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: 1341
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1341
=> 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:1341
=> 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:
FAF1--AL139081.2 ENSEMBL gene 1475 24250 . + . FI_gene_label "FAF1^ENSG00000185104.20" ; ID "FAF1--AL139081.2^FAF1^ENSG00000185104.20" ; exon_id "ENSE00002276283.2" ; exon_number 1 ; gene_id "FAF1--AL139081.2^FAF1^ENSG00000185104.20" ; gene_name FAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007930.7" ; hgnc_id "HGNC:3578" ; level 3 ; orig_coord_info "chr1,50959767,50959787,-" ; protein_id "ENSP00000360843.5" ; tag basic ; transcript_id "FAF1--AL139081.2^ENST00000371778.5" ; transcript_name "FAF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FAF1--AL139081.2 ENSEMBL mRNA 1475 24250 . + . FI_gene_label "FAF1^ENSG00000185104.20" ; ID "FAF1--AL139081.2^ENST00000371778.5" ; Parent "FAF1--AL139081.2^FAF1^ENSG00000185104.20" ; exon_id "ENSE00002276283.2" ; exon_number 1 ; gene_id "FAF1--AL139081.2^FAF1^ENSG00000185104.20" ; gene_name FAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007930.7" ; hgnc_id "HGNC:3578" ; level 3 ; orig_coord_info "chr1,50959767,50959787,-" ; protein_id "ENSP00000360843.5" ; tag basic ; transcript_id "FAF1--AL139081.2^ENST00000371778.5" ; transcript_name "FAF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FAF1--AL139383.1 ENSEMBL gene 1475 24250 . + . FI_gene_label "FAF1^ENSG00000185104.20" ; ID "FAF1--AL139383.1^FAF1^ENSG00000185104.20" ; exon_id "ENSE00002276283.2" ; exon_number 1 ; gene_id "FAF1--AL139383.1^FAF1^ENSG00000185104.20" ; gene_name FAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007930.7" ; hgnc_id "HGNC:3578" ; level 3 ; orig_coord_info "chr1,50959767,50959787,-" ; protein_id "ENSP00000360843.5" ; tag basic ; transcript_id "FAF1--AL139383.1^ENST00000371778.5" ; transcript_name "FAF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FAF1--AL139383.1 ENSEMBL mRNA 1475 24250 . + . FI_gene_label "FAF1^ENSG00000185104.20" ; ID "FAF1--AL139383.1^ENST00000371778.5" ; Parent "FAF1--AL139383.1^FAF1^ENSG00000185104.20" ; exon_id "ENSE00002276283.2" ; exon_number 1 ; gene_id "FAF1--AL139383.1^FAF1^ENSG00000185104.20" ; gene_name FAF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000007930.7" ; hgnc_id "HGNC:3578" ; level 3 ; orig_coord_info "chr1,50959767,50959787,-" ; protein_id "ENSP00000360843.5" ; tag basic ; transcript_id "FAF1--AL139383.1^ENST00000371778.5" ; transcript_name "FAF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
POLD3--NRG1 HAVANA gene 1027 19037 . + . FI_gene_label "POLD3^ENSG00000077514.9" ; ID "POLD3--NRG1^POLD3^ENSG00000077514.9" ; ccdsid "CCDS8233.1" ; exon_id "ENSE00002198152.2" ; exon_number 1 ; gene_id "POLD3--NRG1^POLD3^ENSG00000077514.9" ; gene_name POLD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165621.4" ; havana_transcript "OTTHUMT00000385376.2" ; hgnc_id "HGNC:20932" ; level 2 ; orig_coord_info "chr11,74592659,74592718,+" ; protein_id "ENSP00000263681.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "POLD3--NRG1^ENST00000263681.7" ; transcript_name "POLD3-201" ; transcript_support_level 1 ; transcript_type protein_coding
POLD3--NRG1 HAVANA mRNA 1027 19037 . + . FI_gene_label "POLD3^ENSG00000077514.9" ; ID "POLD3--NRG1^ENST00000263681.7" ; Parent "POLD3--NRG1^POLD3^ENSG00000077514.9" ; ccdsid "CCDS8233.1" ; exon_id "ENSE00002198152.2" ; exon_number 1 ; gene_id "POLD3--NRG1^POLD3^ENSG00000077514.9" ; gene_name POLD3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165621.4" ; havana_transcript "OTTHUMT00000385376.2" ; hgnc_id "HGNC:20932" ; level 2 ; orig_coord_info "chr11,74592659,74592718,+" ; protein_id "ENSP00000263681.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "POLD3--NRG1^ENST00000263681.7" ; transcript_name "POLD3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
