Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/b7b2affc8817f0e4f0b1e92b873517/fi_workdir/tih_rna_sample_00592_B23MVV7LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/a653be7af61cd45745a205e1964b86/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/a653be7af61cd45745a205e1964b86/.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: 1890
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1890
=> 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:1890
=> 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:
AC013268.1--MALL HAVANA gene 16390 22812 . + . FI_gene_label "MALL^ENSG00000144063.4" ; ID "AC013268.1--MALL^MALL^ENSG00000144063.4" ; ccdsid "CCDS2085.1" ; exon_id "ENSE00001129113.3" ; exon_number 1 ; gene_id "AC013268.1--MALL^MALL^ENSG00000144063.4" ; gene_name MALL ; gene_type protein_coding ; havana_gene "OTTHUMG00000131196.3" ; havana_transcript "OTTHUMT00000253921.2" ; hgnc_id "HGNC:6818" ; level 2 ; orig_coord_info "chr2,110115688,110115792,-" ; protein_id "ENSP00000272462.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC013268.1--MALL^ENST00000272462.3" ; transcript_name "MALL-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC013268.1--MALL HAVANA mRNA 16390 22812 . + . FI_gene_label "MALL^ENSG00000144063.4" ; ID "AC013268.1--MALL^ENST00000272462.3" ; Parent "AC013268.1--MALL^MALL^ENSG00000144063.4" ; ccdsid "CCDS2085.1" ; exon_id "ENSE00001129113.3" ; exon_number 1 ; gene_id "AC013268.1--MALL^MALL^ENSG00000144063.4" ; gene_name MALL ; gene_type protein_coding ; havana_gene "OTTHUMG00000131196.3" ; havana_transcript "OTTHUMT00000253921.2" ; hgnc_id "HGNC:6818" ; level 2 ; orig_coord_info "chr2,110115688,110115792,-" ; protein_id "ENSP00000272462.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC013268.1--MALL^ENST00000272462.3" ; transcript_name "MALL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
COX6CP1--COX6C HAVANA gene 4239 10289 . + . FI_gene_label "COX6C^ENSG00000164919.11" ; ID "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; ccdsid "CCDS6284.1" ; exon_id "ENSE00002129072.1" ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6" ; havana_transcript "OTTHUMT00000379835.1" ; hgnc_id "HGNC:2285" ; level 2 ; orig_coord_info "chr8,99891908,99892021,-" ; protein_id "ENSP00000297564.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6" ; transcript_name "COX6C-201" ; transcript_support_level 2 ; transcript_type protein_coding
COX6CP1--COX6C HAVANA mRNA 4239 10289 . + . FI_gene_label "COX6C^ENSG00000164919.11" ; ID "COX6CP1--COX6C^ENST00000297564.6" ; Parent "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; ccdsid "CCDS6284.1" ; exon_id "ENSE00002129072.1" ; exon_number 2 ; gene_id "COX6CP1--COX6C^COX6C^ENSG00000164919.11" ; gene_name COX6C ; gene_type protein_coding ; havana_gene "OTTHUMG00000164703.6" ; havana_transcript "OTTHUMT00000379835.1" ; hgnc_id "HGNC:2285" ; level 2 ; orig_coord_info "chr8,99891908,99892021,-" ; protein_id "ENSP00000297564.2" ; tag alternative_5_UTR basic appris_principal_1 CCDS ; transcript_id "COX6CP1--COX6C^ENST00000297564.6" ; transcript_name "COX6C-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
