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: 3158
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3158
=> 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:3158
=> 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:
AGAP3--BRAF HAVANA gene 30511 64383 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6" ; havana_transcript "OTTHUMT00000496651.1" ; hgnc_id "HGNC:1097" ; level 2 ; orig_coord_info "chr7,140924566,140924703,-" ; protein_id "ENSP00000288602.7" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AGAP3--BRAF^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding
AGAP3--BRAF HAVANA mRNA 30511 64383 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "AGAP3--BRAF^ENST00000288602.11" ; Parent "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "AGAP3--BRAF^BRAF^ENSG00000157764.14" ; gene_name BRAF ; gene_type protein_coding ; havana_gene "OTTHUMG00000157457.6" ; havana_transcript "OTTHUMT00000496651.1" ; hgnc_id "HGNC:1097" ; level 2 ; orig_coord_info "chr7,140924566,140924703,-" ; protein_id "ENSP00000288602.7" ; tag not_organism_supported basic appris_alternative_2 ; transcript_id "AGAP3--BRAF^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AGAP3--BRAF HAVANA gene 6272 14541 . + . FI_gene_label "AGAP3^ENSG00000133612.19" ; ID "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; ccdsid "CCDS78287.1" ; exon_id "ENSE00001339499.3" ; exon_number 1 ; gene_id "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8" ; havana_transcript "OTTHUMT00000351912.1" ; hgnc_id "HGNC:16923" ; level 2 ; orig_coord_info "chr7,151114771,151115641,+" ; protein_id "ENSP00000335589.3" ; tag basic CCDS ; transcript_id "AGAP3--BRAF^ENST00000335367.7" ; transcript_name "AGAP3-201" ; transcript_support_level 1 ; transcript_type protein_coding
AGAP3--BRAF HAVANA mRNA 6272 14541 . + . FI_gene_label "AGAP3^ENSG00000133612.19" ; ID "AGAP3--BRAF^ENST00000335367.7" ; Parent "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; ccdsid "CCDS78287.1" ; exon_id "ENSE00001339499.3" ; exon_number 1 ; gene_id "AGAP3--BRAF^AGAP3^ENSG00000133612.19" ; gene_name AGAP3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000158724.8" ; havana_transcript "OTTHUMT00000351912.1" ; hgnc_id "HGNC:16923" ; level 2 ; orig_coord_info "chr7,151114771,151115641,+" ; protein_id "ENSP00000335589.3" ; tag basic CCDS ; transcript_id "AGAP3--BRAF^ENST00000335367.7" ; transcript_name "AGAP3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ME1--DOP1A ENSEMBL gene 20339 60306 . + . FI_gene_label "DOP1A^ENSG00000083097.14" ; ID "ME1--DOP1A^DOP1A^ENSG00000083097.14" ; ccdsid "CCDS64467.1" ; exon_id "ENSE00001450762.1" ; exon_number 3 ; gene_id "ME1--DOP1A^DOP1A^ENSG00000083097.14" ; gene_name DOP1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000016365.4" ; hgnc_id "HGNC:21194" ; level 3 ; orig_coord_info "chr6,83096978,83097115,+" ; protein_id "ENSP00000237163.6" ; tag basic appris_principal_4 CCDS ; transcript_id "ME1--DOP1A^ENST00000237163.9" ; transcript_name "DOP1A-201" ; transcript_support_level 5 ; transcript_type protein_coding
ME1--DOP1A ENSEMBL mRNA 20339 60306 . + . FI_gene_label "DOP1A^ENSG00000083097.14" ; ID "ME1--DOP1A^ENST00000237163.9" ; Parent "ME1--DOP1A^DOP1A^ENSG00000083097.14" ; ccdsid "CCDS64467.1" ; exon_id "ENSE00001450762.1" ; exon_number 3 ; gene_id "ME1--DOP1A^DOP1A^ENSG00000083097.14" ; gene_name DOP1A ; gene_type protein_coding ; havana_gene "OTTHUMG00000016365.4" ; hgnc_id "HGNC:21194" ; level 3 ; orig_coord_info "chr6,83096978,83097115,+" ; protein_id "ENSP00000237163.6" ; tag basic appris_principal_4 CCDS ; transcript_id "ME1--DOP1A^ENST00000237163.9" ; transcript_name "DOP1A-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
