Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/9bad2e9ad323dc63577fa98ef00650/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/ce7b85f55652164fb1539df5d7a60e/fi_workdir/659_b4x-T1-TRNA-1_B23MHV2LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/9bad2e9ad323dc63577fa98ef00650/.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: 3287
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3287
=> 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:3287
=> 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:
ACOT7--CACNA1D HAVANA gene 21983 87811 . + . FI_gene_label "CACNA1D^ENSG00000157388.19" ; ID "ACOT7--CACNA1D^CACNA1D^ENSG00000157388.19" ; ccdsid "CCDS2872.1" ; exon_id "ENSE00001812671.2" ; exon_number 1 ; gene_id "ACOT7--CACNA1D^CACNA1D^ENSG00000157388.19" ; gene_name CACNA1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000158278.13" ; havana_transcript "OTTHUMT00000350555.6" ; hgnc_id "HGNC:1391" ; level 2 ; orig_coord_info "chr3,53495167,53495233,+" ; protein_id "ENSP00000288139.3" ; tag CAGE_supported_TSS basic MANE_Plus_Clinical appris_principal_4 CCDS ; transcript_id "ACOT7--CACNA1D^ENST00000288139.11" ; transcript_name "CACNA1D-201" ; transcript_support_level 1 ; transcript_type protein_coding
ACOT7--CACNA1D HAVANA mRNA 21983 87811 . + . FI_gene_label "CACNA1D^ENSG00000157388.19" ; ID "ACOT7--CACNA1D^ENST00000288139.11" ; Parent "ACOT7--CACNA1D^CACNA1D^ENSG00000157388.19" ; ccdsid "CCDS2872.1" ; exon_id "ENSE00001812671.2" ; exon_number 1 ; gene_id "ACOT7--CACNA1D^CACNA1D^ENSG00000157388.19" ; gene_name CACNA1D ; gene_type protein_coding ; havana_gene "OTTHUMG00000158278.13" ; havana_transcript "OTTHUMT00000350555.6" ; hgnc_id "HGNC:1391" ; level 2 ; orig_coord_info "chr3,53495167,53495233,+" ; protein_id "ENSP00000288139.3" ; tag CAGE_supported_TSS basic MANE_Plus_Clinical appris_principal_4 CCDS ; transcript_id "ACOT7--CACNA1D^ENST00000288139.11" ; transcript_name "CACNA1D-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ACOT7--CACNA1D HAVANA gene 1001 17497 . + . FI_gene_label "ACOT7^ENSG00000097021.20" ; ID "ACOT7--CACNA1D^ACOT7^ENSG00000097021.20" ; ccdsid "CCDS30573.1" ; exon_id "ENSE00001257465.4" ; exon_number 1 ; gene_id "ACOT7--CACNA1D^ACOT7^ENSG00000097021.20" ; gene_name ACOT7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000001295.8" ; havana_transcript "OTTHUMT00000003778.2" ; hgnc_id "HGNC:24157" ; level 2 ; orig_coord_info "chr1,6393257,6393399,-" ; protein_id "ENSP00000354615.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "ACOT7--CACNA1D^ENST00000361521.9" ; transcript_name "ACOT7-201" ; transcript_support_level 1 ; transcript_type protein_coding
ACOT7--CACNA1D HAVANA mRNA 1001 17497 . + . FI_gene_label "ACOT7^ENSG00000097021.20" ; ID "ACOT7--CACNA1D^ENST00000361521.9" ; Parent "ACOT7--CACNA1D^ACOT7^ENSG00000097021.20" ; ccdsid "CCDS30573.1" ; exon_id "ENSE00001257465.4" ; exon_number 1 ; gene_id "ACOT7--CACNA1D^ACOT7^ENSG00000097021.20" ; gene_name ACOT7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000001295.8" ; havana_transcript "OTTHUMT00000003778.2" ; hgnc_id "HGNC:24157" ; level 2 ; orig_coord_info "chr1,6393257,6393399,-" ; protein_id "ENSP00000354615.4" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "ACOT7--CACNA1D^ENST00000361521.9" ; transcript_name "ACOT7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KMT2C--PRKAG2 HAVANA gene 1639 75258 . + . FI_gene_label "KMT2C^ENSG00000055609.20" ; ID "KMT2C--PRKAG2^KMT2C^ENSG00000055609.20" ; ccdsid "CCDS5931.1" ; exon_id "ENSE00003850683.1" ; exon_number 1 ; gene_id "KMT2C--PRKAG2^KMT2C^ENSG00000055609.20" ; gene_name KMT2C ; gene_type protein_coding ; havana_gene "OTTHUMG00000150553.7" ; havana_transcript "OTTHUMT00000318887.4" ; hgnc_id "HGNC:13726" ; level 2 ; orig_coord_info "chr7,152435626,152435786,-" ; protein_id "ENSP00000262189.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "KMT2C--PRKAG2^ENST00000262189.11" ; transcript_name "KMT2C-201" ; transcript_support_level 1 ; transcript_type protein_coding