EPS8L2--DRD4 HAVANA gene 18006 20976 . + . FI_gene_label "DRD4^ENSG00000069696.7" ; ID "EPS8L2--DRD4^DRD4^ENSG00000069696.7" ; ccdsid "CCDS7710.1" ; exon_id "ENSE00000438635.3" ; exon_number 1 ; gene_id "EPS8L2--DRD4^DRD4^ENSG00000069696.7" ; gene_name DRD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133312.3" ; havana_transcript "OTTHUMT00000257109.2" ; hgnc_id "HGNC:3025" ; level 2 ; orig_coord_info "chr11,637305,637589,+" ; protein_id "ENSP00000176183.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EPS8L2--DRD4^ENST00000176183.6" ; transcript_name "DRD4-201" ; transcript_support_level 1 ; transcript_type protein_coding
EPS8L2--DRD4 HAVANA mRNA 18006 20976 . + . FI_gene_label "DRD4^ENSG00000069696.7" ; ID "EPS8L2--DRD4^ENST00000176183.6" ; Parent "EPS8L2--DRD4^DRD4^ENSG00000069696.7" ; ccdsid "CCDS7710.1" ; exon_id "ENSE00000438635.3" ; exon_number 1 ; gene_id "EPS8L2--DRD4^DRD4^ENSG00000069696.7" ; gene_name DRD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133312.3" ; havana_transcript "OTTHUMT00000257109.2" ; hgnc_id "HGNC:3025" ; level 2 ; orig_coord_info "chr11,637305,637589,+" ; protein_id "ENSP00000176183.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EPS8L2--DRD4^ENST00000176183.6" ; transcript_name "DRD4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EPS8L2--DRD4 HAVANA gene 3053 15005 . + . FI_gene_label "EPS8L2^ENSG00000177106.16" ; ID "EPS8L2--DRD4^EPS8L2^ENSG00000177106.16" ; ccdsid "CCDS31328.1" ; exon_id "ENSE00003542299.1" ; exon_number 2 ; gene_id "EPS8L2--DRD4^EPS8L2^ENSG00000177106.16" ; gene_name EPS8L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165165.12" ; havana_transcript "OTTHUMT00000382343.2" ; hgnc_id "HGNC:21296" ; level 2 ; orig_coord_info "chr11,709408,709451,+" ; protein_id "ENSP00000320828.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EPS8L2--DRD4^ENST00000318562.13" ; transcript_name "EPS8L2-201" ; transcript_support_level 1 ; transcript_type protein_coding
EPS8L2--DRD4 HAVANA mRNA 3053 15005 . + . FI_gene_label "EPS8L2^ENSG00000177106.16" ; ID "EPS8L2--DRD4^ENST00000318562.13" ; Parent "EPS8L2--DRD4^EPS8L2^ENSG00000177106.16" ; ccdsid "CCDS31328.1" ; exon_id "ENSE00003542299.1" ; exon_number 2 ; gene_id "EPS8L2--DRD4^EPS8L2^ENSG00000177106.16" ; gene_name EPS8L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165165.12" ; havana_transcript "OTTHUMT00000382343.2" ; hgnc_id "HGNC:21296" ; level 2 ; orig_coord_info "chr11,709408,709451,+" ; protein_id "ENSP00000320828.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EPS8L2--DRD4^ENST00000318562.13" ; transcript_name "EPS8L2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
LINC01002--TERT HAVANA gene 29208 48641 . + . FI_gene_label "TERT^ENSG00000164362.21" ; ID "LINC01002--TERT^TERT^ENSG00000164362.21" ; ccdsid "CCDS3861.2" ; exon_id "ENSE00003896691.1" ; exon_number 1 ; gene_id "LINC01002--TERT^TERT^ENSG00000164362.21" ; gene_name TERT ; gene_type protein_coding ; havana_gene "OTTHUMG00000090357.9" ; havana_transcript "OTTHUMT00000206729.4" ; hgnc_id "HGNC:11730" ; level 2 ; orig_coord_info "chr5,1294771,1294989,-" ; protein_id "ENSP00000309572.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "LINC01002--TERT^ENST00000310581.10" ; transcript_name "TERT-201" ; transcript_support_level 1 ; transcript_type protein_coding
