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: 2755
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2755
=> 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:2755
=> 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 2 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:
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:
PEDS1--LINC01728 HAVANA gene 1001 9520 . + . FI_gene_label "PEDS1^ENSG00000240849.11" ; ID "PEDS1--LINC01728^PEDS1^ENSG00000240849.11" ; ccdsid "CCDS54473.1" ; exon_id "ENSE00001455768.1" ; exon_number 1 ; gene_id "PEDS1--LINC01728^PEDS1^ENSG00000240849.11" ; gene_name PEDS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152625.5" ; havana_transcript "OTTHUMT00000080533.1" ; hgnc_id "HGNC:16735" ; level 2 ; orig_coord_info "chr20,50153517,50153637,-" ; protein_id "ENSP00000360713.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "PEDS1--LINC01728^ENST00000371650.9" ; transcript_name "PEDS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PEDS1--LINC01728 HAVANA mRNA 1001 9520 . + . FI_gene_label "PEDS1^ENSG00000240849.11" ; ID "PEDS1--LINC01728^ENST00000371650.9" ; Parent "PEDS1--LINC01728^PEDS1^ENSG00000240849.11" ; ccdsid "CCDS54473.1" ; exon_id "ENSE00001455768.1" ; exon_number 1 ; gene_id "PEDS1--LINC01728^PEDS1^ENSG00000240849.11" ; gene_name PEDS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152625.5" ; havana_transcript "OTTHUMT00000080533.1" ; hgnc_id "HGNC:16735" ; level 2 ; orig_coord_info "chr20,50153517,50153637,-" ; protein_id "ENSP00000360713.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "PEDS1--LINC01728^ENST00000371650.9" ; transcript_name "PEDS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PEDS1--RNU6-639P HAVANA gene 1001 9520 . + . FI_gene_label "PEDS1^ENSG00000240849.11" ; ID "PEDS1--RNU6-639P^PEDS1^ENSG00000240849.11" ; ccdsid "CCDS54473.1" ; exon_id "ENSE00001455768.1" ; exon_number 1 ; gene_id "PEDS1--RNU6-639P^PEDS1^ENSG00000240849.11" ; gene_name PEDS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152625.5" ; havana_transcript "OTTHUMT00000080533.1" ; hgnc_id "HGNC:16735" ; level 2 ; orig_coord_info "chr20,50153517,50153637,-" ; protein_id "ENSP00000360713.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "PEDS1--RNU6-639P^ENST00000371650.9" ; transcript_name "PEDS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PEDS1--RNU6-639P HAVANA mRNA 1001 9520 . + . FI_gene_label "PEDS1^ENSG00000240849.11" ; ID "PEDS1--RNU6-639P^ENST00000371650.9" ; Parent "PEDS1--RNU6-639P^PEDS1^ENSG00000240849.11" ; ccdsid "CCDS54473.1" ; exon_id "ENSE00001455768.1" ; exon_number 1 ; gene_id "PEDS1--RNU6-639P^PEDS1^ENSG00000240849.11" ; gene_name PEDS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000152625.5" ; havana_transcript "OTTHUMT00000080533.1" ; hgnc_id "HGNC:16735" ; level 2 ; orig_coord_info "chr20,50153517,50153637,-" ; protein_id "ENSP00000360713.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "PEDS1--RNU6-639P^ENST00000371650.9" ; transcript_name "PEDS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PPME1--TCF7L2 HAVANA gene 38381 46571 . + . FI_gene_label "TCF7L2^ENSG00000148737.17" ; ID "PPME1--TCF7L2^TCF7L2^ENSG00000148737.17" ; exon_id "ENSE00001738678.1" ; exon_number 1 ; gene_id "PPME1--TCF7L2^TCF7L2^ENSG00000148737.17" ; gene_name TCF7L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019070.11" ; havana_transcript "OTTHUMT00000050420.2" ; hgnc_id "HGNC:11641" ; level 2 ; orig_coord_info "chr10,113146072,113146097,+" ; protein_id "ENSP00000277945.7" ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "PPME1--TCF7L2^ENST00000277945.11" ; transcript_name "TCF7L2-201" ; transcript_support_level 5 ; transcript_type protein_coding
