  ; exon_id "ENSE00003538346.1"  ; exon_number 2 ; gene_id "ARHGAP11B--ULK4^ULK4^ENSG00000168038.11"  ; gene_name ULK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156210.4"  ; havana_transcript "OTTHUMT00000343490.2"  ; hgnc_id "HGNC:15784"  ; level 2 ; orig_coord_info "chr3,41954622,41954759,-"  ; protein_id "ENSP00000301831.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGAP11B--ULK4^ENST00000301831.9"  ; transcript_name "ULK4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
ARHGAP11B--ULK4	HAVANA	mRNA	9770	54792	.	+	.	FI_gene_label "ULK4^ENSG00000168038.11"  ; ID "ARHGAP11B--ULK4^ENST00000301831.9"  ; Parent "ARHGAP11B--ULK4^ULK4^ENSG00000168038.11"  ; ccdsid "CCDS43071.1"  ; exon_id "ENSE00003538346.1"  ; exon_number 2 ; gene_id "ARHGAP11B--ULK4^ULK4^ENSG00000168038.11"  ; gene_name ULK4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156210.4"  ; havana_transcript "OTTHUMT00000343490.2"  ; hgnc_id "HGNC:15784"  ; level 2 ; orig_coord_info "chr3,41954622,41954759,-"  ; protein_id "ENSP00000301831.4"  ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ARHGAP11B--ULK4^ENST00000301831.9"  ; transcript_name "ULK4-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B	HAVANA	mRNA	18631	44079	.	+	.	FI_gene_label "SEC16B^ENSG00000120341.18"  ; ID "CRYZL2P--SEC16B^ENST00000308284.10"  ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; ccdsid "CCDS44281.1"  ; exon_id "ENSE00003707644.1"  ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18"  ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20"  ; havana_transcript "OTTHUMT00000084773.22"  ; hgnc_id "HGNC:30301"  ; level 2 ; orig_coord_info "chr1,177967683,177967981,-"  ; protein_id "ENSP00000308339.6"  ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10"  ; transcript_name "SEC16B-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
NLRP2--ADAMTS13	HAVANA	gene	3577	21684	.	+	.	FI_gene_label "NLRP2^ENSG00000022556.16"  ; ID "NLRP2--ADAMTS13^NLRP2^ENSG00000022556.16"  ; ccdsid "CCDS86807.1"  ; exon_id "ENSE00003505640.1"  ; exon_number 2 ; gene_id "NLRP2--ADAMTS13^NLRP2^ENSG00000022556.16"  ; gene_name NLRP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167763.7"  ; havana_transcript "OTTHUMT00000396158.1"  ; hgnc_id "HGNC:22948"  ; level 2 ; orig_coord_info "chr19,54970016,54970295,+"  ; protein_id "ENSP00000263437.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NLRP2--ADAMTS13^ENST00000263437.10"  ; transcript_name "NLRP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
NLRP2--ADAMTS13	HAVANA	mRNA	3577	21684	.	+	.	FI_gene_label "NLRP2^ENSG00000022556.16"  ; ID "NLRP2--ADAMTS13^ENST00000263437.10"  ; Parent "NLRP2--ADAMTS13^NLRP2^ENSG00000022556.16"  ; ccdsid "CCDS86807.1"  ; exon_id "ENSE00003505640.1"  ; exon_number 2 ; gene_id "NLRP2--ADAMTS13^NLRP2^ENSG00000022556.16"  ; gene_name NLRP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167763.7"  ; havana_transcript "OTTHUMT00000396158.1"  ; hgnc_id "HGNC:22948"  ; level 2 ; orig_coord_info "chr19,54970016,54970295,+"  ; protein_id "ENSP00000263437.6"  ; tag basic appris_alternative_2 CCDS ; transcript_id "NLRP2--ADAMTS13^ENST00000263437.10"  ; transcript_name "NLRP2-201"  ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created: 