LINC01002--TERT HAVANA mRNA 29208 48641 . + . FI_gene_label "TERT^ENSG00000164362.21" ; ID "LINC01002--TERT^ENST00000310581.10" ; Parent "LINC01002--TERT^TERT^ENSG00000164362.21" ; ccdsid "CCDS3861.2" ; exon_id "ENSE00003896691.1" ; exon_number 1 ; gene_id "LINC01002--TERT^TERT^ENSG00000164362.21" ; gene_name TERT ; gene_type protein_coding ; havana_gene "OTTHUMG00000090357.9" ; havana_transcript "OTTHUMT00000206729.4" ; hgnc_id "HGNC:11730" ; level 2 ; orig_coord_info "chr5,1294771,1294989,-" ; protein_id "ENSP00000309572.5" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "LINC01002--TERT^ENST00000310581.10" ; transcript_name "TERT-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SVIL-AS1--LYZL1 ENSEMBL gene 17555 21678 . + . FI_gene_label "LYZL1^ENSG00000120563.10" ; ID "SVIL-AS1--LYZL1^LYZL1^ENSG00000120563.10" ; ccdsid "CCDS31174.1" ; exon_id "ENSE00002455236.1" ; exon_number 1 ; gene_id "SVIL-AS1--LYZL1^LYZL1^ENSG00000120563.10" ; gene_name LYZL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017880.5" ; hgnc_id "HGNC:30502" ; level 3 ; orig_coord_info "chr10,29289118,29289230,+" ; protein_id "ENSP00000364650.3" ; tag basic CCDS ; transcript_id "SVIL-AS1--LYZL1^ENST00000375500.8" ; transcript_name "LYZL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SVIL-AS1--LYZL1 ENSEMBL mRNA 17555 21678 . + . FI_gene_label "LYZL1^ENSG00000120563.10" ; ID "SVIL-AS1--LYZL1^ENST00000375500.8" ; Parent "SVIL-AS1--LYZL1^LYZL1^ENSG00000120563.10" ; ccdsid "CCDS31174.1" ; exon_id "ENSE00002455236.1" ; exon_number 1 ; gene_id "SVIL-AS1--LYZL1^LYZL1^ENSG00000120563.10" ; gene_name LYZL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017880.5" ; hgnc_id "HGNC:30502" ; level 3 ; orig_coord_info "chr10,29289118,29289230,+" ; protein_id "ENSP00000364650.3" ; tag basic CCDS ; transcript_id "SVIL-AS1--LYZL1^ENST00000375500.8" ; transcript_name "LYZL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--LINC01347 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--LINC01347^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--LINC01347 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--LINC01347^ENST00000326270.13" ; Parent "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--LINC01347^ENST00000326270.13" ; transcript_name "TLK2-201" ; 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:
ZC3H6--ZC3H8 ENSEMBL gene 25567 37214 . + . FI_gene_label "ZC3H8^ENSG00000144161.13" ; ID "ZC3H6--ZC3H8^ZC3H8^ENSG00000144161.13" ; exon_id "ENSE00001292436.4" ; exon_number 1 ; gene_id "ZC3H6--ZC3H8^ZC3H8^ENSG00000144161.13" ; gene_name ZC3H8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153270.4" ; hgnc_id "HGNC:30941" ; level 3 ; orig_coord_info "chr2,112254908,112254981,-" ; protein_id "ENSP00000272570.5" ; tag basic appris_principal_2 ; transcript_id "ZC3H6--ZC3H8^ENST00000272570.9" ; transcript_name "ZC3H8-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZC3H6--ZC3H8 ENSEMBL mRNA 25567 37214 . + . FI_gene_label "ZC3H8^ENSG00000144161.13" ; ID "ZC3H6--ZC3H8^ENST00000272570.9" ; Parent "ZC3H6--ZC3H8^ZC3H8^ENSG00000144161.13" ; exon_id "ENSE00001292436.4" ; exon_number 1 ; gene_id "ZC3H6--ZC3H8^ZC3H8^ENSG00000144161.13" ; gene_name ZC3H8 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153270.4" ; hgnc_id "HGNC:30941" ; level 3 ; orig_coord_info "chr2,112254908,112254981,-" ; protein_id "ENSP00000272570.5" ; tag basic appris_principal_2 ; transcript_id "ZC3H6--ZC3H8^ENST00000272570.9" ; transcript_name "ZC3H8-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZC3H6--ZC3H8 