PPME1--TCF7L2 HAVANA mRNA 38381 46571 . + . FI_gene_label "TCF7L2^ENSG00000148737.17" ; ID "PPME1--TCF7L2^ENST00000277945.11" ; Parent "PPME1--TCF7L2^TCF7L2^ENSG00000148737.17" ; exon_id "ENSE00001738678.1" ; exon_number 1 ; gene_id "PPME1--TCF7L2^TCF7L2^ENSG00000148737.17" ; gene_name TCF7L2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019070.11" ; havana_transcript "OTTHUMT00000050420.2" ; hgnc_id "HGNC:11641" ; level 2 ; orig_coord_info "chr10,113146072,113146097,+" ; protein_id "ENSP00000277945.7" ; tag mRNA_start_NF mRNA_end_NF cds_start_NF cds_end_NF ; transcript_id "PPME1--TCF7L2^ENST00000277945.11" ; transcript_name "TCF7L2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PPME1--TCF7L2 HAVANA gene 1023 20839 . + . FI_gene_label "PPME1^ENSG00000214517.10" ; ID "PPME1--TCF7L2^PPME1^ENSG00000214517.10" ; ccdsid "CCDS44678.1" ; exon_id "ENSE00002301751.2" ; exon_number 1 ; gene_id "PPME1--TCF7L2^PPME1^ENSG00000214517.10" ; gene_name PPME1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168115.5" ; havana_transcript "OTTHUMT00000398254.2" ; hgnc_id "HGNC:30178" ; level 2 ; orig_coord_info "chr11,74171422,74171522,+" ; protein_id "ENSP00000329867.8" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPME1--TCF7L2^ENST00000328257.13" ; transcript_name "PPME1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PPME1--TCF7L2 HAVANA mRNA 1023 20839 . + . FI_gene_label "PPME1^ENSG00000214517.10" ; ID "PPME1--TCF7L2^ENST00000328257.13" ; Parent "PPME1--TCF7L2^PPME1^ENSG00000214517.10" ; ccdsid "CCDS44678.1" ; exon_id "ENSE00002301751.2" ; exon_number 1 ; gene_id "PPME1--TCF7L2^PPME1^ENSG00000214517.10" ; gene_name PPME1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168115.5" ; havana_transcript "OTTHUMT00000398254.2" ; hgnc_id "HGNC:30178" ; level 2 ; orig_coord_info "chr11,74171422,74171522,+" ; protein_id "ENSP00000329867.8" ; tag non_canonical_U12 basic MANE_Select appris_principal_1 CCDS ; transcript_id "PPME1--TCF7L2^ENST00000328257.13" ; transcript_name "PPME1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PTBP3--HSDL2 HAVANA gene 1636 7412 . + . FI_gene_label "PTBP3^ENSG00000119314.16" ; ID "PTBP3--HSDL2^PTBP3^ENSG00000119314.16" ; exon_id "ENSE00001333878.4" ; exon_number 1 ; gene_id "PTBP3--HSDL2^PTBP3^ENSG00000119314.16" ; gene_name PTBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020503.3" ; havana_transcript "OTTHUMT00000053674.2" ; hgnc_id "HGNC:10253" ; level 2 ; orig_coord_info "chr9,112332784,112332843,-" ; protein_id "ENSP00000210227.4" ; tag mRNA_end_NF cds_end_NF ; transcript_id "PTBP3--HSDL2^ENST00000210227.4" ; transcript_name "PTBP3-201" ; transcript_support_level 2 ; transcript_type protein_coding
PTBP3--HSDL2 HAVANA mRNA 1636 7412 . + . FI_gene_label "PTBP3^ENSG00000119314.16" ; ID "PTBP3--HSDL2^ENST00000210227.4" ; Parent "PTBP3--HSDL2^PTBP3^ENSG00000119314.16" ; exon_id "ENSE00001333878.4" ; exon_number 1 ; gene_id "PTBP3--HSDL2^PTBP3^ENSG00000119314.16" ; gene_name PTBP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020503.3" ; havana_transcript "OTTHUMT00000053674.2" ; hgnc_id "HGNC:10253" ; level 2 ; orig_coord_info "chr9,112332784,112332843,-" ; protein_id "ENSP00000210227.4" ; tag mRNA_end_NF cds_end_NF ; transcript_id "PTBP3--HSDL2^ENST00000210227.4" ; transcript_name "PTBP3-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