ME1--DOP1A HAVANA gene 1001 17338 . + . FI_gene_label "ME1^ENSG00000065833.9" ; ID "ME1--DOP1A^ME1^ENSG00000065833.9" ; ccdsid "CCDS34492.1" ; exon_id "ENSE00000760044.5" ; exon_number 1 ; gene_id "ME1--DOP1A^ME1^ENSG00000065833.9" ; gene_name ME1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015111.3" ; havana_transcript "OTTHUMT00000041350.3" ; hgnc_id "HGNC:6983" ; level 2 ; orig_coord_info "chr6,83430877,83430954,-" ; protein_id "ENSP00000358719.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ME1--DOP1A^ENST00000369705.4" ; transcript_name "ME1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ME1--DOP1A HAVANA mRNA 1001 17338 . + . FI_gene_label "ME1^ENSG00000065833.9" ; ID "ME1--DOP1A^ENST00000369705.4" ; Parent "ME1--DOP1A^ME1^ENSG00000065833.9" ; ccdsid "CCDS34492.1" ; exon_id "ENSE00000760044.5" ; exon_number 1 ; gene_id "ME1--DOP1A^ME1^ENSG00000065833.9" ; gene_name ME1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015111.3" ; havana_transcript "OTTHUMT00000041350.3" ; hgnc_id "HGNC:6983" ; level 2 ; orig_coord_info "chr6,83430877,83430954,-" ; protein_id "ENSP00000358719.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ME1--DOP1A^ENST00000369705.4" ; transcript_name "ME1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SYNE2--MTHFD1 HAVANA gene 2580 12840 . + . FI_gene_label "SYNE2^ENSG00000054654.19" ; ID "SYNE2--MTHFD1^SYNE2^ENSG00000054654.19" ; exon_id "ENSE00003737812.1" ; exon_number 2 ; gene_id "SYNE2--MTHFD1^SYNE2^ENSG00000054654.19" ; gene_name SYNE2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140349.6" ; havana_transcript "OTTHUMT00000411904.2" ; hgnc_id "HGNC:17084" ; level 1 ; orig_coord_info "chr14,63909149,63909227,+" ; protein_id "ENSP00000344528.5" ; tag basic exp_conf ; transcript_id "SYNE2--MTHFD1^ENST00000341472.9" ; transcript_name "SYNE2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SYNE2--MTHFD1 HAVANA mRNA 2580 12840 . + . FI_gene_label "SYNE2^ENSG00000054654.19" ; ID "SYNE2--MTHFD1^ENST00000341472.9" ; Parent "SYNE2--MTHFD1^SYNE2^ENSG00000054654.19" ; exon_id "ENSE00003737812.1" ; exon_number 2 ; gene_id "SYNE2--MTHFD1^SYNE2^ENSG00000054654.19" ; gene_name SYNE2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000140349.6" ; havana_transcript "OTTHUMT00000411904.2" ; hgnc_id "HGNC:17084" ; level 1 ; orig_coord_info "chr14,63909149,63909227,+" ; protein_id "ENSP00000344528.5" ; tag basic exp_conf ; transcript_id "SYNE2--MTHFD1^ENST00000341472.9" ; transcript_name "SYNE2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SYNE2--MTHFD1 HAVANA gene 141022 177439 . + . FI_gene_label "MTHFD1^ENSG00000100714.17" ; ID "SYNE2--MTHFD1^MTHFD1^ENSG00000100714.17" ; exon_id "ENSE00002279035.1" ; exon_number 1 ; gene_id "SYNE2--MTHFD1^MTHFD1^ENSG00000100714.17" ; gene_name MTHFD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000141309.15" ; havana_transcript "OTTHUMT00000412167.3" ; hgnc_id "HGNC:7432" ; level 1 ; orig_coord_info "chr14,64388428,64388468,+" ; protein_id "ENSP00000438588.2" ; tag upstream_ATG 3_standard_supported_extension basic exp_conf ; transcript_id "SYNE2--MTHFD1^ENST00000545908.6" ; transcript_name "MTHFD1-201" ; transcript_support_level 2 ; transcript_type protein_coding
SYNE2--MTHFD1 HAVANA mRNA 141022 177439 . + . FI_gene_label "MTHFD1^ENSG00000100714.17" ; ID "SYNE2--MTHFD1^ENST00000545908.6" ; Parent "SYNE2--MTHFD1^MTHFD1^ENSG00000100714.17" ; exon_id "ENSE00002279035.1" ; exon_number 1 ; gene_id "SYNE2--MTHFD1^MTHFD1^ENSG00000100714.17" ; gene_name MTHFD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000141309.15" ; havana_transcript "OTTHUMT00000412167.3" ; hgnc_id "HGNC:7432" ; level 1 ; orig_coord_info "chr14,64388428,64388468,+" ; protein_id "ENSP00000438588.2" ; tag upstream_ATG 3_standard_supported_extension basic exp_conf ; transcript_id "SYNE2--MTHFD1^ENST00000545908.6" ; transcript_name "MTHFD1-201" ; transcript_support_level 2 ; 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
121 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 ------------------------------
269 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 6 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