NLRP2--ADAMTS13	HAVANA	gene	26346	51698	.	+	.	FI_gene_label "ADAMTS13^ENSG00000160323.19"  ; ID "NLRP2--ADAMTS13^ADAMTS13^ENSG00000160323.19"  ; ccdsid "CCDS6972.1"  ; exon_id "ENSE00003904238.1"  ; exon_number 1 ; gene_id "NLRP2--ADAMTS13^ADAMTS13^ENSG00000160323.19"  ; gene_name ADAMTS13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020876.4"  ; havana_transcript "OTTHUMT00000054921.1"  ; hgnc_id "HGNC:1366"  ; level 2 ; orig_coord_info "chr9,133422444,133422548,+"  ; protein_id "ENSP00000347927.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NLRP2--ADAMTS13^ENST00000355699.7"  ; transcript_name "ADAMTS13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
NLRP2--ADAMTS13	HAVANA	mRNA	26346	51698	.	+	.	FI_gene_label "ADAMTS13^ENSG00000160323.19"  ; ID "NLRP2--ADAMTS13^ENST00000355699.7"  ; Parent "NLRP2--ADAMTS13^ADAMTS13^ENSG00000160323.19"  ; ccdsid "CCDS6972.1"  ; exon_id "ENSE00003904238.1"  ; exon_number 1 ; gene_id "NLRP2--ADAMTS13^ADAMTS13^ENSG00000160323.19"  ; gene_name ADAMTS13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020876.4"  ; havana_transcript "OTTHUMT00000054921.1"  ; hgnc_id "HGNC:1366"  ; level 2 ; orig_coord_info "chr9,133422444,133422548,+"  ; protein_id "ENSP00000347927.2"  ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NLRP2--ADAMTS13^ENST00000355699.7"  ; transcript_name "ADAMTS13-201"  ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created: 
PDXDC1--NPIPB5	ENSEMBL	gene	1610	14305	.	+	.	FI_gene_label "PDXDC1^ENSG00000179889.19"  ; ID "PDXDC1--NPIPB5^PDXDC1^ENSG00000179889.19"  ; exon_id "ENSE00002269182.2"  ; exon_number 1 ; gene_id "PDXDC1--NPIPB5^PDXDC1^ENSG00000179889.19"  ; gene_name PDXDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166304.6"  ; hgnc_id "HGNC:28995"  ; level 3 ; orig_coord_info "chr16,14975200,14975220,+"  ; protein_id "ENSP00000322807.8"  ; tag basic ; transcript_id "PDXDC1--NPIPB5^ENST00000325823.11"  ; transcript_name "PDXDC1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
PDXDC1--NPIPB5	ENSEMBL	mRNA	1610	14305	.	+	.	FI_gene_label "PDXDC1^ENSG00000179889.19"  ; ID "PDXDC1--NPIPB5^ENST00000325823.11"  ; Parent "PDXDC1--NPIPB5^PDXDC1^ENSG00000179889.19"  ; exon_id "ENSE00002269182.2"  ; exon_number 1 ; gene_id "PDXDC1--NPIPB5^PDXDC1^ENSG00000179889.19"  ; gene_name PDXDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166304.6"  ; hgnc_id "HGNC:28995"  ; level 3 ; orig_coord_info "chr16,14975200,14975220,+"  ; protein_id "ENSP00000322807.8"  ; tag basic ; transcript_id "PDXDC1--NPIPB5^ENST00000325823.11"  ; transcript_name "PDXDC1-201"  ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created: 
PDXDC1--NPIPB5	HAVANA	gene	43624	46955	.	+	.	FI_gene_label "NPIPB5^ENSG00000243716.10"  ; ID "PDXDC1--NPIPB5^NPIPB5^ENSG00000243716.10"  ; exon_id "ENSE00002265272.1"  ; exon_number 3 ; gene_id "PDXDC1--NPIPB5^NPIPB5^ENSG00000243716.10"  ; gene_name NPIPB5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163573.6"  ; havana_transcript "OTTHUMT00000403183.2"  ; hgnc_id "HGNC:37233"  ; level 2 ; orig_coord_info "chr16,22513802,22513834,+"  ; protein_id "ENSP00000440137.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "PDXDC1--NPIPB5^ENST00000356156.7"  ; transcript_name "NPIPB5-201"  ; transcript_support_level 4 ; transcript_type protein_coding