ENSEMBL gene 1005 22517 . + . FI_gene_label "ZC3H6^ENSG00000188177.14" ; ID "ZC3H6--ZC3H8^ZC3H6^ENSG00000188177.14" ; exon_id "ENSE00001529616.1" ; exon_number 1 ; gene_id "ZC3H6--ZC3H8^ZC3H6^ENSG00000188177.14" ; gene_name ZC3H6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153286.4" ; hgnc_id "HGNC:24762" ; level 3 ; orig_coord_info "chr2,112275995,112276026,+" ; protein_id "ENSP00000340298.4" ; tag basic appris_principal_1 ; transcript_id "ZC3H6--ZC3H8^ENST00000343936.4" ; transcript_name "ZC3H6-201" ; transcript_support_level 2 ; transcript_type protein_coding
ZC3H6--ZC3H8 ENSEMBL mRNA 1005 22517 . + . FI_gene_label "ZC3H6^ENSG00000188177.14" ; ID "ZC3H6--ZC3H8^ENST00000343936.4" ; Parent "ZC3H6--ZC3H8^ZC3H6^ENSG00000188177.14" ; exon_id "ENSE00001529616.1" ; exon_number 1 ; gene_id "ZC3H6--ZC3H8^ZC3H6^ENSG00000188177.14" ; gene_name ZC3H6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153286.4" ; hgnc_id "HGNC:24762" ; level 3 ; orig_coord_info "chr2,112275995,112276026,+" ; protein_id "ENSP00000340298.4" ; tag basic appris_principal_1 ; transcript_id "ZC3H6--ZC3H8^ENST00000343936.4" ; transcript_name "ZC3H6-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
AC013268.1--MALL HAVANA gene 3129 10448 . + . FI_gene_label "AC013268.1^ENSG00000186148.13" ; ID "AC013268.1--MALL^AC013268.1^ENSG00000186148.13" ; exon_id "ENSE00002526923.1" ; exon_number 1 ; gene_id "AC013268.1--MALL^AC013268.1^ENSG00000186148.13" ; gene_name "AC013268.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191773.2" ; havana_transcript "OTTHUMT00000330194.1" ; level 2 ; orig_coord_info "chr2,109936342,109938072,+" ; transcript_id "AC013268.1--MALL^ENST00000417926.5" ; transcript_name "AC013268.1-202" ; transcript_support_level 2 ; transcript_type processed_transcript
AC013268.1--MALL HAVANA RNA 3129 10448 . + . FI_gene_label "AC013268.1^ENSG00000186148.13" ; ID "AC013268.1--MALL^ENST00000417926.5" ; Parent "AC013268.1--MALL^AC013268.1^ENSG00000186148.13" ; exon_id "ENSE00002526923.1" ; exon_number 1 ; gene_id "AC013268.1--MALL^AC013268.1^ENSG00000186148.13" ; gene_name "AC013268.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000191773.2" ; havana_transcript "OTTHUMT00000330194.1" ; level 2 ; orig_coord_info "chr2,109936342,109938072,+" ; transcript_id "AC013268.1--MALL^ENST00000417926.5" ; transcript_name "AC013268.1-202" ; transcript_support_level 2 ; transcript_type processed_transcript
L1 and L2 created:
AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
COX6CP1--COX6C HAVANA gene 1001 1215 . + . FI_gene_label "COX6CP1^ENSG00000260318.1" ; ID "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; exon_id "ENSE00002587981.1" ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1" ; havana_transcript "OTTHUMT00000421521.1" ; hgnc_id "HGNC:2286" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,11903923,11904137,-" ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1" ; transcript_name "COX6CP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
COX6CP1--COX6C HAVANA RNA 1001 1215 . + . FI_gene_label "COX6CP1^ENSG00000260318.1" ; ID "COX6CP1--COX6C^ENST00000564972.1" ; Parent "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; exon_id "ENSE00002587981.1" ; exon_number 1 ; gene_id "COX6CP1--COX6C^COX6CP1^ENSG00000260318.1" ; gene_name COX6CP1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000172958.1" ; havana_transcript "OTTHUMT00000421521.1" ; hgnc_id "HGNC:2286" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr16,11903923,11904137,-" ; tag pseudo_consens basic ; transcript_id "COX6CP1--COX6C^ENST00000564972.1" ; transcript_name "COX6CP1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
