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: 1551
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1551
=> 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:1551
=> 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 0 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:
CRYZL2P--SEC16B HAVANA gene 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CRYZL2P--SEC16B HAVANA mRNA 18631 44079 . + . FI_gene_label "SEC16B^ENSG00000120341.18" ; ID "CRYZL2P--SEC16B^ENST00000308284.10" ; Parent "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; ccdsid "CCDS44281.1" ; exon_id "ENSE00003707644.1" ; exon_number 2 ; gene_id "CRYZL2P--SEC16B^SEC16B^ENSG00000120341.18" ; gene_name SEC16B ; gene_type protein_coding ; havana_gene "OTTHUMG00000167206.20" ; havana_transcript "OTTHUMT00000084773.22" ; hgnc_id "HGNC:30301" ; level 2 ; orig_coord_info "chr1,177967683,177967981,-" ; protein_id "ENSP00000308339.6" ; tag basic appris_principal_2 CCDS ; transcript_id "CRYZL2P--SEC16B^ENST00000308284.10" ; transcript_name "SEC16B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FBXO25--AC240565.1 HAVANA gene 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding
FBXO25--AC240565.1 HAVANA mRNA 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^ENST00000276326.9" ; Parent "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STRN--ALK HAVANA gene 1001 31439 . + . FI_gene_label "STRN^ENSG00000115808.12" ; ID "STRN--ALK^STRN^ENSG00000115808.12" ; ccdsid "CCDS1784.1" ; exon_id "ENSE00001140050.2" ; exon_number 1 ; gene_id "STRN--ALK^STRN^ENSG00000115808.12" ; gene_name STRN ; gene_type protein_coding ; havana_gene "OTTHUMG00000100959.3" ; havana_transcript "OTTHUMT00000218568.2" ; hgnc_id "HGNC:11424" ; level 2 ; orig_coord_info "chr2,36966230,36966463,-" ; protein_id "ENSP00000263918.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STRN--ALK^ENST00000263918.9" ; transcript_name "STRN-201" ; transcript_support_level 1 ; transcript_type protein_coding
STRN--ALK HAVANA mRNA 1001 31439 . + . FI_gene_label "STRN^ENSG00000115808.12" ; ID "STRN--ALK^ENST00000263918.9" ; Parent "STRN--ALK^STRN^ENSG00000115808.12" ; ccdsid "CCDS1784.1" ; exon_id "ENSE00001140050.2" ; exon_number 1 ; gene_id "STRN--ALK^STRN^ENSG00000115808.12" ; gene_name STRN ; gene_type protein_coding ; havana_gene "OTTHUMG00000100959.3" ; havana_transcript "OTTHUMT00000218568.2" ; hgnc_id "HGNC:11424" ; level 2 ; orig_coord_info "chr2,36966230,36966463,-" ; protein_id "ENSP00000263918.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STRN--ALK^ENST00000263918.9" ; transcript_name "STRN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STRN--ALK HAVANA gene 34440 69444 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "STRN--ALK^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "STRN--ALK^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STRN--ALK^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding
STRN--ALK HAVANA mRNA 34440 69444 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "STRN--ALK^ENST00000389048.8" ; Parent "STRN--ALK^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "STRN--ALK^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STRN--ALK^ENST00000389048.8" ; transcript_name "ALK-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--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^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:
WWOX--CLEC3A HAVANA gene 32903 37792 . + . FI_gene_label "CLEC3A^ENSG00000166509.12" ; ID "WWOX--CLEC3A^CLEC3A^ENSG00000166509.12" ; exon_id "ENSE00003895828.1" ; exon_number 1 ; gene_id "WWOX--CLEC3A^CLEC3A^ENSG00000166509.12" ; gene_name CLEC3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000137620.5" ; havana_transcript "OTTHUMT00000269041.4" ; hgnc_id "HGNC:2052" ; level 2 ; orig_coord_info "chr16,78022627,78022741,+" ; protein_id "ENSP00000299642.5" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "WWOX--CLEC3A^ENST00000299642.10" ; transcript_name "CLEC3A-201" ; transcript_support_level 1 ; transcript_type protein_coding