KMT2C--PRKAG2 HAVANA mRNA 1639 75258 . + . FI_gene_label "KMT2C^ENSG00000055609.20" ; ID "KMT2C--PRKAG2^ENST00000262189.11" ; Parent "KMT2C--PRKAG2^KMT2C^ENSG00000055609.20" ; ccdsid "CCDS5931.1" ; exon_id "ENSE00003850683.1" ; exon_number 1 ; gene_id "KMT2C--PRKAG2^KMT2C^ENSG00000055609.20" ; gene_name KMT2C ; gene_type protein_coding ; havana_gene "OTTHUMG00000150553.7" ; havana_transcript "OTTHUMT00000318887.4" ; hgnc_id "HGNC:13726" ; level 2 ; orig_coord_info "chr7,152435626,152435786,-" ; protein_id "ENSP00000262189.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "KMT2C--PRKAG2^ENST00000262189.11" ; transcript_name "KMT2C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
KMT2C--PRKAG2 HAVANA gene 78272 115673 . + . FI_gene_label "PRKAG2^ENSG00000106617.15" ; ID "KMT2C--PRKAG2^PRKAG2^ENSG00000106617.15" ; ccdsid "CCDS5928.1" ; exon_id "ENSE00003552936.2" ; exon_number 1 ; gene_id "KMT2C--PRKAG2^PRKAG2^ENSG00000106617.15" ; gene_name PRKAG2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157324.26" ; havana_transcript "OTTHUMT00000348440.4" ; hgnc_id "HGNC:9386" ; level 2 ; orig_coord_info "chr7,151876507,151876620,-" ; protein_id "ENSP00000287878.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_4 CCDS ; transcript_id "KMT2C--PRKAG2^ENST00000287878.9" ; transcript_name "PRKAG2-201" ; transcript_support_level 1 ; transcript_type protein_coding
KMT2C--PRKAG2 HAVANA mRNA 78272 115673 . + . FI_gene_label "PRKAG2^ENSG00000106617.15" ; ID "KMT2C--PRKAG2^ENST00000287878.9" ; Parent "KMT2C--PRKAG2^PRKAG2^ENSG00000106617.15" ; ccdsid "CCDS5928.1" ; exon_id "ENSE00003552936.2" ; exon_number 1 ; gene_id "KMT2C--PRKAG2^PRKAG2^ENSG00000106617.15" ; gene_name PRKAG2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157324.26" ; havana_transcript "OTTHUMT00000348440.4" ; hgnc_id "HGNC:9386" ; level 2 ; orig_coord_info "chr7,151876507,151876620,-" ; protein_id "ENSP00000287878.3" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_4 CCDS ; transcript_id "KMT2C--PRKAG2^ENST00000287878.9" ; transcript_name "PRKAG2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SEMA3F--TATDN2 HAVANA gene 1280 14797 . + . FI_gene_label "SEMA3F^ENSG00000001617.12" ; ID "SEMA3F--TATDN2^SEMA3F^ENSG00000001617.12" ; ccdsid "CCDS2811.1" ; exon_id "ENSE00002021109.1" ; exon_number 2 ; gene_id "SEMA3F--TATDN2^SEMA3F^ENSG00000001617.12" ; gene_name SEMA3F ; gene_type protein_coding ; havana_gene "OTTHUMG00000156806.9" ; havana_transcript "OTTHUMT00000345929.2" ; hgnc_id "HGNC:10728" ; level 2 ; orig_coord_info "chr3,50159623,50159734,+" ; protein_id "ENSP00000002829.3" ; tag basic MANE_Select CCDS ; transcript_id "SEMA3F--TATDN2^ENST00000002829.8" ; transcript_name "SEMA3F-201" ; transcript_support_level 1 ; transcript_type protein_coding
SEMA3F--TATDN2 HAVANA mRNA 1280 14797 . + . FI_gene_label "SEMA3F^ENSG00000001617.12" ; ID "SEMA3F--TATDN2^ENST00000002829.8" ; Parent "SEMA3F--TATDN2^SEMA3F^ENSG00000001617.12" ; ccdsid "CCDS2811.1" ; exon_id "ENSE00002021109.1" ; exon_number 2 ; gene_id "SEMA3F--TATDN2^SEMA3F^ENSG00000001617.12" ; gene_name SEMA3F ; gene_type protein_coding ; havana_gene "OTTHUMG00000156806.9" ; havana_transcript "OTTHUMT00000345929.2" ; hgnc_id "HGNC:10728" ; level 2 ; orig_coord_info "chr3,50159623,50159734,+" ; protein_id "ENSP00000002829.3" ; tag basic MANE_Select CCDS ; transcript_id "SEMA3F--TATDN2^ENST00000002829.8" ; transcript_name "SEMA3F-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SEMA3F--TATDN2 HAVANA gene 17798 27874 . + . FI_gene_label "TATDN2^ENSG00000157014.11" ; ID "SEMA3F--TATDN2^TATDN2^ENSG00000157014.11" ; ccdsid "CCDS33698.1" ; exon_id "ENSE00001029764.3" ; exon_number 2 ; gene_id "SEMA3F--TATDN2^TATDN2^ENSG00000157014.11" ; gene_name TATDN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155361.2" ; havana_transcript "OTTHUMT00000339641.1" ; hgnc_id "HGNC:28988" ; level 2 ; orig_coord_info "chr3,10249201,10249614,+" ; protein_id "ENSP00000287652.4" ; tag basic appris_principal_1 CCDS ; transcript_id "SEMA3F--TATDN2^ENST00000287652.8" ; transcript_name "TATDN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
SEMA3F--TATDN2 HAVANA mRNA 17798 27874 . + . FI_gene_label "TATDN2^ENSG00000157014.11" ; ID "SEMA3F--TATDN2^ENST00000287652.8" ; Parent "SEMA3F--TATDN2^TATDN2^ENSG00000157014.11" ; ccdsid "CCDS33698.1" ; exon_id "ENSE00001029764.3" ; exon_number 2 ; gene_id "SEMA3F--TATDN2^TATDN2^ENSG00000157014.11" ; gene_name TATDN2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000155361.2" ; havana_transcript "OTTHUMT00000339641.1" ; hgnc_id "HGNC:28988" ; level 2 ; orig_coord_info "chr3,10249201,10249614,+" ; protein_id "ENSP00000287652.4" ; tag basic appris_principal_1 CCDS ; transcript_id "SEMA3F--TATDN2^ENST00000287652.8" ; transcript_name "TATDN2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SND1--BRAF HAVANA gene 40810 74682 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "SND1--BRAF^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "SND1--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 "SND1--BRAF^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding
SND1--BRAF HAVANA mRNA 40810 74682 . + . FI_gene_label "BRAF^ENSG00000157764.14" ; ID "SND1--BRAF^ENST00000288602.11" ; Parent "SND1--BRAF^BRAF^ENSG00000157764.14" ; exon_id "ENSE00003826734.1" ; exon_number 1 ; gene_id "SND1--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 "SND1--BRAF^ENST00000288602.11" ; transcript_name "BRAF-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SND1--BRAF HAVANA gene 1001 37596 . + . FI_gene_label "SND1^ENSG00000197157.11" ; ID "SND1--BRAF^SND1^ENSG00000197157.11" ; ccdsid "CCDS34747.1" ; exon_id "ENSE00001903029.2" ; exon_number 1 ; gene_id "SND1--BRAF^SND1^ENSG00000197157.11" ; gene_name SND1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157560.3" ; havana_transcript "OTTHUMT00000349148.2" ; hgnc_id "HGNC:30646" ; level 2 ; orig_coord_info "chr7,127652374,127652451,+" ; protein_id "ENSP00000346762.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SND1--BRAF^ENST00000354725.8" ; transcript_name "SND1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SND1--BRAF HAVANA mRNA 1001 37596 . + . FI_gene_label "SND1^ENSG00000197157.11" ; ID "SND1--BRAF^ENST00000354725.8" ; Parent "SND1--BRAF^SND1^ENSG00000197157.11" ; ccdsid "CCDS34747.1" ; exon_id "ENSE00001903029.2" ; exon_number 1 ; gene_id "SND1--BRAF^SND1^ENSG00000197157.11" ; gene_name SND1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157560.3" ; havana_transcript "OTTHUMT00000349148.2" ; hgnc_id "HGNC:30646" ; level 2 ; orig_coord_info "chr7,127652374,127652451,+" ; protein_id "ENSP00000346762.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SND1--BRAF^ENST00000354725.8" ; transcript_name "SND1-201" ; transcript_support_level 1 ; transcript_type protein_coding
153 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 ------------------------------
283 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 1 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 1 second) ------
GFF3 file parsed