LINC01002--TERT HAVANA gene 19738 21175 . + . FI_gene_label "LINC01002^ENSG00000282508.2" ; ID "LINC01002--TERT^LINC01002^ENSG00000282508.2" ; exon_id "ENSE00003775674.1" ; exon_number 1 ; gene_id "LINC01002--TERT^LINC01002^ENSG00000282508.2" ; gene_name LINC01002 ; gene_type lncRNA ; havana_gene "OTTHUMG00000188608.6" ; havana_transcript "OTTHUMT00000475123.1" ; hgnc_id "HGNC:38538" ; level 2 ; orig_coord_info "chr19,205170,205411,-" ; transcript_id "LINC01002--TERT^ENST00000631401.1" ; transcript_name "LINC01002-201" ; transcript_support_level 5 ; transcript_type retained_intron
LINC01002--TERT HAVANA RNA 19738 21175 . + . FI_gene_label "LINC01002^ENSG00000282508.2" ; ID "LINC01002--TERT^ENST00000631401.1" ; Parent "LINC01002--TERT^LINC01002^ENSG00000282508.2" ; exon_id "ENSE00003775674.1" ; exon_number 1 ; gene_id "LINC01002--TERT^LINC01002^ENSG00000282508.2" ; gene_name LINC01002 ; gene_type lncRNA ; havana_gene "OTTHUMG00000188608.6" ; havana_transcript "OTTHUMT00000475123.1" ; hgnc_id "HGNC:38538" ; level 2 ; orig_coord_info "chr19,205170,205411,-" ; transcript_id "LINC01002--TERT^ENST00000631401.1" ; transcript_name "LINC01002-201" ; transcript_support_level 5 ; transcript_type retained_intron
L1 and L2 created:
SVIL-AS1--AL158167.1 HAVANA gene 1138 14554 . + . FI_gene_label "SVIL-AS1^ENSG00000224597.10" ; ID "SVIL-AS1--AL158167.1^SVIL-AS1^ENSG00000224597.10" ; exon_id "ENSE00001729842.1" ; exon_number 1 ; gene_id "SVIL-AS1--AL158167.1^SVIL-AS1^ENSG00000224597.10" ; gene_name "SVIL-AS1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000017881.6" ; havana_transcript "OTTHUMT00000047388.1" ; hgnc_id "HGNC:51219" ; level 2 ; orig_coord_info "chr10,29409539,29409658,+" ; tag basic ; transcript_id "SVIL-AS1--AL158167.1^ENST00000413405.5" ; transcript_name "SVIL-AS1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
SVIL-AS1--AL158167.1 HAVANA RNA 1138 14554 . + . FI_gene_label "SVIL-AS1^ENSG00000224597.10" ; ID "SVIL-AS1--AL158167.1^ENST00000413405.5" ; Parent "SVIL-AS1--AL158167.1^SVIL-AS1^ENSG00000224597.10" ; exon_id "ENSE00001729842.1" ; exon_number 1 ; gene_id "SVIL-AS1--AL158167.1^SVIL-AS1^ENSG00000224597.10" ; gene_name "SVIL-AS1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000017881.6" ; havana_transcript "OTTHUMT00000047388.1" ; hgnc_id "HGNC:51219" ; level 2 ; orig_coord_info "chr10,29409539,29409658,+" ; tag basic ; transcript_id "SVIL-AS1--AL158167.1^ENST00000413405.5" ; transcript_name "SVIL-AS1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
SVIL-AS1--AL158167.1 HAVANA gene 17555 21075 . + . FI_gene_label "AL158167.1^ENSG00000287402.1" ; ID "SVIL-AS1--AL158167.1^AL158167.1^ENSG00000287402.1" ; exon_id "ENSE00003867079.1" ; exon_number 1 ; gene_id "SVIL-AS1--AL158167.1^AL158167.1^ENSG00000287402.1" ; gene_name "AL158167.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195149.1" ; havana_transcript "OTTHUMT00000524836.1" ; level 2 ; orig_coord_info "chr10,29408245,29409366,-" ; tag basic TAGENE ; transcript_id "SVIL-AS1--AL158167.1^ENST00000658254.1" ; transcript_name "AL158167.1-201" ; transcript_type lncRNA