PTBP3--HSDL2 HAVANA gene 25263 39686 . + . FI_gene_label "HSDL2^ENSG00000119471.15" ; ID "PTBP3--HSDL2^HSDL2^ENSG00000119471.15" ; ccdsid "CCDS56582.1" ; exon_id "ENSE00001534957.1" ; exon_number 1 ; gene_id "PTBP3--HSDL2^HSDL2^ENSG00000119471.15" ; gene_name HSDL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020504.6" ; havana_transcript "OTTHUMT00000053680.1" ; hgnc_id "HGNC:18572" ; level 2 ; orig_coord_info "chr9,112380164,112380180,+" ; protein_id "ENSP00000381783.1" ; tag basic CCDS ; transcript_id "PTBP3--HSDL2^ENST00000398803.1" ; transcript_name "HSDL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PTBP3--HSDL2 HAVANA mRNA 25263 39686 . + . FI_gene_label "HSDL2^ENSG00000119471.15" ; ID "PTBP3--HSDL2^ENST00000398803.1" ; Parent "PTBP3--HSDL2^HSDL2^ENSG00000119471.15" ; ccdsid "CCDS56582.1" ; exon_id "ENSE00001534957.1" ; exon_number 1 ; gene_id "PTBP3--HSDL2^HSDL2^ENSG00000119471.15" ; gene_name HSDL2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020504.6" ; havana_transcript "OTTHUMT00000053680.1" ; hgnc_id "HGNC:18572" ; level 2 ; orig_coord_info "chr9,112380164,112380180,+" ; protein_id "ENSP00000381783.1" ; tag basic CCDS ; transcript_id "PTBP3--HSDL2^ENST00000398803.1" ; transcript_name "HSDL2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RBMS1--AFF3 ENSEMBL gene 33105 78008 . + . FI_gene_label "AFF3^ENSG00000144218.20" ; ID "RBMS1--AFF3^AFF3^ENSG00000144218.20" ; ccdsid "CCDS42723.1" ; exon_id "ENSE00003790625.1" ; exon_number 3 ; gene_id "RBMS1--AFF3^AFF3^ENSG00000144218.20" ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13" ; hgnc_id "HGNC:6473" ; level 3 ; orig_coord_info "chr2,100104402,100104454,-" ; protein_id "ENSP00000317421.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "RBMS1--AFF3^ENST00000317233.8" ; transcript_name "AFF3-201" ; transcript_support_level 5 ; transcript_type protein_coding
RBMS1--AFF3 ENSEMBL mRNA 33105 78008 . + . FI_gene_label "AFF3^ENSG00000144218.20" ; ID "RBMS1--AFF3^ENST00000317233.8" ; Parent "RBMS1--AFF3^AFF3^ENSG00000144218.20" ; ccdsid "CCDS42723.1" ; exon_id "ENSE00003790625.1" ; exon_number 3 ; gene_id "RBMS1--AFF3^AFF3^ENSG00000144218.20" ; gene_name AFF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000153011.13" ; hgnc_id "HGNC:6473" ; level 3 ; orig_coord_info "chr2,100104402,100104454,-" ; protein_id "ENSP00000317421.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "RBMS1--AFF3^ENST00000317233.8" ; transcript_name "AFF3-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
RBMS1--AFF3 HAVANA gene 1001 28645 . + . FI_gene_label "RBMS1^ENSG00000153250.20" ; ID "RBMS1--AFF3^RBMS1^ENSG00000153250.20" ; ccdsid "CCDS2213.1" ; exon_id "ENSE00002037352.2" ; exon_number 1 ; gene_id "RBMS1--AFF3^RBMS1^ENSG00000153250.20" ; gene_name RBMS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132031.10" ; havana_transcript "OTTHUMT00000255043.5" ; hgnc_id "HGNC:9907" ; level 2 ; orig_coord_info "chr2,160493289,160493363,-" ; protein_id "ENSP00000294904.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBMS1--AFF3^ENST00000348849.8" ; transcript_name "RBMS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RBMS1--AFF3 HAVANA mRNA 1001 28645 . + . FI_gene_label "RBMS1^ENSG00000153250.20" ; ID "RBMS1--AFF3^ENST00000348849.8" ; Parent "RBMS1--AFF3^RBMS1^ENSG00000153250.20" ; ccdsid "CCDS2213.1" ; exon_id "ENSE00002037352.2" ; exon_number 1 ; gene_id "RBMS1--AFF3^RBMS1^ENSG00000153250.20" ; gene_name RBMS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132031.10" ; havana_transcript "OTTHUMT00000255043.5" ; hgnc_id "HGNC:9907" ; level 2 ; orig_coord_info "chr2,160493289,160493363,-" ; protein_id "ENSP00000294904.