PDXDC1--NPIPB5	HAVANA	mRNA	43624	46955	.	+	.	FI_gene_label "NPIPB5^ENSG00000243716.10"  ; ID "PDXDC1--NPIPB5^ENST00000356156.7"  ; Parent "PDXDC1--NPIPB5^NPIPB5^ENSG00000243716.10"  ; exon_id "ENSE00002265272.1"  ; exon_number 3 ; gene_id "PDXDC1--NPIPB5^NPIPB5^ENSG00000243716.10"  ; gene_name NPIPB5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163573.6"  ; havana_transcript "OTTHUMT00000403183.2"  ; hgnc_id "HGNC:37233"  ; level 2 ; orig_coord_info "chr16,22513802,22513834,+"  ; protein_id "ENSP00000440137.1"  ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "PDXDC1--NPIPB5^ENST00000356156.7"  ; transcript_name "NPIPB5-201"  ; transcript_support_level 4 ; 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: 
AC015911.9--SLFN12L	HAVANA	gene	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
AC015911.9--SLFN12L	HAVANA	RNA	1001	1691	.	+	.	FI_gene_label "AC015911.9^ENSG00000286030.2"  ; ID "AC015911.9--SLFN12L^ENST00000650652.2"  ; Parent "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; exon_id "ENSE00003850003.2"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^AC015911.9^ENSG00000286030.2"  ; gene_name "AC015911.9"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000193507.2"  ; havana_transcript "OTTHUMT00000502481.2"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr17,35522279,35522969,-"  ; tag basic ; transcript_id "AC015911.9--SLFN12L^ENST00000650652.2"  ; transcript_name "AC015911.9-201"  ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
AC015911.9--SLFN12L	ENSEMBL	gene	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
AC015911.9--SLFN12L	ENSEMBL	RNA	5824	9825	.	+	.	FI_gene_label "SLFN12L^ENSG00000286065.2"  ; ID "AC015911.9--SLFN12L^ENST00000675965.1"  ; Parent "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; exon_id "ENSE00003899764.1"  ; exon_number 1 ; gene_id "AC015911.9--SLFN12L^SLFN12L^ENSG00000286065.2"  ; gene_name SLFN12L ; gene_type lncRNA ; havana_gene "OTTHUMG00000167707.2"  ; hgnc_id "HGNC:33920"  ; level 3 ; orig_coord_info "chr17,35480502,35480513,-"  ; transcript_id "AC015911.9--SLFN12L^ENST00000675965.1"  ; transcript_name "SLFN12L-206"  ; transcript_type lncRNA
L1 and L2 created: 
AC091057.6--CHRFAM7A	HAVANA	gene	2089	6675	.	+	.	FI_gene_label "AC091057.6^ENSG00000285035.1"  ; ID "AC091057.6--CHRFAM7A^AC091057.6^ENSG00000285035.1"  ; exon_id "ENSE00002630084.1"  ; exon_number 1 ; gene_id "AC091057.6--CHRFAM7A^AC091057.6^ENSG00000285035.1"  ; gene_name "AC091057.6"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192492.2"  ; havana_transcript "OTTHUMT00000494948.1"  ; level 2 ; orig_coord_info "chr15,30646132,30646295,+"  ; tag basic ; transcript_id "AC091057.6--CHRFAM7A^ENST00000566548.5"  ; transcript_name "AC091057.6-202"  ; transcript_support_level 3 ; transcript_type processed_transcript
