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: 1625
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1625
=> 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:1625
=> 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:
BCAP31--PDZD4 HAVANA gene 13982 22356 . + . FI_gene_label "PDZD4^ENSG00000067840.12" ; ID "BCAP31--PDZD4^PDZD4^ENSG00000067840.12" ; ccdsid "CCDS14732.1" ; exon_id "ENSE00001892310.1" ; exon_number 1 ; gene_id "BCAP31--PDZD4^PDZD4^ENSG00000067840.12" ; gene_name PDZD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000024209.4" ; havana_transcript "OTTHUMT00000061013.3" ; hgnc_id "HGNC:21167" ; level 2 ; orig_coord_info "chrX,153830239,153830298,-" ; protein_id "ENSP00000164640.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "BCAP31--PDZD4^ENST00000164640.8" ; transcript_name "PDZD4-201" ; transcript_support_level 1 ; transcript_type protein_coding
BCAP31--PDZD4 HAVANA mRNA 13982 22356 . + . FI_gene_label "PDZD4^ENSG00000067840.12" ; ID "BCAP31--PDZD4^ENST00000164640.8" ; Parent "BCAP31--PDZD4^PDZD4^ENSG00000067840.12" ; ccdsid "CCDS14732.1" ; exon_id "ENSE00001892310.1" ; exon_number 1 ; gene_id "BCAP31--PDZD4^PDZD4^ENSG00000067840.12" ; gene_name PDZD4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000024209.4" ; havana_transcript "OTTHUMT00000061013.3" ; hgnc_id "HGNC:21167" ; level 2 ; orig_coord_info "chrX,153830239,153830298,-" ; protein_id "ENSP00000164640.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "BCAP31--PDZD4^ENST00000164640.8" ; transcript_name "PDZD4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BCAP31--PDZD4 HAVANA gene 1179 10906 . + . FI_gene_label "BCAP31^ENSG00000185825.17" ; ID "BCAP31--PDZD4^BCAP31^ENSG00000185825.17" ; ccdsid "CCDS14727.1" ; exon_id "ENSE00003485532.1" ; exon_number 2 ; gene_id "BCAP31--PDZD4^BCAP31^ENSG00000185825.17" ; gene_name BCAP31 ; gene_type protein_coding ; havana_gene "OTTHUMG00000024218.5" ; havana_transcript "OTTHUMT00000061071.3" ; hgnc_id "HGNC:16695" ; level 2 ; orig_coord_info "chrX,153723153,153723244,-" ; protein_id "ENSP00000343458.6" ; tag CAGE_supported_TSS 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCAP31--PDZD4^ENST00000345046.12" ; transcript_name "BCAP31-201" ; transcript_support_level 1 ; transcript_type protein_coding
BCAP31--PDZD4 HAVANA mRNA 1179 10906 . + . FI_gene_label "BCAP31^ENSG00000185825.17" ; ID "BCAP31--PDZD4^ENST00000345046.12" ; Parent "BCAP31--PDZD4^BCAP31^ENSG00000185825.17" ; ccdsid "CCDS14727.1" ; exon_id "ENSE00003485532.1" ; exon_number 2 ; gene_id "BCAP31--PDZD4^BCAP31^ENSG00000185825.17" ; gene_name BCAP31 ; gene_type protein_coding ; havana_gene "OTTHUMG00000024218.5" ; havana_transcript "OTTHUMT00000061071.3" ; hgnc_id "HGNC:16695" ; level 2 ; orig_coord_info "chrX,153723153,153723244,-" ; protein_id "ENSP00000343458.6" ; tag CAGE_supported_TSS 3_standard_supported_extension basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCAP31--PDZD4^ENST00000345046.12" ; transcript_name "BCAP31-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FGFR3--TACC3 HAVANA gene 1020 10219 . + . FI_gene_label "FGFR3^ENSG00000068078.20" ; ID "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; exon_id "ENSE00001596390.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7" ; havana_transcript "OTTHUMT00000495785.1" ; hgnc_id "HGNC:3690" ; level 2 ; orig_coord_info "chr4,1793935,1794043,+" ; protein_id "ENSP00000260795.3" ; transcript_id "FGFR3--TACC3^ENST00000260795.8" ; transcript_name "FGFR3-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
