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: 1449
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1449
=> 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:1449
=> 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:
CLIP2--GTF2I HAVANA gene 1001 24520 . + . FI_gene_label "CLIP2^ENSG00000106665.16" ; ID "CLIP2--GTF2I^CLIP2^ENSG00000106665.16" ; ccdsid "CCDS5569.1" ; exon_id "ENSE00001128453.3" ; exon_number 2 ; gene_id "CLIP2--GTF2I^CLIP2^ENSG00000106665.16" ; gene_name CLIP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022980.5" ; havana_transcript "OTTHUMT00000252556.3" ; hgnc_id "HGNC:2586" ; level 2 ; orig_coord_info "chr7,74317547,74317667,+" ; protein_id "ENSP00000223398.6" ; tag RNA_Seq_supported_partial basic MANE_Select appris_principal_3 CCDS ; transcript_id "CLIP2--GTF2I^ENST00000223398.11" ; transcript_name "CLIP2-201" ; transcript_support_level 5 ; transcript_type protein_coding
CLIP2--GTF2I HAVANA mRNA 1001 24520 . + . FI_gene_label "CLIP2^ENSG00000106665.16" ; ID "CLIP2--GTF2I^ENST00000223398.11" ; Parent "CLIP2--GTF2I^CLIP2^ENSG00000106665.16" ; ccdsid "CCDS5569.1" ; exon_id "ENSE00001128453.3" ; exon_number 2 ; gene_id "CLIP2--GTF2I^CLIP2^ENSG00000106665.16" ; gene_name CLIP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000022980.5" ; havana_transcript "OTTHUMT00000252556.3" ; hgnc_id "HGNC:2586" ; level 2 ; orig_coord_info "chr7,74317547,74317667,+" ; protein_id "ENSP00000223398.6" ; tag RNA_Seq_supported_partial basic MANE_Select appris_principal_3 CCDS ; transcript_id "CLIP2--GTF2I^ENST00000223398.11" ; transcript_name "CLIP2-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
CLIP2--GTF2I HAVANA gene 31184 34755 . + . FI_gene_label "GTF2I^ENSG00000263001.7" ; ID "CLIP2--GTF2I^GTF2I^ENSG00000263001.7" ; exon_id "ENSE00003732947.1" ; exon_number 2 ; gene_id "CLIP2--GTF2I^GTF2I^ENSG00000263001.7" ; gene_name GTF2I ; gene_type protein_coding ; havana_gene "OTTHUMG00000156237.8" ; havana_transcript "OTTHUMT00000343534.2" ; hgnc_id "HGNC:4659" ; level 2 ; orig_coord_info "chr7,74689129,74689227,+" ; protein_id "ENSP00000405022.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "CLIP2--GTF2I^ENST00000432143.2" ; transcript_name "GTF2I-201" ; transcript_support_level 4 ; transcript_type protein_coding
CLIP2--GTF2I HAVANA mRNA 31184 34755 . + . FI_gene_label "GTF2I^ENSG00000263001.7" ; ID "CLIP2--GTF2I^ENST00000432143.2" ; Parent "CLIP2--GTF2I^GTF2I^ENSG00000263001.7" ; exon_id "ENSE00003732947.1" ; exon_number 2 ; gene_id "CLIP2--GTF2I^GTF2I^ENSG00000263001.7" ; gene_name GTF2I ; gene_type protein_coding ; havana_gene "OTTHUMG00000156237.8" ; havana_transcript "OTTHUMT00000343534.2" ; hgnc_id "HGNC:4659" ; level 2 ; orig_coord_info "chr7,74689129,74689227,+" ; protein_id "ENSP00000405022.1" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "CLIP2--GTF2I^ENST00000432143.2" ; transcript_name "GTF2I-201" ; transcript_support_level 4 ; transcript_type protein_coding
L1 and L2 created:
CTBP2--FAM53B HAVANA gene 31381 38491 . + . FI_gene_label "FAM53B^ENSG00000189319.14" ; ID "CTBP2--FAM53B^FAM53B^ENSG00000189319.14" ; exon_id "ENSE00003607391.1" ; exon_number 2 ; gene_id "CTBP2--FAM53B^FAM53B^ENSG00000189319.14" ; gene_name FAM53B ; gene_type protein_coding ; havana_gene "OTTHUMG00000019215.3" ; havana_transcript "OTTHUMT00000050881.1" ; hgnc_id "HGNC:28968" ; level 1 ; orig_coord_info "chr10,124706636,124706713,-" ; protein_id "ENSP00000280780.6" ; tag basic appris_alternative_2 exp_conf ; transcript_id "CTBP2--FAM53B^ENST00000280780.6" ; transcript_name "FAM53B-201" ; transcript_support_level 1 ; transcript_type protein_coding
