Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/48e1a8acd66a786443a118575cbf70/fi_workdir/tih_rna_sample_00575_B23MVV7LT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/dae028ae9805ce55e56b769a05fd6c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/dae028ae9805ce55e56b769a05fd6c/.command.run ==> STAGING COMPLETE (3 inputs) 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: 175 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 175 => 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:175 => 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: TRIM33--VTCN1 ENSEMBL gene 30623 40648 . + . FI_gene_label "VTCN1^ENSG00000134258.17" ; ID "TRIM33--VTCN1^VTCN1^ENSG00000134258.17" ; ccdsid "CCDS58020.1" ; exon_id "ENSE00003733740.1" ; exon_number 1 ; gene_id "TRIM33--VTCN1^VTCN1^ENSG00000134258.17" ; gene_name VTCN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012118.4" ; hgnc_id "HGNC:28873" ; level 3 ; orig_coord_info "chr1,117210824,117210855,-" ; protein_id "ENSP00000328168.3" ; tag basic CCDS ; transcript_id "TRIM33--VTCN1^ENST00000328189.7" ; transcript_name "VTCN1-201" ; transcript_support_level 5 ; transcript_type protein_coding TRIM33--VTCN1 ENSEMBL mRNA 30623 40648 . + . FI_gene_label "VTCN1^ENSG00000134258.17" ; ID "TRIM33--VTCN1^ENST00000328189.7" ; Parent "TRIM33--VTCN1^VTCN1^ENSG00000134258.17" ; ccdsid "CCDS58020.1" ; exon_id "ENSE00003733740.1" ; exon_number 1 ; gene_id "TRIM33--VTCN1^VTCN1^ENSG00000134258.17" ; gene_name VTCN1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000012118.4" ; hgnc_id "HGNC:28873" ; level 3 ; orig_coord_info "chr1,117210824,117210855,-" ; protein_id "ENSP00000328168.3" ; tag basic CCDS ; transcript_id "TRIM33--VTCN1^ENST00000328189.7" ; transcript_name "VTCN1-201" ; transcript_support_level 5 ; transcript_type protein_coding L1 and L2 created: TRIM33--VTCN1 HAVANA gene 1001 27622 . + . FI_gene_label "TRIM33^ENSG00000197323.12" ; ID "TRIM33--VTCN1^TRIM33^ENSG00000197323.12" ; ccdsid "CCDS872.1" ; exon_id "ENSE00003846759.1" ; exon_number 1 ; gene_id "TRIM33--VTCN1^TRIM33^ENSG00000197323.12" ; gene_name TRIM33 ; gene_type protein_coding ; havana_gene "OTTHUMG00000011891.3" ; havana_transcript "OTTHUMT00000032854.2" ; hgnc_id "HGNC:16290" ; level 2 ; orig_coord_info "chr1,114510551,114511076,-" ; protein_id "ENSP00000351250.2" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "TRIM33--VTCN1^ENST00000358465.7" ; transcript_name "TRIM33-201" ; transcript_support_level 1 ; transcript_type protein_coding TRIM33--VTCN1 HAVANA mRNA 1001 27622 . + . FI_gene_label "TRIM33^ENSG00000197323.12" ; ID "TRIM33--VTCN1^ENST00000358465.7" ; Parent "TRIM33--VTCN1^TRIM33^ENSG00000197323.12" ; ccdsid "CCDS872.1" ; exon_id "ENSE00003846759.1" ; exon_number 1 ; gene_id "TRIM33--VTCN1^TRIM33^ENSG00000197323.12" ; gene_name TRIM33 ; gene_type protein_coding ; havana_gene "OTTHUMG00000011891.3" ; havana_transcript "OTTHUMT00000032854.2" ; hgnc_id "HGNC:16290" ; level 2 ; orig_coord_info "chr1,114510551,114511076,-" ; protein_id "ENSP00000351250.2" ; tag basic MANE_Select appris_alternative_2 CCDS ; transcript_id "TRIM33--VTCN1^ENST00000358465.7" ; transcript_name "TRIM33-201" ; transcript_support_level 1 ; transcript_type protein_coding 13 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 ------------------------------ 21 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 1 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