FGFR3--TACC3 HAVANA mRNA 1020 10219 . + . FI_gene_label "FGFR3^ENSG00000068078.20" ; ID "FGFR3--TACC3^ENST00000260795.8" ; Parent "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; exon_id "ENSE00001596390.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^FGFR3^ENSG00000068078.20" ; gene_name FGFR3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000121148.7" ; havana_transcript "OTTHUMT00000495785.1" ; hgnc_id "HGNC:3690" ; level 2 ; orig_coord_info "chr4,1793935,1794043,+" ; protein_id "ENSP00000260795.3" ; transcript_id "FGFR3--TACC3^ENST00000260795.8" ; transcript_name "FGFR3-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
FGFR3--TACC3 HAVANA gene 16535 31742 . + . FI_gene_label "TACC3^ENSG00000013810.20" ; ID "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; ccdsid "CCDS3352.1" ; exon_id "ENSE00003597099.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25" ; havana_transcript "OTTHUMT00000203730.4" ; hgnc_id "HGNC:11524" ; level 2 ; orig_coord_info "chr4,1723422,1723583,+" ; protein_id "ENSP00000326550.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9" ; transcript_name "TACC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
FGFR3--TACC3 HAVANA mRNA 16535 31742 . + . FI_gene_label "TACC3^ENSG00000013810.20" ; ID "FGFR3--TACC3^ENST00000313288.9" ; Parent "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; ccdsid "CCDS3352.1" ; exon_id "ENSE00003597099.1" ; exon_number 2 ; gene_id "FGFR3--TACC3^TACC3^ENSG00000013810.20" ; gene_name TACC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000089535.25" ; havana_transcript "OTTHUMT00000203730.4" ; hgnc_id "HGNC:11524" ; level 2 ; orig_coord_info "chr4,1723422,1723583,+" ; protein_id "ENSP00000326550.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "FGFR3--TACC3^ENST00000313288.9" ; transcript_name "TACC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GUCY1B2--NKAIN2 HAVANA gene 24657 32303 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
GUCY1B2--NKAIN2 HAVANA mRNA 24657 32303 . + . FI_gene_label "NKAIN2^ENSG00000188580.15" ; ID "GUCY1B2--NKAIN2^ENST00000368416.5" ; Parent "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; exon_id "ENSE00003552753.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^NKAIN2^ENSG00000188580.15" ; gene_name NKAIN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015500.3" ; havana_transcript "OTTHUMT00000042056.1" ; hgnc_id "HGNC:16443" ; level 2 ; orig_coord_info "chr6,123804201,123804254,+" ; protein_id "ENSP00000357401.1" ; tag basic ; transcript_id "GUCY1B2--NKAIN2^ENST00000368416.5" ; transcript_name "NKAIN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SCX--AC234917.3 HAVANA gene 1001 3029 . + . FI_gene_label "SCX^ENSG00000260428.3" ; ID "SCX--AC234917.3^SCX^ENSG00000260428.3" ; ccdsid "CCDS43779.1" ; exon_id "ENSE00002607285.3" ; exon_number 1 ; gene_id "SCX--AC234917.3^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--AC234917.3^ENST00000567180.3" ; transcript_name "SCX-201" ; transcript_support_level 1 ; transcript_type protein_coding
SCX--AC234917.3 HAVANA mRNA 1001 3029 . + . FI_gene_label "SCX^ENSG00000260428.3" ; ID "SCX--AC234917.3^ENST00000567180.3" ; Parent "SCX--AC234917.3^SCX^ENSG00000260428.3" ; ccdsid "CCDS43779.1" ; exon_id "ENSE00002607285.3" ; exon_number 1 ; gene_id "SCX--AC234917.3^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--AC234917.3^ENST00000567180.3" ; transcript_name "SCX-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SNU13--LLPH HAVANA gene 4331 9276 . + . FI_gene_label "SNU13^ENSG00000100138.15" ; ID "SNU13--LLPH^SNU13^ENSG00000100138.15" ; ccdsid "CCDS14022.1" ; exon_id "ENSE00001388935.4" ; exon_number 1 ; gene_id "SNU13--LLPH^SNU13^ENSG00000100138.15" ; gene_name SNU13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151189.9" ; havana_transcript "OTTHUMT00000321683.2" ; hgnc_id "HGNC:7819" ; level 2 ; orig_coord_info "chr22,41682356,41682358,-" ; protein_id "ENSP00000215956.5" ; tag basic appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000215956.10" ; transcript_name "SNU13-201" ; transcript_support_level 1 ; transcript_type protein_coding
