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: 1345
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1345
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:1345
=> 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:
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:
CCDC6--RET HAVANA gene 1001 16128 . + . FI_gene_label "CCDC6^ENSG00000108091.11" ; ID "CCDC6--RET^CCDC6^ENSG00000108091.11" ; ccdsid "CCDS7257.1" ; exon_id "ENSE00001950758.3" ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11" ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3" ; havana_transcript "OTTHUMT00000048176.3" ; hgnc_id "HGNC:18782" ; level 2 ; orig_coord_info "chr10,59906122,59906424,-" ; protein_id "ENSP00000263102.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7" ; transcript_name "CCDC6-201" ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET HAVANA mRNA 1001 16128 . + . FI_gene_label "CCDC6^ENSG00000108091.11" ; ID "CCDC6--RET^ENST00000263102.7" ; Parent "CCDC6--RET^CCDC6^ENSG00000108091.11" ; ccdsid "CCDS7257.1" ; exon_id "ENSE00001950758.3" ; exon_number 1 ; gene_id "CCDC6--RET^CCDC6^ENSG00000108091.11" ; gene_name CCDC6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018284.3" ; havana_transcript "OTTHUMT00000048176.3" ; hgnc_id "HGNC:18782" ; level 2 ; orig_coord_info "chr10,59906122,59906424,-" ; protein_id "ENSP00000263102.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CCDC6--RET^ENST00000263102.7" ; transcript_name "CCDC6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CCDC6--RET HAVANA gene 19134 39754 . + . FI_gene_label "RET^ENSG00000165731.20" ; ID "CCDC6--RET^RET^ENSG00000165731.20" ; ccdsid "CCDS53525.1" ; exon_id "ENSE00003744437.1" ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20" ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7" ; havana_transcript "OTTHUMT00000358138.3" ; hgnc_id "HGNC:9967" ; level 2 ; orig_coord_info "chr10,43077259,43077331,+" ; protein_id "ENSP00000344798.4" ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6" ; transcript_name "RET-201" ; transcript_support_level 1 ; transcript_type protein_coding
CCDC6--RET HAVANA mRNA 19134 39754 . + . FI_gene_label "RET^ENSG00000165731.20" ; ID "CCDC6--RET^ENST00000340058.6" ; Parent "CCDC6--RET^RET^ENSG00000165731.20" ; ccdsid "CCDS53525.1" ; exon_id "ENSE00003744437.1" ; exon_number 1 ; gene_id "CCDC6--RET^RET^ENSG00000165731.20" ; gene_name RET ; gene_type protein_coding ; havana_gene "OTTHUMG00000018024.7" ; havana_transcript "OTTHUMT00000358138.3" ; hgnc_id "HGNC:9967" ; level 2 ; orig_coord_info "chr10,43077259,43077331,+" ; protein_id "ENSP00000344798.4" ; tag basic CCDS ; transcript_id "CCDC6--RET^ENST00000340058.6" ; transcript_name "RET-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DNAJC1--C10orf143 HAVANA gene 1040 14616 . + . FI_gene_label "DNAJC1^ENSG00000136770.11" ; ID "DNAJC1--C10orf143^DNAJC1^ENSG00000136770.11" ; ccdsid "CCDS7136.1" ; exon_id "ENSE00001940957.2" ; exon_number 1 ; gene_id "DNAJC1--C10orf143^DNAJC1^ENSG00000136770.11" ; gene_name DNAJC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017800.6" ; havana_transcript "OTTHUMT00000047149.2" ; hgnc_id "HGNC:20090" ; level 2 ; orig_coord_info "chr10,22003213,22003434,-" ; protein_id "ENSP00000366179.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJC1--C10orf143^ENST00000376980.8" ; transcript_name "DNAJC1-202" ; transcript_support_level 1 ; transcript_type protein_coding
DNAJC1--C10orf143 HAVANA mRNA 1040 14616 . + . FI_gene_label "DNAJC1^ENSG00000136770.11" ; ID "DNAJC1--C10orf143^ENST00000376980.8" ; Parent "DNAJC1--C10orf143^DNAJC1^ENSG00000136770.11" ; ccdsid "CCDS7136.1" ; exon_id "ENSE00001940957.2" ; exon_number 1 ; gene_id "DNAJC1--C10orf143^DNAJC1^ENSG00000136770.11" ; gene_name DNAJC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000017800.6" ; havana_transcript "OTTHUMT00000047149.2" ; hgnc_id "HGNC:20090" ; level 2 ; orig_coord_info "chr10,22003213,22003434,-" ; protein_id "ENSP00000366179.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DNAJC1--C10orf143^ENST00000376980.8" ; transcript_name "DNAJC1-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DNAJC1--C10orf143 HAVANA gene 17630 24580 . + . FI_gene_label "C10orf143^ENSG00000237489.5" ; ID "DNAJC1--C10orf143^C10orf143^ENSG00000237489.5" ; exon_id "ENSE00001671572.1" ; exon_number 1 ; gene_id "DNAJC1--C10orf143^C10orf143^ENSG00000237489.5" ; gene_name C10orf143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019268.5" ; havana_transcript "OTTHUMT00000051025.2" ; hgnc_id "HGNC:48677" ; level 2 ; orig_coord_info "chr10,130110704,130110772,-" ; protein_id "ENSP00000489817.1" ; transcript_id "DNAJC1--C10orf143^ENST00000456581.1" ; transcript_name "C10orf143-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