AC091057.6--CHRFAM7A	HAVANA	RNA	2089	6675	.	+	.	FI_gene_label "AC091057.6^ENSG00000285035.1"  ; ID "AC091057.6--CHRFAM7A^ENST00000566548.5"  ; Parent "AC091057.6--CHRFAM7A^AC091057.6^ENSG00000285035.1"  ; exon_id "ENSE00002630084.1"  ; exon_number 1 ; gene_id "AC091057.6--CHRFAM7A^AC091057.6^ENSG00000285035.1"  ; gene_name "AC091057.6"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192492.2"  ; havana_transcript "OTTHUMT00000494948.1"  ; level 2 ; orig_coord_info "chr15,30646132,30646295,+"  ; tag basic ; transcript_id "AC091057.6--CHRFAM7A^ENST00000566548.5"  ; transcript_name "AC091057.6-202"  ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created: 
AC091057.6--ULK4	HAVANA	gene	2089	6675	.	+	.	FI_gene_label "AC091057.6^ENSG00000285035.1"  ; ID "AC091057.6--ULK4^AC091057.6^ENSG00000285035.1"  ; exon_id "ENSE00002630084.1"  ; exon_number 1 ; gene_id "AC091057.6--ULK4^AC091057.6^ENSG00000285035.1"  ; gene_name "AC091057.6"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192492.2"  ; havana_transcript "OTTHUMT00000494948.1"  ; level 2 ; orig_coord_info "chr15,30646132,30646295,+"  ; tag basic ; transcript_id "AC091057.6--ULK4^ENST00000566548.5"  ; transcript_name "AC091057.6-202"  ; transcript_support_level 3 ; transcript_type processed_transcript
AC091057.6--ULK4	HAVANA	RNA	2089	6675	.	+	.	FI_gene_label "AC091057.6^ENSG00000285035.1"  ; ID "AC091057.6--ULK4^ENST00000566548.5"  ; Parent "AC091057.6--ULK4^AC091057.6^ENSG00000285035.1"  ; exon_id "ENSE00002630084.1"  ; exon_number 1 ; gene_id "AC091057.6--ULK4^AC091057.6^ENSG00000285035.1"  ; gene_name "AC091057.6"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000192492.2"  ; havana_transcript "OTTHUMT00000494948.1"  ; level 2 ; orig_coord_info "chr15,30646132,30646295,+"  ; tag basic ; transcript_id "AC091057.6--ULK4^ENST00000566548.5"  ; transcript_name "AC091057.6-202"  ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created: 
ARHGAP11A--ULK4P2	HAVANA	gene	18855	25850	.	+	.	FI_gene_label "ULK4P2^ENSG00000260128.6"  ; ID "ARHGAP11A--ULK4P2^ULK4P2^ENSG00000260128.6"  ; exon_id "ENSE00002597383.1"  ; exon_number 1 ; gene_id "ARHGAP11A--ULK4P2^ULK4P2^ENSG00000260128.6"  ; gene_name ULK4P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000175653.1"  ; havana_transcript "OTTHUMT00000430720.1"  ; hgnc_id "HGNC:15776"  ; level 2 ; orig_coord_info "chr15,30572765,30573016,+"  ; transcript_id "ARHGAP11A--ULK4P2^ENST00000561753.5"  ; transcript_name "ULK4P2-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
ARHGAP11A--ULK4P2	HAVANA	RNA	18855	25850	.	+	.	FI_gene_label "ULK4P2^ENSG00000260128.6"  ; ID "ARHGAP11A--ULK4P2^ENST00000561753.5"  ; Parent "ARHGAP11A--ULK4P2^ULK4P2^ENSG00000260128.6"  ; exon_id "ENSE00002597383.1"  ; exon_number 1 ; gene_id "ARHGAP11A--ULK4P2^ULK4P2^ENSG00000260128.6"  ; gene_name ULK4P2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000175653.1"  ; havana_transcript "OTTHUMT00000430720.1"  ; hgnc_id "HGNC:15776"  ; level 2 ; orig_coord_info "chr15,30572765,30573016,+"  ; transcript_id "ARHGAP11A--ULK4P2^ENST00000561753.5"  ; transcript_name "ULK4P2-201"  ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created: 