SNU13--LLPH HAVANA mRNA 4331 9276 . + . FI_gene_label "SNU13^ENSG00000100138.15" ; ID "SNU13--LLPH^ENST00000215956.10" ; Parent "SNU13--LLPH^SNU13^ENSG00000100138.15" ; ccdsid "CCDS14022.1" ; exon_id "ENSE00001388935.4" ; exon_number 1 ; gene_id "SNU13--LLPH^SNU13^ENSG00000100138.15" ; gene_name SNU13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151189.9" ; havana_transcript "OTTHUMT00000321683.2" ; hgnc_id "HGNC:7819" ; level 2 ; orig_coord_info "chr22,41682356,41682358,-" ; protein_id "ENSP00000215956.5" ; tag basic appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000215956.10" ; transcript_name "SNU13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SNU13--LLPH HAVANA gene 13051 23027 . + . FI_gene_label "LLPH^ENSG00000139233.7" ; ID "SNU13--LLPH^LLPH^ENSG00000139233.7" ; ccdsid "CCDS8974.1" ; exon_id "ENSE00003592110.1" ; exon_number 2 ; gene_id "SNU13--LLPH^LLPH^ENSG00000139233.7" ; gene_name LLPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000168959.4" ; havana_transcript "OTTHUMT00000401752.4" ; hgnc_id "HGNC:28229" ; level 2 ; orig_coord_info "chr12,66128896,66129106,-" ; protein_id "ENSP00000266604.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000266604.7" ; transcript_name "LLPH-201" ; transcript_support_level 1 ; transcript_type protein_coding
SNU13--LLPH HAVANA mRNA 13051 23027 . + . FI_gene_label "LLPH^ENSG00000139233.7" ; ID "SNU13--LLPH^ENST00000266604.7" ; Parent "SNU13--LLPH^LLPH^ENSG00000139233.7" ; ccdsid "CCDS8974.1" ; exon_id "ENSE00003592110.1" ; exon_number 2 ; gene_id "SNU13--LLPH^LLPH^ENSG00000139233.7" ; gene_name LLPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000168959.4" ; havana_transcript "OTTHUMT00000401752.4" ; hgnc_id "HGNC:28229" ; level 2 ; orig_coord_info "chr12,66128896,66129106,-" ; protein_id "ENSP00000266604.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SNU13--LLPH^ENST00000266604.7" ; transcript_name "LLPH-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:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
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:
AC243829.5--AC233699.1 HAVANA gene 5248 14222 . + . FI_gene_label "AC233699.1^ENSG00000261499.2" ; ID "AC243829.5--AC233699.1^AC233699.1^ENSG00000261499.2" ; exon_id "ENSE00002600750.2" ; exon_number 1 ; gene_id "AC243829.5--AC233699.1^AC233699.1^ENSG00000261499.2" ; gene_name "AC233699.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188425.1" ; havana_transcript "OTTHUMT00000477176.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr17,36274191,36274283,+" ; tag basic ; transcript_id "AC243829.5--AC233699.1^ENST00000569955.2" ; transcript_name "AC233699.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC243829.5--AC233699.1 HAVANA RNA 5248 14222 . + . FI_gene_label "AC233699.1^ENSG00000261499.2" ; ID "AC243829.5--AC233699.1^ENST00000569955.2" ; Parent "AC243829.5--AC233699.1^AC233699.1^ENSG00000261499.2" ; exon_id "ENSE00002600750.2" ; exon_number 1 ; gene_id "AC243829.5--AC233699.1^AC233699.1^ENSG00000261499.2" ; gene_name "AC233699.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000188425.1" ; havana_transcript "OTTHUMT00000477176.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr17,36274191,36274283,+" ; tag basic ; transcript_id "AC243829.5--AC233699.1^ENST00000569955.2" ; transcript_name "AC233699.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AC243829.5--AC233699.1 HAVANA gene 1001 2247 . + . FI_gene_label "AC243829.5^ENSG00000278097.1" ; ID "AC243829.5--AC233699.1^AC243829.5^ENSG00000278097.1" ; exon_id "ENSE00002266549.2" ; exon_number 1 ; gene_id "AC243829.5--AC233699.1^AC243829.5^ENSG00000278097.1" ; gene_name "AC243829.5" ; gene_type lncRNA ; havana_gene "OTTHUMG00000188421.1" ; havana_transcript "OTTHUMT00000477171.1" ; level 2 ; orig_coord_info "chr17,36226685,36226807,-" ; tag basic ; transcript_id "AC243829.5--AC233699.1^ENST00000578447.2" ; transcript_name "AC243829.5-201" ; transcript_support_level 5 ; transcript_type lncRNA