CTBP2--FAM53B HAVANA mRNA 31381 38491 . + . FI_gene_label "FAM53B^ENSG00000189319.14" ; ID "CTBP2--FAM53B^ENST00000280780.6" ; Parent "CTBP2--FAM53B^FAM53B^ENSG00000189319.14" ; exon_id "ENSE00003607391.1" ; exon_number 2 ; gene_id "CTBP2--FAM53B^FAM53B^ENSG00000189319.14" ; gene_name FAM53B ; gene_type protein_coding ; havana_gene "OTTHUMG00000019215.3" ; havana_transcript "OTTHUMT00000050881.1" ; hgnc_id "HGNC:28968" ; level 1 ; orig_coord_info "chr10,124706636,124706713,-" ; protein_id "ENSP00000280780.6" ; tag basic appris_alternative_2 exp_conf ; transcript_id "CTBP2--FAM53B^ENST00000280780.6" ; transcript_name "FAM53B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CTBP2--FAM53B HAVANA gene 12532 28271 . + . FI_gene_label "CTBP2^ENSG00000175029.17" ; ID "CTBP2--FAM53B^CTBP2^ENSG00000175029.17" ; ccdsid "CCDS7644.1" ; exon_id "ENSE00001191639.9" ; exon_number 1 ; gene_id "CTBP2--FAM53B^CTBP2^ENSG00000175029.17" ; gene_name CTBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019224.9" ; havana_transcript "OTTHUMT00000050905.2" ; hgnc_id "HGNC:2495" ; level 2 ; orig_coord_info "chr10,125026082,125027759,-" ; protein_id "ENSP00000311825.6" ; tag basic MANE_Select CCDS ; transcript_id "CTBP2--FAM53B^ENST00000309035.11" ; transcript_name "CTBP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CTBP2--FAM53B HAVANA mRNA 12532 28271 . + . FI_gene_label "CTBP2^ENSG00000175029.17" ; ID "CTBP2--FAM53B^ENST00000309035.11" ; Parent "CTBP2--FAM53B^CTBP2^ENSG00000175029.17" ; ccdsid "CCDS7644.1" ; exon_id "ENSE00001191639.9" ; exon_number 1 ; gene_id "CTBP2--FAM53B^CTBP2^ENSG00000175029.17" ; gene_name CTBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019224.9" ; havana_transcript "OTTHUMT00000050905.2" ; hgnc_id "HGNC:2495" ; level 2 ; orig_coord_info "chr10,125026082,125027759,-" ; protein_id "ENSP00000311825.6" ; tag basic MANE_Select CCDS ; transcript_id "CTBP2--FAM53B^ENST00000309035.11" ; transcript_name "CTBP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PLEKHG1--MTHFD1L HAVANA gene 11157 31558 . + . FI_gene_label "PLEKHG1^ENSG00000120278.16" ; ID "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16" ; ccdsid "CCDS34552.1" ; exon_id "ENSE00001444243.1" ; exon_number 2 ; gene_id "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16" ; gene_name PLEKHG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015824.7" ; havana_transcript "OTTHUMT00000042691.3" ; hgnc_id "HGNC:20884" ; level 2 ; orig_coord_info "chr6,150733682,150734092,+" ; protein_id "ENSP00000351318.2" ; tag basic appris_principal_1 CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000358517.6" ; transcript_name "PLEKHG1-201" ; transcript_support_level 5 ; transcript_type protein_coding
PLEKHG1--MTHFD1L HAVANA mRNA 11157 31558 . + . FI_gene_label "PLEKHG1^ENSG00000120278.16" ; ID "PLEKHG1--MTHFD1L^ENST00000358517.6" ; Parent "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16" ; ccdsid "CCDS34552.1" ; exon_id "ENSE00001444243.1" ; exon_number 2 ; gene_id "PLEKHG1--MTHFD1L^PLEKHG1^ENSG00000120278.16" ; gene_name PLEKHG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015824.7" ; havana_transcript "OTTHUMT00000042691.3" ; hgnc_id "HGNC:20884" ; level 2 ; orig_coord_info "chr6,150733682,150734092,+" ; protein_id "ENSP00000351318.2" ; tag basic appris_principal_1 CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000358517.6" ; transcript_name "PLEKHG1-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
PLEKHG1--MTHFD1L HAVANA gene 34596 42321 . + . FI_gene_label "MTHFD1L^ENSG00000120254.16" ; ID "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16" ; ccdsid "CCDS56457.1" ; exon_id "ENSE00003713432.1" ; exon_number 1 ; gene_id "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16" ; gene_name MTHFD1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000015828.4" ; havana_transcript "OTTHUMT00000474291.1" ; hgnc_id "HGNC:21055" ; level 2 ; orig_coord_info "chr6,150865823,150866049,+" ; protein_id "ENSP00000356276.4" ; tag basic CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000367307.8" ; transcript_name "MTHFD1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