WWOX--CLEC3A HAVANA mRNA 32903 37792 . + . FI_gene_label "CLEC3A^ENSG00000166509.12" ; ID "WWOX--CLEC3A^ENST00000299642.10" ; Parent "WWOX--CLEC3A^CLEC3A^ENSG00000166509.12" ; exon_id "ENSE00003895828.1" ; exon_number 1 ; gene_id "WWOX--CLEC3A^CLEC3A^ENSG00000166509.12" ; gene_name CLEC3A ; gene_type protein_coding ; havana_gene "OTTHUMG00000137620.5" ; havana_transcript "OTTHUMT00000269041.4" ; hgnc_id "HGNC:2052" ; level 2 ; orig_coord_info "chr16,78022627,78022741,+" ; protein_id "ENSP00000299642.5" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "WWOX--CLEC3A^ENST00000299642.10" ; transcript_name "CLEC3A-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
WWOX--CLEC3A HAVANA gene 1250 18768 . + . FI_gene_label "WWOX^ENSG00000186153.17" ; ID "WWOX--CLEC3A^WWOX^ENSG00000186153.17" ; ccdsid "CCDS42197.1" ; exon_id "ENSE00002598693.1" ; exon_number 1 ; gene_id "WWOX--CLEC3A^WWOX^ENSG00000186153.17" ; gene_name WWOX ; gene_type protein_coding ; havana_gene "OTTHUMG00000176851.3" ; havana_transcript "OTTHUMT00000434020.1" ; hgnc_id "HGNC:12799" ; level 2 ; orig_coord_info "chr16,78099779,78099885,+" ; protein_id "ENSP00000348119.3" ; tag basic CCDS ; transcript_id "WWOX--CLEC3A^ENST00000355860.7" ; transcript_name "WWOX-201" ; transcript_support_level 1 ; transcript_type protein_coding
WWOX--CLEC3A HAVANA mRNA 1250 18768 . + . FI_gene_label "WWOX^ENSG00000186153.17" ; ID "WWOX--CLEC3A^ENST00000355860.7" ; Parent "WWOX--CLEC3A^WWOX^ENSG00000186153.17" ; ccdsid "CCDS42197.1" ; exon_id "ENSE00002598693.1" ; exon_number 1 ; gene_id "WWOX--CLEC3A^WWOX^ENSG00000186153.17" ; gene_name WWOX ; gene_type protein_coding ; havana_gene "OTTHUMG00000176851.3" ; havana_transcript "OTTHUMT00000434020.1" ; hgnc_id "HGNC:12799" ; level 2 ; orig_coord_info "chr16,78099779,78099885,+" ; protein_id "ENSP00000348119.3" ; tag basic CCDS ; transcript_id "WWOX--CLEC3A^ENST00000355860.7" ; transcript_name "WWOX-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC006453.1--FAM230C HAVANA gene 11227 20685 . + . FI_gene_label "FAM230C^ENSG00000279516.2" ; ID "AC006453.1--FAM230C^FAM230C^ENSG00000279516.2" ; exon_id "ENSE00003758598.1" ; exon_number 1 ; gene_id "AC006453.1--FAM230C^FAM230C^ENSG00000279516.2" ; gene_name FAM230C ; gene_type lncRNA ; havana_gene "OTTHUMG00000189381.2" ; havana_transcript "OTTHUMT00000479522.1" ; hgnc_id "HGNC:24482" ; level 2 ; orig_coord_info "chr13,18195297,18195411,+" ; tag basic ; transcript_id "AC006453.1--FAM230C^ENST00000623511.1" ; transcript_name "FAM230C-201" ; transcript_support_level 1 ; transcript_type lncRNA
AC006453.1--FAM230C HAVANA RNA 11227 20685 . + . FI_gene_label "FAM230C^ENSG00000279516.2" ; ID "AC006453.1--FAM230C^ENST00000623511.1" ; Parent "AC006453.1--FAM230C^FAM230C^ENSG00000279516.2" ; exon_id "ENSE00003758598.1" ; exon_number 1 ; gene_id "AC006453.1--FAM230C^FAM230C^ENSG00000279516.2" ; gene_name FAM230C ; gene_type lncRNA ; havana_gene "OTTHUMG00000189381.2" ; havana_transcript "OTTHUMT00000479522.1" ; hgnc_id "HGNC:24482" ; level 2 ; orig_coord_info "chr13,18195297,18195411,+" ; tag basic ; transcript_id "AC006453.1--FAM230C^ENST00000623511.1" ; transcript_name "FAM230C-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
AC006453.1--FAM230C HAVANA gene 1001 8226 . + . FI_gene_label "AC006453.1^ENSG00000283132.1" ; ID "AC006453.1--FAM230C^AC006453.1^ENSG00000283132.1" ; exon_id "ENSE00003797054.1" ; exon_number 1 ; gene_id "AC006453.1--FAM230C^AC006453.1^ENSG00000283132.1" ; gene_name "AC006453.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191643.1" ; havana_transcript "OTTHUMT00000489004.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr2,89640438,89640635,-" ; tag basic ; transcript_id "AC006453.1--FAM230C^ENST00000636037.1" ; transcript_name "AC006453.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC006453.1--FAM230C HAVANA RNA 1001 8226 . + . FI_gene_label "AC006453.1^ENSG00000283132.1" ; ID "AC006453.1--FAM230C^ENST00000636037.1" ; Parent "AC006453.1--FAM230C^AC006453.1^ENSG00000283132.1" ; exon_id "ENSE00003797054.1" ; exon_number 1 ; gene_id "AC006453.1--FAM230C^AC006453.1^ENSG00000283132.1" ; gene_name "AC006453.1" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000191643.1" ; havana_transcript "OTTHUMT00000489004.1" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr2,89640438,89640635,-" ; tag basic ; transcript_id "AC006453.1--FAM230C^ENST00000636037.1" ; transcript_name "AC006453.1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AC136431.1--PKD1P1 HAVANA gene 9015 27073 . + . FI_gene_label "PKD1P1^ENSG00000244257.5" ; ID "AC136431.1--PKD1P1^PKD1P1^ENSG00000244257.5" ; exon_id "ENSE00001787767.1" ; exon_number 1 ; gene_id "AC136431.1--PKD1P1^PKD1P1^ENSG00000244257.5" ; gene_name PKD1P1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000133625.1" ; havana_transcript "OTTHUMT00000257767.1" ; hgnc_id "HGNC:30065" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr16,16310341,16310562,+" ; tag basic ; transcript_id "AC136431.1--PKD1P1^ENST00000458669.1" ; transcript_name "PKD1P1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