DNAJC1--C10orf143 HAVANA mRNA 17630 24580 . + . FI_gene_label "C10orf143^ENSG00000237489.5" ; ID "DNAJC1--C10orf143^ENST00000456581.1" ; Parent "DNAJC1--C10orf143^C10orf143^ENSG00000237489.5" ; exon_id "ENSE00001671572.1" ; exon_number 1 ; gene_id "DNAJC1--C10orf143^C10orf143^ENSG00000237489.5" ; gene_name C10orf143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019268.5" ; havana_transcript "OTTHUMT00000051025.2" ; hgnc_id "HGNC:48677" ; level 2 ; orig_coord_info "chr10,130110704,130110772,-" ; protein_id "ENSP00000489817.1" ; transcript_id "DNAJC1--C10orf143^ENST00000456581.1" ; transcript_name "C10orf143-201" ; transcript_support_level 2 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
ECHS1--NEBL HAVANA gene 1001 8479 . + . FI_gene_label "ECHS1^ENSG00000127884.5" ; ID "ECHS1--NEBL^ECHS1^ENSG00000127884.5" ; ccdsid "CCDS7681.1" ; exon_id "ENSE00001447396.4" ; exon_number 1 ; gene_id "ECHS1--NEBL^ECHS1^ENSG00000127884.5" ; gene_name ECHS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019320.2" ; havana_transcript "OTTHUMT00000051156.2" ; hgnc_id "HGNC:3151" ; level 2 ; orig_coord_info "chr10,133373246,133373333,-" ; protein_id "ENSP00000357535.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ECHS1--NEBL^ENST00000368547.4" ; transcript_name "ECHS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ECHS1--NEBL HAVANA mRNA 1001 8479 . + . FI_gene_label "ECHS1^ENSG00000127884.5" ; ID "ECHS1--NEBL^ENST00000368547.4" ; Parent "ECHS1--NEBL^ECHS1^ENSG00000127884.5" ; ccdsid "CCDS7681.1" ; exon_id "ENSE00001447396.4" ; exon_number 1 ; gene_id "ECHS1--NEBL^ECHS1^ENSG00000127884.5" ; gene_name ECHS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019320.2" ; havana_transcript "OTTHUMT00000051156.2" ; hgnc_id "HGNC:3151" ; level 2 ; orig_coord_info "chr10,133373246,133373333,-" ; protein_id "ENSP00000357535.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ECHS1--NEBL^ENST00000368547.4" ; transcript_name "ECHS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ECHS1--NEBL HAVANA gene 36322 73814 . + . FI_gene_label "NEBL^ENSG00000078114.19" ; ID "ECHS1--NEBL^NEBL^ENSG00000078114.19" ; ccdsid "CCDS7134.1" ; exon_id "ENSE00001376454.2" ; exon_number 1 ; gene_id "ECHS1--NEBL^NEBL^ENSG00000078114.19" ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5" ; havana_transcript "OTTHUMT00000047113.1" ; hgnc_id "HGNC:16932" ; level 2 ; orig_coord_info "chr10,20897125,20897205,-" ; protein_id "ENSP00000366326.4" ; tag basic MANE_Select CCDS ; transcript_id "ECHS1--NEBL^ENST00000377122.9" ; transcript_name "NEBL-202" ; transcript_support_level 1 ; transcript_type protein_coding
ECHS1--NEBL HAVANA mRNA 36322 73814 . + . FI_gene_label "NEBL^ENSG00000078114.19" ; ID "ECHS1--NEBL^ENST00000377122.9" ; Parent "ECHS1--NEBL^NEBL^ENSG00000078114.19" ; ccdsid "CCDS7134.1" ; exon_id "ENSE00001376454.2" ; exon_number 1 ; gene_id "ECHS1--NEBL^NEBL^ENSG00000078114.19" ; gene_name NEBL ; gene_type protein_coding ; havana_gene "OTTHUMG00000017786.5" ; havana_transcript "OTTHUMT00000047113.1" ; hgnc_id "HGNC:16932" ; level 2 ; orig_coord_info "chr10,20897125,20897205,-" ; protein_id "ENSP00000366326.4" ; tag basic MANE_Select CCDS ; transcript_id "ECHS1--NEBL^ENST00000377122.9" ; transcript_name "NEBL-202" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KLRC4--KLRK1 HAVANA gene 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1 HAVANA mRNA 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^ENST00000240618.11" ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KLRC4--KLRK1 HAVANA gene 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
KLRC4--KLRK1 HAVANA mRNA 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^ENST00000309384.2" ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; 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:
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:
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
120 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
241 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 11 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 0 second) ------
GFF3 file parsed