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RBMS1--AFF3^ENST00000348849.8" ; transcript_name "RBMS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RPN2--PTPRT HAVANA gene 1921 21709 . + . FI_gene_label "RPN2^ENSG00000118705.17" ; ID "RPN2--PTPRT^RPN2^ENSG00000118705.17" ; ccdsid "CCDS13291.1" ; exon_id "ENSE00001369190.4" ; exon_number 1 ; gene_id "RPN2--PTPRT^RPN2^ENSG00000118705.17" ; gene_name RPN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032409.6" ; havana_transcript "OTTHUMT00000079076.4" ; hgnc_id "HGNC:10382" ; level 2 ; orig_coord_info "chr20,37179357,37179369,+" ; protein_id "ENSP00000237530.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RPN2--PTPRT^ENST00000237530.11" ; transcript_name "RPN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
RPN2--PTPRT HAVANA mRNA 1921 21709 . + . FI_gene_label "RPN2^ENSG00000118705.17" ; ID "RPN2--PTPRT^ENST00000237530.11" ; Parent "RPN2--PTPRT^RPN2^ENSG00000118705.17" ; ccdsid "CCDS13291.1" ; exon_id "ENSE00001369190.4" ; exon_number 1 ; gene_id "RPN2--PTPRT^RPN2^ENSG00000118705.17" ; gene_name RPN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032409.6" ; havana_transcript "OTTHUMT00000079076.4" ; hgnc_id "HGNC:10382" ; level 2 ; orig_coord_info "chr20,37179357,37179369,+" ; protein_id "ENSP00000237530.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RPN2--PTPRT^ENST00000237530.11" ; transcript_name "RPN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RPN2--PTPRT HAVANA gene 24947 70206 . + . FI_gene_label "PTPRT^ENSG00000196090.12" ; ID "RPN2--PTPRT^PTPRT^ENSG00000196090.12" ; exon_id "ENSE00001299020.1" ; exon_number 1 ; gene_id "RPN2--PTPRT^PTPRT^ENSG00000196090.12" ; gene_name PTPRT ; gene_type protein_coding ; havana_gene "OTTHUMG00000033040.5" ; havana_transcript "OTTHUMT00000080317.1" ; hgnc_id "HGNC:9682" ; level 2 ; orig_coord_info "chr20,43189646,43189733,-" ; protein_id "ENSP00000348408.2" ; tag dotter_confirmed not_organism_supported basic appris_alternative_2 ; transcript_id "RPN2--PTPRT^ENST00000356100.6" ; transcript_name "PTPRT-201" ; transcript_support_level 5 ; transcript_type protein_coding
RPN2--PTPRT HAVANA mRNA 24947 70206 . + . FI_gene_label "PTPRT^ENSG00000196090.12" ; ID "RPN2--PTPRT^ENST00000356100.6" ; Parent "RPN2--PTPRT^PTPRT^ENSG00000196090.12" ; exon_id "ENSE00001299020.1" ; exon_number 1 ; gene_id "RPN2--PTPRT^PTPRT^ENSG00000196090.12" ; gene_name PTPRT ; gene_type protein_coding ; havana_gene "OTTHUMG00000033040.5" ; havana_transcript "OTTHUMT00000080317.1" ; hgnc_id "HGNC:9682" ; level 2 ; orig_coord_info "chr20,43189646,43189733,-" ; protein_id "ENSP00000348408.2" ; tag dotter_confirmed not_organism_supported basic appris_alternative_2 ; transcript_id "RPN2--PTPRT^ENST00000356100.6" ; transcript_name "PTPRT-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
USP12--MTIF3 HAVANA gene 1001 14211 . + . FI_gene_label "USP12^ENSG00000152484.14" ; ID "USP12--MTIF3^USP12^ENSG00000152484.14" ; ccdsid "CCDS31952.1" ; exon_id "ENSE00001488438.3" ; exon_number 1 ; gene_id "USP12--MTIF3^USP12^ENSG00000152484.14" ; gene_name USP12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016626.5" ; havana_transcript "OTTHUMT00000044264.3" ; hgnc_id "HGNC:20485" ; level 2 ; orig_coord_info "chr13,27171592,27171639,-" ; protein_id "ENSP00000282344.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "USP12--MTIF3^ENST00000282344.11" ; transcript_name "USP12-201" ; transcript_support_level 1 ; transcript_type protein_coding