AC243829.5--AC233699.1 HAVANA RNA 1001 2247 . + . FI_gene_label "AC243829.5^ENSG00000278097.1" ; ID "AC243829.5--AC233699.1^ENST00000578447.2" ; Parent "AC243829.5--AC233699.1^AC243829.5^ENSG00000278097.1" ; exon_id "ENSE00002266549.2" ; exon_number 1 ; gene_id "AC243829.5--AC233699.1^AC243829.5^ENSG00000278097.1" ; gene_name "AC243829.5" ; gene_type lncRNA ; havana_gene "OTTHUMG00000188421.1" ; havana_transcript "OTTHUMT00000477171.1" ; level 2 ; orig_coord_info "chr17,36226685,36226807,-" ; tag basic ; transcript_id "AC243829.5--AC233699.1^ENST00000578447.2" ; transcript_name "AC243829.5-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
GUCY1B2--NKAIN2 HAVANA gene 2157 15439 . + . FI_gene_label "GUCY1B2^ENSG00000123201.14" ; ID "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; exon_id "ENSE00001531871.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5" ; havana_transcript "OTTHUMT00000045017.2" ; hgnc_id "HGNC:4686" ; level 2 ; orig_coord_info "chr13,51065951,51066207,-" ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6" ; transcript_name "GUCY1B2-201" ; transcript_support_level 5 ; transcript_type processed_transcript
GUCY1B2--NKAIN2 HAVANA RNA 2157 15439 . + . FI_gene_label "GUCY1B2^ENSG00000123201.14" ; ID "GUCY1B2--NKAIN2^ENST00000389600.6" ; Parent "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; exon_id "ENSE00001531871.1" ; exon_number 1 ; gene_id "GUCY1B2--NKAIN2^GUCY1B2^ENSG00000123201.14" ; gene_name GUCY1B2 ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000016940.5" ; havana_transcript "OTTHUMT00000045017.2" ; hgnc_id "HGNC:4686" ; level 2 ; orig_coord_info "chr13,51065951,51066207,-" ; transcript_id "GUCY1B2--NKAIN2^ENST00000389600.6" ; transcript_name "GUCY1B2-201" ; transcript_support_level 5 ; transcript_type processed_transcript
L1 and L2 created:
SCX--AC234917.3 HAVANA gene 6030 9373 . + . FI_gene_label "AC234917.3^ENSG00000287222.1" ; ID "SCX--AC234917.3^AC234917.3^ENSG00000287222.1" ; exon_id "ENSE00003851445.1" ; exon_number 1 ; gene_id "SCX--AC234917.3^AC234917.3^ENSG00000287222.1" ; gene_name "AC234917.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195627.1" ; havana_transcript "OTTHUMT00000527893.1" ; level 2 ; orig_coord_info "chr8,143829518,143830038,+" ; tag basic TAGENE ; transcript_id "SCX--AC234917.3^ENST00000654408.1" ; transcript_name "AC234917.3-201" ; transcript_type lncRNA
SCX--AC234917.3 HAVANA RNA 6030 9373 . + . FI_gene_label "AC234917.3^ENSG00000287222.1" ; ID "SCX--AC234917.3^ENST00000654408.1" ; Parent "SCX--AC234917.3^AC234917.3^ENSG00000287222.1" ; exon_id "ENSE00003851445.1" ; exon_number 1 ; gene_id "SCX--AC234917.3^AC234917.3^ENSG00000287222.1" ; gene_name "AC234917.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000195627.1" ; havana_transcript "OTTHUMT00000527893.1" ; level 2 ; orig_coord_info "chr8,143829518,143830038,+" ; tag basic TAGENE ; transcript_id "SCX--AC234917.3^ENST00000654408.1" ; transcript_name "AC234917.3-201" ; transcript_type lncRNA
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
143 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 ------------------------------
278 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 12 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