AC136431.1--PKD1P1 HAVANA RNA 9015 27073 . + . FI_gene_label "PKD1P1^ENSG00000244257.5" ; ID "AC136431.1--PKD1P1^ENST00000458669.1" ; Parent "AC136431.1--PKD1P1^PKD1P1^ENSG00000244257.5" ; exon_id "ENSE00001787767.1" ; exon_number 1 ; gene_id "AC136431.1--PKD1P1^PKD1P1^ENSG00000244257.5" ; gene_name PKD1P1 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000133625.1" ; havana_transcript "OTTHUMT00000257767.1" ; hgnc_id "HGNC:30065" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr16,16310341,16310562,+" ; tag basic ; transcript_id "AC136431.1--PKD1P1^ENST00000458669.1" ; transcript_name "PKD1P1-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene
L1 and L2 created:
AC136431.1--PKD1P1 HAVANA gene 1001 6014 . + . FI_gene_label "AC136431.1^ENSG00000260126.2" ; ID "AC136431.1--PKD1P1^AC136431.1^ENSG00000260126.2" ; exon_id "ENSE00003856180.1" ; exon_number 1 ; gene_id "AC136431.1--PKD1P1^AC136431.1^ENSG00000260126.2" ; gene_name "AC136431.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000177276.2" ; havana_transcript "OTTHUMT00000436080.2" ; level 2 ; orig_coord_info "chr16,16499533,16499619,+" ; tag basic TAGENE ; transcript_id "AC136431.1--PKD1P1^ENST00000567465.2" ; transcript_name "AC136431.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
AC136431.1--PKD1P1 HAVANA RNA 1001 6014 . + . FI_gene_label "AC136431.1^ENSG00000260126.2" ; ID "AC136431.1--PKD1P1^ENST00000567465.2" ; Parent "AC136431.1--PKD1P1^AC136431.1^ENSG00000260126.2" ; exon_id "ENSE00003856180.1" ; exon_number 1 ; gene_id "AC136431.1--PKD1P1^AC136431.1^ENSG00000260126.2" ; gene_name "AC136431.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000177276.2" ; havana_transcript "OTTHUMT00000436080.2" ; level 2 ; orig_coord_info "chr16,16499533,16499619,+" ; tag basic TAGENE ; transcript_id "AC136431.1--PKD1P1^ENST00000567465.2" ; transcript_name "AC136431.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
CRYZL2P--SEC16B HAVANA gene 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
CRYZL2P--SEC16B HAVANA RNA 1005 12289 . + . FI_gene_label "CRYZL2P^ENSG00000242193.11" ; ID "CRYZL2P--SEC16B^ENST00000462729.2" ; Parent "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; exon_id "ENSE00001918901.2" ; exon_number 1 ; gene_id "CRYZL2P--SEC16B^CRYZL2P^ENSG00000242193.11" ; gene_name CRYZL2P ; gene_type transcribed_unitary_pseudogene ; havana_gene "OTTHUMG00000154878.4" ; havana_transcript "OTTHUMT00000337460.2" ; hgnc_id "HGNC:52164" ; level 2 ; orig_coord_info "chr1,178037897,178037946,-" ; tag basic ; transcript_id "CRYZL2P--SEC16B^ENST00000462729.2" ; transcript_name "CRYZL2P-201" ; transcript_support_level NA ; transcript_type transcribed_unitary_pseudogene
L1 and L2 created:
FBXO25--AC240565.1 HAVANA gene 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--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 "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
FBXO25--AC240565.1 HAVANA RNA 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^ENST00000624936.2" ; Parent "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--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 "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
L1 and L2 created:
TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
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
127 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 ------------------------------
248 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------
------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
------------------------ Check12: all level1 locations -------------------------
We fixed 11 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 0 second) ------
GFF3 file parsed