POLD3--NRG1 HAVANA gene 31078 55871 . + . FI_gene_label "NRG1^ENSG00000157168.20" ; ID "POLD3--NRG1^NRG1^ENSG00000157168.20" ; ccdsid "CCDS6083.1" ; exon_id "ENSE00003752907.2" ; exon_number 1 ; gene_id "POLD3--NRG1^NRG1^ENSG00000157168.20" ; gene_name NRG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163918.29" ; havana_transcript "OTTHUMT00000483442.1" ; hgnc_id "HGNC:7997" ; level 2 ; orig_coord_info "chr8,32548727,32548826,+" ; protein_id "ENSP00000287842.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "POLD3--NRG1^ENST00000287842.7" ; transcript_name "NRG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
POLD3--NRG1 HAVANA mRNA 31078 55871 . + . FI_gene_label "NRG1^ENSG00000157168.20" ; ID "POLD3--NRG1^ENST00000287842.7" ; Parent "POLD3--NRG1^NRG1^ENSG00000157168.20" ; ccdsid "CCDS6083.1" ; exon_id "ENSE00003752907.2" ; exon_number 1 ; gene_id "POLD3--NRG1^NRG1^ENSG00000157168.20" ; gene_name NRG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163918.29" ; havana_transcript "OTTHUMT00000483442.1" ; hgnc_id "HGNC:7997" ; level 2 ; orig_coord_info "chr8,32548727,32548826,+" ; protein_id "ENSP00000287842.4" ; tag basic appris_alternative_2 CCDS ; transcript_id "POLD3--NRG1^ENST00000287842.7" ; transcript_name "NRG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC7A1--FLT3 HAVANA gene 23039 46183 . + . FI_gene_label "FLT3^ENSG00000122025.15" ; ID "SLC7A1--FLT3^FLT3^ENSG00000122025.15" ; ccdsid "CCDS31953.1" ; exon_id "ENSE00003896396.1" ; exon_number 1 ; gene_id "SLC7A1--FLT3^FLT3^ENSG00000122025.15" ; gene_name FLT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016646.4" ; havana_transcript "OTTHUMT00000044319.3" ; hgnc_id "HGNC:3765" ; level 2 ; orig_coord_info "chr13,28100468,28100510,-" ; protein_id "ENSP00000241453.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC7A1--FLT3^ENST00000241453.12" ; transcript_name "FLT3-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC7A1--FLT3 HAVANA mRNA 23039 46183 . + . FI_gene_label "FLT3^ENSG00000122025.15" ; ID "SLC7A1--FLT3^ENST00000241453.12" ; Parent "SLC7A1--FLT3^FLT3^ENSG00000122025.15" ; ccdsid "CCDS31953.1" ; exon_id "ENSE00003896396.1" ; exon_number 1 ; gene_id "SLC7A1--FLT3^FLT3^ENSG00000122025.15" ; gene_name FLT3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016646.4" ; havana_transcript "OTTHUMT00000044319.3" ; hgnc_id "HGNC:3765" ; level 2 ; orig_coord_info "chr13,28100468,28100510,-" ; protein_id "ENSP00000241453.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC7A1--FLT3^ENST00000241453.12" ; transcript_name "FLT3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SLC7A1--FLT3 HAVANA gene 1001 20022 . + . FI_gene_label "SLC7A1^ENSG00000139514.13" ; ID "SLC7A1--FLT3^SLC7A1^ENSG00000139514.13" ; ccdsid "CCDS9333.1" ; exon_id "ENSE00001486219.1" ; exon_number 3 ; gene_id "SLC7A1--FLT3^SLC7A1^ENSG00000139514.13" ; gene_name SLC7A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016658.6" ; havana_transcript "OTTHUMT00000044337.3" ; hgnc_id "HGNC:11057" ; level 2 ; orig_coord_info "chr13,29535819,29536188,-" ; protein_id "ENSP00000370128.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC7A1--FLT3^ENST00000380752.10" ; transcript_name "SLC7A1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SLC7A1--FLT3 HAVANA mRNA 1001 20022 . + . FI_gene_label "SLC7A1^ENSG00000139514.13" ; ID "SLC7A1--FLT3^ENST00000380752.10" ; Parent "SLC7A1--FLT3^SLC7A1^ENSG00000139514.13" ; ccdsid "CCDS9333.1" ; exon_id "ENSE00001486219.1" ; exon_number 3 ; gene_id "SLC7A1--FLT3^SLC7A1^ENSG00000139514.13" ; gene_name SLC7A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016658.6" ; havana_transcript "OTTHUMT00000044337.3" ; hgnc_id "HGNC:11057" ; level 2 ; orig_coord_info "chr13,29535819,29536188,-" ; protein_id "ENSP00000370128.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SLC7A1--FLT3^ENST00000380752.10" ; transcript_name "SLC7A1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TPCN2--PPME1 HAVANA gene 1001 22333 . + . FI_gene_label "TPCN2^ENSG00000162341.18" ; ID "TPCN2--PPME1^TPCN2^ENSG00000162341.18" ; ccdsid "CCDS8189.1" ; exon_id "ENSE00003799742.1" ; exon_number 1 ; gene_id "TPCN2--PPME1^TPCN2^ENSG00000162341.18" ; gene_name TPCN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000193817.1" ; havana_transcript "OTTHUMT00000396878.3" ; hgnc_id "HGNC:20820" ; level 2 ; orig_coord_info "chr11,69048998,69049106,+" ; protein_id "ENSP00000294309.