USP12--MTIF3 HAVANA mRNA 1001 14211 . + . FI_gene_label "USP12^ENSG00000152484.14" ; ID "USP12--MTIF3^ENST00000282344.11" ; Parent "USP12--MTIF3^USP12^ENSG00000152484.14" ; ccdsid "CCDS31952.1" ; exon_id "ENSE00001488438.3" ; exon_number 1 ; gene_id "USP12--MTIF3^USP12^ENSG00000152484.14" ; gene_name USP12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016626.5" ; havana_transcript "OTTHUMT00000044264.3" ; hgnc_id "HGNC:20485" ; level 2 ; orig_coord_info "chr13,27171592,27171639,-" ; protein_id "ENSP00000282344.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "USP12--MTIF3^ENST00000282344.11" ; transcript_name "USP12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
USP12--MTIF3 HAVANA gene 17239 23686 . + . FI_gene_label "MTIF3^ENSG00000122033.15" ; ID "USP12--MTIF3^MTIF3^ENSG00000122033.15" ; ccdsid "CCDS9322.1" ; exon_id "ENSE00003664514.1" ; exon_number 5 ; gene_id "USP12--MTIF3^MTIF3^ENSG00000122033.15" ; gene_name MTIF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016633.2" ; havana_transcript "OTTHUMT00000044300.1" ; hgnc_id "HGNC:29788" ; level 2 ; orig_coord_info "chr13,27439989,27440448,-" ; protein_id "ENSP00000370508.1" ; tag basic appris_principal_1 CCDS ; transcript_id "USP12--MTIF3^ENST00000381116.5" ; transcript_name "MTIF3-201" ; transcript_support_level 5 ; transcript_type protein_coding
USP12--MTIF3 HAVANA mRNA 17239 23686 . + . FI_gene_label "MTIF3^ENSG00000122033.15" ; ID "USP12--MTIF3^ENST00000381116.5" ; Parent "USP12--MTIF3^MTIF3^ENSG00000122033.15" ; ccdsid "CCDS9322.1" ; exon_id "ENSE00003664514.1" ; exon_number 5 ; gene_id "USP12--MTIF3^MTIF3^ENSG00000122033.15" ; gene_name MTIF3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016633.2" ; havana_transcript "OTTHUMT00000044300.1" ; hgnc_id "HGNC:29788" ; level 2 ; orig_coord_info "chr13,27439989,27440448,-" ; protein_id "ENSP00000370508.1" ; tag basic appris_principal_1 CCDS ; transcript_id "USP12--MTIF3^ENST00000381116.5" ; transcript_name "MTIF3-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
USP12--RNU6-63P HAVANA gene 1001 14211 . + . FI_gene_label "USP12^ENSG00000152484.14" ; ID "USP12--RNU6-63P^USP12^ENSG00000152484.14" ; ccdsid "CCDS31952.1" ; exon_id "ENSE00001488438.3" ; exon_number 1 ; gene_id "USP12--RNU6-63P^USP12^ENSG00000152484.14" ; gene_name USP12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016626.5" ; havana_transcript "OTTHUMT00000044264.3" ; hgnc_id "HGNC:20485" ; level 2 ; orig_coord_info "chr13,27171592,27171639,-" ; protein_id "ENSP00000282344.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "USP12--RNU6-63P^ENST00000282344.11" ; transcript_name "USP12-201" ; transcript_support_level 1 ; transcript_type protein_coding
USP12--RNU6-63P HAVANA mRNA 1001 14211 . + . FI_gene_label "USP12^ENSG00000152484.14" ; ID "USP12--RNU6-63P^ENST00000282344.11" ; Parent "USP12--RNU6-63P^USP12^ENSG00000152484.14" ; ccdsid "CCDS31952.1" ; exon_id "ENSE00001488438.3" ; exon_number 1 ; gene_id "USP12--RNU6-63P^USP12^ENSG00000152484.14" ; gene_name USP12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016626.5" ; havana_transcript "OTTHUMT00000044264.3" ; hgnc_id "HGNC:20485" ; level 2 ; orig_coord_info "chr13,27171592,27171639,-" ; protein_id "ENSP00000282344.