ARHGAP11B--AC019322.1	HAVANA	gene	3795	6742	.	+	.	FI_gene_label "ARHGAP11B^ENSG00000285077.2"  ; ID "ARHGAP11B--AC019322.1^ARHGAP11B^ENSG00000285077.2"  ; exon_id "ENSE00002622270.1"  ; exon_number 1 ; gene_id "ARHGAP11B--AC019322.1^ARHGAP11B^ENSG00000285077.2"  ; gene_name ARHGAP11B ; gene_type protein_coding ; havana_gene "OTTHUMG00000192491.3"  ; havana_transcript "OTTHUMT00000494704.1"  ; hgnc_id "HGNC:15782"  ; level 2 ; orig_coord_info "chr15,30630724,30630773,+"  ; transcript_id "ARHGAP11B--AC019322.1^ENST00000566362.1"  ; transcript_name "ARHGAP11B-203"  ; transcript_support_level 3 ; transcript_type processed_transcript
ARHGAP11B--AC019322.1	HAVANA	RNA	3795	6742	.	+	.	FI_gene_label "ARHGAP11B^ENSG00000285077.2"  ; ID "ARHGAP11B--AC019322.1^ENST00000566362.1"  ; Parent "ARHGAP11B--AC019322.1^ARHGAP11B^ENSG00000285077.2"  ; exon_id "ENSE00002622270.1"  ; exon_number 1 ; gene_id "ARHGAP11B--AC019322.1^ARHGAP11B^ENSG00000285077.2"  ; gene_name ARHGAP11B ; gene_type protein_coding ; havana_gene "OTTHUMG00000192491.3"  ; havana_transcript "OTTHUMT00000494704.1"  ; hgnc_id "HGNC:15782"  ; level 2 ; orig_coord_info "chr15,30630724,30630773,+"  ; transcript_id "ARHGAP11B--AC019322.1^ENST00000566362.1"  ; transcript_name "ARHGAP11B-203"  ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created: 
ARHGAP11B--AC019322.1	HAVANA	gene	9743	13131	.	+	.	FI_gene_label "AC019322.1^ENSG00000263070.1"  ; ID "ARHGAP11B--AC019322.1^AC019322.1^ENSG00000263070.1"  ; exon_id "ENSE00002671292.1"  ; exon_number 1 ; gene_id "ARHGAP11B--AC019322.1^AC019322.1^ENSG00000263070.1"  ; gene_name "AC019322.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000177735.1"  ; havana_transcript "OTTHUMT00000438770.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr15,30386884,30386987,-"  ; tag basic ; transcript_id "ARHGAP11B--AC019322.1^ENST00000571869.1"  ; transcript_name "AC019322.1-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
ARHGAP11B--AC019322.1	HAVANA	RNA	9743	13131	.	+	.	FI_gene_label "AC019322.1^ENSG00000263070.1"  ; ID "ARHGAP11B--AC019322.1^ENST00000571869.1"  ; Parent "ARHGAP11B--AC019322.1^AC019322.1^ENSG00000263070.1"  ; exon_id "ENSE00002671292.1"  ; exon_number 1 ; gene_id "ARHGAP11B--AC019322.1^AC019322.1^ENSG00000263070.1"  ; gene_name "AC019322.1"  ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000177735.1"  ; havana_transcript "OTTHUMT00000438770.1"  ; level 2 ; ont "PGO:0000005"  "PGO:0000019"  ; orig_coord_info "chr15,30386884,30386987,-"  ; tag basic ; transcript_id "ARHGAP11B--AC019322.1^ENST00000571869.1"  ; transcript_name "AC019322.1-201"  ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created: 
ARHGAP11B--CHRFAM7A	HAVANA	gene	3795	6742	.	+	.	FI_gene_label "ARHGAP11B^ENSG00000285077.2"  ; ID "ARHGAP11B--CHRFAM7A^ARHGAP11B^ENSG00000285077.2"  ; exon_id "ENSE00002622270.1"  ; exon_number 1 ; gene_id "ARHGAP11B--CHRFAM7A^ARHGAP11B^ENSG00000285077.2"  ; gene_name ARHGAP11B ; gene_type protein_coding ; havana_gene "OTTHUMG00000192491.3"  ; havana_transcript "OTTHUMT00000494704.1"  ; hgnc_id "HGNC:15782"  ; level 2 ; orig_coord_info "chr15,30630724,30630773,+"  ; transcript_id "ARHGAP11B--CHRFAM7A^ENST00000566362.1"  ; transcript_name "ARHGAP11B-203"  ; transcript_support_level 3 ; transcript_type processed_transcript