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TPCN2--PPME1^ENST00000294309.8" ; transcript_name "TPCN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TPCN2--PPME1 HAVANA mRNA 1001 22333 . + . FI_gene_label "TPCN2^ENSG00000162341.18" ; ID "TPCN2--PPME1^ENST00000294309.8" ; Parent "TPCN2--PPME1^TPCN2^ENSG00000162341.18" ; ccdsid "CCDS8189.1" ; exon_id "ENSE00003799742.1" ; exon_number 1 ; gene_id "TPCN2--PPME1^TPCN2^ENSG00000162341.18" ; gene_name TPCN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000193817.1" ; havana_transcript "OTTHUMT00000396878.3" ; hgnc_id "HGNC:20820" ; level 2 ; orig_coord_info "chr11,69048998,69049106,+" ; protein_id "ENSP00000294309.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TPCN2--PPME1^ENST00000294309.8" ; transcript_name "TPCN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TPCN2--PPME1 HAVANA gene 29521 49337 . + . FI_gene_label "PPME1^ENSG00000214517.10" ; ID "TPCN2--PPME1^PPME1^ENSG00000214517.10" ; ccdsid "CCDS44678.1" ; exon_id "ENSE00002301751.2" ; exon_number 1 ; gene_id "TPCN2--PPME1^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 "TPCN2--PPME1^ENST00000328257.13" ; transcript_name "PPME1-201" ; transcript_support_level 1 ; transcript_type protein_coding
TPCN2--PPME1 HAVANA mRNA 29521 49337 . + . FI_gene_label "PPME1^ENSG00000214517.10" ; ID "TPCN2--PPME1^ENST00000328257.13" ; Parent "TPCN2--PPME1^PPME1^ENSG00000214517.10" ; ccdsid "CCDS44678.1" ; exon_id "ENSE00002301751.2" ; exon_number 1 ; gene_id "TPCN2--PPME1^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 "TPCN2--PPME1^ENST00000328257.13" ; transcript_name "PPME1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FAF1--AL139081.2 HAVANA gene 31499 33252 . + . FI_gene_label "AL139081.2^ENSG00000286779.1" ; ID "FAF1--AL139081.2^AL139081.2^ENSG00000286779.1" ; exon_id "ENSE00003882665.1" ; exon_number 1 ; gene_id "FAF1--AL139081.2^AL139081.2^ENSG00000286779.1" ; gene_name "AL139081.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000194672.1" ; havana_transcript "OTTHUMT00000520533.1" ; level 2 ; orig_coord_info "chr13,33800138,33800255,+" ; tag basic TAGENE ; transcript_id "FAF1--AL139081.2^ENST00000667510.1" ; transcript_name "AL139081.2-201" ; transcript_type lncRNA
FAF1--AL139081.2 HAVANA RNA 31499 33252 . + . FI_gene_label "AL139081.2^ENSG00000286779.1" ; ID "FAF1--AL139081.2^ENST00000667510.1" ; Parent "FAF1--AL139081.2^AL139081.2^ENSG00000286779.1" ; exon_id "ENSE00003882665.1" ; exon_number 1 ; gene_id "FAF1--AL139081.2^AL139081.2^ENSG00000286779.1" ; gene_name "AL139081.2" ; gene_type lncRNA ; havana_gene "OTTHUMG00000194672.1" ; havana_transcript "OTTHUMT00000520533.1" ; level 2 ; orig_coord_info "chr13,33800138,33800255,+" ; tag basic TAGENE ; transcript_id "FAF1--AL139081.2^ENST00000667510.1" ; transcript_name "AL139081.2-201" ; transcript_type lncRNA
L1 and L2 created:
FAF1--AL139383.1 HAVANA gene 43798 46152 . + . FI_gene_label "AL139383.1^ENSG00000230490.3" ; ID "FAF1--AL139383.1^AL139383.1^ENSG00000230490.3" ; exon_id "ENSE00001757467.1" ; exon_number 1 ; gene_id "FAF1--AL139383.1^AL139383.1^ENSG00000230490.3" ; gene_name "AL139383.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000016714.6" ; havana_transcript "OTTHUMT00000044449.1" ; level 2 ; orig_coord_info "chr13,33524238,33524322,-" ; tag basic ; transcript_id "FAF1--AL139383.1^ENST00000437698.1" ; transcript_name "AL139383.1-202" ; transcript_support_level 3 ; transcript_type lncRNA
FAF1--AL139383.1 HAVANA RNA 43798 46152 . + . FI_gene_label "AL139383.1^ENSG00000230490.3" ; ID "FAF1--AL139383.1^ENST00000437698.1" ; Parent "FAF1--AL139383.1^AL139383.1^ENSG00000230490.3" ; exon_id "ENSE00001757467.1" ; exon_number 1 ; gene_id "FAF1--AL139383.1^AL139383.1^ENSG00000230490.3" ; gene_name "AL139383.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000016714.6" ; havana_transcript "OTTHUMT00000044449.1" ; level 2 ; orig_coord_info "chr13,33524238,33524322,-" ; tag basic ; transcript_id "FAF1--AL139383.1^ENST00000437698.1" ; transcript_name "AL139383.1-202" ; transcript_support_level 3 ; transcript_type lncRNA
87 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 ------------------------------
135 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 8 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