PLEKHG1--MTHFD1L HAVANA mRNA 34596 42321 . + . FI_gene_label "MTHFD1L^ENSG00000120254.16" ; ID "PLEKHG1--MTHFD1L^ENST00000367307.8" ; Parent "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16" ; ccdsid "CCDS56457.1" ; exon_id "ENSE00003713432.1" ; exon_number 1 ; gene_id "PLEKHG1--MTHFD1L^MTHFD1L^ENSG00000120254.16" ; gene_name MTHFD1L ; gene_type protein_coding ; havana_gene "OTTHUMG00000015828.4" ; havana_transcript "OTTHUMT00000474291.1" ; hgnc_id "HGNC:21055" ; level 2 ; orig_coord_info "chr6,150865823,150866049,+" ; protein_id "ENSP00000356276.4" ; tag basic CCDS ; transcript_id "PLEKHG1--MTHFD1L^ENST00000367307.8" ; transcript_name "MTHFD1L-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TCF25--TUBB3 HAVANA gene 1023 25151 . + . FI_gene_label "TCF25^ENSG00000141002.20" ; ID "TCF25--TUBB3^TCF25^ENSG00000141002.20" ; ccdsid "CCDS10987.1" ; exon_id "ENSE00002624794.2" ; exon_number 1 ; gene_id "TCF25--TUBB3^TCF25^ENSG00000141002.20" ; gene_name TCF25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000138986.6" ; havana_transcript "OTTHUMT00000272875.4" ; hgnc_id "HGNC:29181" ; level 2 ; orig_coord_info "chr16,89873668,89873859,+" ; protein_id "ENSP00000263346.8" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TCF25--TUBB3^ENST00000263346.13" ; transcript_name "TCF25-201" ; transcript_support_level 1 ; transcript_type protein_coding
TCF25--TUBB3 HAVANA mRNA 1023 25151 . + . FI_gene_label "TCF25^ENSG00000141002.20" ; ID "TCF25--TUBB3^ENST00000263346.13" ; Parent "TCF25--TUBB3^TCF25^ENSG00000141002.20" ; ccdsid "CCDS10987.1" ; exon_id "ENSE00002624794.2" ; exon_number 1 ; gene_id "TCF25--TUBB3^TCF25^ENSG00000141002.20" ; gene_name TCF25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000138986.6" ; havana_transcript "OTTHUMT00000272875.4" ; hgnc_id "HGNC:29181" ; level 2 ; orig_coord_info "chr16,89873668,89873859,+" ; protein_id "ENSP00000263346.8" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "TCF25--TUBB3^ENST00000263346.13" ; transcript_name "TCF25-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TCF25--TUBB3 HAVANA gene 32148 40269 . + . FI_gene_label "TUBB3^ENSG00000258947.8" ; ID "TCF25--TUBB3^TUBB3^ENSG00000258947.8" ; ccdsid "CCDS10988.1" ; exon_id "ENSE00002473274.1" ; exon_number 1 ; gene_id "TCF25--TUBB3^TUBB3^ENSG00000258947.8" ; gene_name TUBB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000138985.4" ; havana_transcript "OTTHUMT00000272874.2" ; hgnc_id "HGNC:20772" ; level 2 ; orig_coord_info "chr16,89923402,89923458,+" ; protein_id "ENSP00000320295.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TCF25--TUBB3^ENST00000315491.12" ; transcript_name "TUBB3-201" ; transcript_support_level 1 ; transcript_type protein_coding
TCF25--TUBB3 HAVANA mRNA 32148 40269 . + . FI_gene_label "TUBB3^ENSG00000258947.8" ; ID "TCF25--TUBB3^ENST00000315491.12" ; Parent "TCF25--TUBB3^TUBB3^ENSG00000258947.8" ; ccdsid "CCDS10988.1" ; exon_id "ENSE00002473274.1" ; exon_number 1 ; gene_id "TCF25--TUBB3^TUBB3^ENSG00000258947.8" ; gene_name TUBB3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000138985.4" ; havana_transcript "OTTHUMT00000272874.2" ; hgnc_id "HGNC:20772" ; level 2 ; orig_coord_info "chr16,89923402,89923458,+" ; protein_id "ENSP00000320295.7" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TCF25--TUBB3^ENST00000315491.12" ; transcript_name "TUBB3-201" ; transcript_support_level 1 ; transcript_type protein_coding
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
113 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 ------------------------------
177 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 7 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
Lets remove isoform PLEKHG1--MTHFD1L^ENST00000643692.1
1 identical isoforms removed
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 0 second) ------
GFF3 file parsed