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "USP12--RNU6-63P^ENST00000282344.11" ; transcript_name "USP12-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PEDS1--LINC01728 HAVANA gene 18004 18752 . + . FI_gene_label "LINC01728^ENSG00000233277.1" ; ID "PEDS1--LINC01728^LINC01728^ENSG00000233277.1" ; exon_id "ENSE00001721147.1" ; exon_number 1 ; gene_id "PEDS1--LINC01728^LINC01728^ENSG00000233277.1" ; gene_name LINC01728 ; gene_type lncRNA ; havana_gene "OTTHUMG00000032515.1" ; havana_transcript "OTTHUMT00000079327.1" ; hgnc_id "HGNC:52516" ; level 1 ; orig_coord_info "chr20,43894720,43894797,+" ; tag basic exp_conf ; transcript_id "PEDS1--LINC01728^ENST00000428529.1" ; transcript_name "LINC01728-201" ; transcript_support_level 2 ; transcript_type lncRNA
PEDS1--LINC01728 HAVANA RNA 18004 18752 . + . FI_gene_label "LINC01728^ENSG00000233277.1" ; ID "PEDS1--LINC01728^ENST00000428529.1" ; Parent "PEDS1--LINC01728^LINC01728^ENSG00000233277.1" ; exon_id "ENSE00001721147.1" ; exon_number 1 ; gene_id "PEDS1--LINC01728^LINC01728^ENSG00000233277.1" ; gene_name LINC01728 ; gene_type lncRNA ; havana_gene "OTTHUMG00000032515.1" ; havana_transcript "OTTHUMT00000079327.1" ; hgnc_id "HGNC:52516" ; level 1 ; orig_coord_info "chr20,43894720,43894797,+" ; tag basic exp_conf ; transcript_id "PEDS1--LINC01728^ENST00000428529.1" ; transcript_name "LINC01728-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
PEDS1--RNU6-639P ENSEMBL gene 18004 18110 . + . FI_gene_label "RNU6-639P^ENSG00000206801.1" ; ID "PEDS1--RNU6-639P^RNU6-639P^ENSG00000206801.1" ; exon_id "ENSE00001808797.1" ; exon_number 1 ; gene_id "PEDS1--RNU6-639P^RNU6-639P^ENSG00000206801.1" ; gene_name "RNU6-639P" ; gene_type snRNA ; hgnc_id "HGNC:47602" ; level 3 ; orig_coord_info "chr20,43796437,43796543,-" ; tag basic ; transcript_id "PEDS1--RNU6-639P^ENST00000384074.1" ; transcript_name "RNU6-639P-201" ; transcript_support_level NA ; transcript_type snRNA
PEDS1--RNU6-639P ENSEMBL RNA 18004 18110 . + . FI_gene_label "RNU6-639P^ENSG00000206801.1" ; ID "PEDS1--RNU6-639P^ENST00000384074.1" ; Parent "PEDS1--RNU6-639P^RNU6-639P^ENSG00000206801.1" ; exon_id "ENSE00001808797.1" ; exon_number 1 ; gene_id "PEDS1--RNU6-639P^RNU6-639P^ENSG00000206801.1" ; gene_name "RNU6-639P" ; gene_type snRNA ; hgnc_id "HGNC:47602" ; level 3 ; orig_coord_info "chr20,43796437,43796543,-" ; tag basic ; transcript_id "PEDS1--RNU6-639P^ENST00000384074.1" ; transcript_name "RNU6-639P-201" ; transcript_support_level NA ; transcript_type snRNA
L1 and L2 created:
USP12--RNU6-63P ENSEMBL gene 17212 17306 . + . FI_gene_label "RNU6-63P^ENSG00000252499.1" ; ID "USP12--RNU6-63P^RNU6-63P^ENSG00000252499.1" ; exon_id "ENSE00002088967.1" ; exon_number 1 ; gene_id "USP12--RNU6-63P^RNU6-63P^ENSG00000252499.1" ; gene_name "RNU6-63P" ; gene_type snRNA ; hgnc_id "HGNC:42553" ; level 3 ; orig_coord_info "chr13,27488138,27488232,+" ; tag basic ; transcript_id "USP12--RNU6-63P^ENST00000516690.1" ; transcript_name "RNU6-63P-201" ; transcript_support_level NA ; transcript_type snRNA
USP12--RNU6-63P ENSEMBL RNA 17212 17306 . + . FI_gene_label "RNU6-63P^ENSG00000252499.1" ; ID "USP12--RNU6-63P^ENST00000516690.1" ; Parent "USP12--RNU6-63P^RNU6-63P^ENSG00000252499.1" ; exon_id "ENSE00002088967.1" ; exon_number 1 ; gene_id "USP12--RNU6-63P^RNU6-63P^ENSG00000252499.1" ; gene_name "RNU6-63P" ; gene_type snRNA ; hgnc_id "HGNC:42553" ; level 3 ; orig_coord_info "chr13,27488138,27488232,+" ; tag basic ; transcript_id "USP12--RNU6-63P^ENST00000516690.1" ; transcript_name "RNU6-63P-201" ; transcript_support_level NA ; transcript_type snRNA
171 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------
------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
311 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