ARHGAP11B--CHRFAM7A	HAVANA	RNA	3795	6742	.	+	.	FI_gene_label "ARHGAP11B^ENSG00000285077.2"  ; ID "ARHGAP11B--CHRFAM7A^ENST00000566362.1"  ; Parent "ARHGAP11B--CHRFAM7A^ARHGAP11B^ENSG00000285077.2"  ; exon_id "ENSE00002622270.1"  ; exon_number 1 ; gene_id "ARHGAP11B--CHRFAM7A^ARHGAP11B^ENSG00000285077.2"  ; gene_name ARHGAP11B ; gene_type protein_coding ; havana_gene "OTTHUMG00000192491.3"  ; havana_transcript "OTTHUMT00000494704.1"  ; hgnc_id "HGNC:15782"  ; level 2 ; orig_coord_info "chr15,30630724,30630773,+"  ; transcript_id "ARHGAP11B--CHRFAM7A^ENST00000566362.1"  ; transcript_name "ARHGAP11B-203"  ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created: 
ARHGAP11B--ULK4	HAVANA	gene	3795	6742	.	+	.	FI_gene_label "ARHGAP11B^ENSG00000285077.2"  ; ID "ARHGAP11B--ULK4^ARHGAP11B^ENSG00000285077.2"  ; exon_id "ENSE00002622270.1"  ; exon_number 1 ; gene_id "ARHGAP11B--ULK4^ARHGAP11B^ENSG00000285077.2"  ; gene_name ARHGAP11B ; gene_type protein_coding ; havana_gene "OTTHUMG00000192491.3"  ; havana_transcript "OTTHUMT00000494704.1"  ; hgnc_id "HGNC:15782"  ; level 2 ; orig_coord_info "chr15,30630724,30630773,+"  ; transcript_id "ARHGAP11B--ULK4^ENST00000566362.1"  ; transcript_name "ARHGAP11B-203"  ; transcript_support_level 3 ; transcript_type processed_transcript
ARHGAP11B--ULK4	HAVANA	RNA	3795	6742	.	+	.	FI_gene_label "ARHGAP11B^ENSG00000285077.2"  ; ID "ARHGAP11B--ULK4^ENST00000566362.1"  ; Parent "ARHGAP11B--ULK4^ARHGAP11B^ENSG00000285077.2"  ; exon_id "ENSE00002622270.1"  ; exon_number 1 ; gene_id "ARHGAP11B--ULK4^ARHGAP11B^ENSG00000285077.2"  ; gene_name ARHGAP11B ; gene_type protein_coding ; havana_gene "OTTHUMG00000192491.3"  ; havana_transcript "OTTHUMT00000494704.1"  ; hgnc_id "HGNC:15782"  ; level 2 ; orig_coord_info "chr15,30630724,30630773,+"  ; transcript_id "ARHGAP11B--ULK4^ENST00000566362.1"  ; transcript_name "ARHGAP11B-203"  ; transcript_support_level 3 ; transcript_type processed_transcript
L1 and L2 created: 
CRYZL2P--SEC16B	HAVANA	gene	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B	HAVANA	RNA	1005	12289	.	+	.	FI_gene_label "CRYZL2P^ENSG00000242193.11"  ; ID "CRYZL2P--SEC16B^ENST00000462729.2"  ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; exon_id "ENSE00001918901.2"  ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11"  ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4"  ; havana_transcript "OTTHUMT00000337460.2"  ; hgnc_id "HGNC:52164"  ; level 2 ; orig_coord_info "chr1,178037897,178037946,-"  ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2"  ; transcript_name "CRYZL2P-201"  ; transcript_support_level NA ; transcript_type transcribed_unitary_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
175 cases fixed where L3 features have parent feature(s) missing
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--------------------------- 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 ------------------------------
354 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 20 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