SVIL-AS1--AL158167.1 HAVANA RNA 17555 21075 . + . FI_gene_label "AL158167.1^ENSG00000287402.1" ; ID "SVIL-AS1--AL158167.1^ENST00000658254.1" ; Parent "SVIL-AS1--AL158167.1^AL158167.1^ENSG00000287402.1" ; exon_id "ENSE00003867079.1" ; exon_number 1 ; gene_id "SVIL-AS1--AL158167.1^AL158167.1^ENSG00000287402.1" ; gene_name "AL158167.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195149.1" ; havana_transcript "OTTHUMT00000524836.1" ; level 2 ; orig_coord_info "chr10,29408245,29409366,-" ; tag basic TAGENE ; transcript_id "SVIL-AS1--AL158167.1^ENST00000658254.1" ; transcript_name "AL158167.1-201" ; transcript_type lncRNA
L1 and L2 created:
SVIL-AS1--LYZL1 HAVANA gene 1138 14554 . + . FI_gene_label "SVIL-AS1^ENSG00000224597.10" ; ID "SVIL-AS1--LYZL1^SVIL-AS1^ENSG00000224597.10" ; exon_id "ENSE00001729842.1" ; exon_number 1 ; gene_id "SVIL-AS1--LYZL1^SVIL-AS1^ENSG00000224597.10" ; gene_name "SVIL-AS1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000017881.6" ; havana_transcript "OTTHUMT00000047388.1" ; hgnc_id "HGNC:51219" ; level 2 ; orig_coord_info "chr10,29409539,29409658,+" ; tag basic ; transcript_id "SVIL-AS1--LYZL1^ENST00000413405.5" ; transcript_name "SVIL-AS1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
SVIL-AS1--LYZL1 HAVANA RNA 1138 14554 . + . FI_gene_label "SVIL-AS1^ENSG00000224597.10" ; ID "SVIL-AS1--LYZL1^ENST00000413405.5" ; Parent "SVIL-AS1--LYZL1^SVIL-AS1^ENSG00000224597.10" ; exon_id "ENSE00001729842.1" ; exon_number 1 ; gene_id "SVIL-AS1--LYZL1^SVIL-AS1^ENSG00000224597.10" ; gene_name "SVIL-AS1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000017881.6" ; havana_transcript "OTTHUMT00000047388.1" ; hgnc_id "HGNC:51219" ; level 2 ; orig_coord_info "chr10,29409539,29409658,+" ; tag basic ; transcript_id "SVIL-AS1--LYZL1^ENST00000413405.5" ; transcript_name "SVIL-AS1-201" ; transcript_support_level 1 ; transcript_type processed_transcript
L1 and L2 created:
TLK2--LINC01347 HAVANA gene 41405 47393 . + . FI_gene_label "LINC01347^ENSG00000214837.8" ; ID "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; exon_id "ENSE00002389344.1" ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5" ; havana_transcript "OTTHUMT00000481524.1" ; hgnc_id "HGNC:50566" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,243097190,243097299,-" ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2" ; transcript_name "LINC01347-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TLK2--LINC01347 HAVANA RNA 41405 47393 . + . FI_gene_label "LINC01347^ENSG00000214837.8" ; ID "TLK2--LINC01347^ENST00000417964.2" ; Parent "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; exon_id "ENSE00002389344.1" ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5" ; havana_transcript "OTTHUMT00000481524.1" ; hgnc_id "HGNC:50566" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,243097190,243097299,-" ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2" ; transcript_name "LINC01347-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_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
217 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 ------------------------------
310 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 18 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