[root@7f6d1fb335c2 10:35:58 /work/desaturase/01.data_prepare]# genome=Homo_sapiens.GRCh38.dna.toplevel.fa.gz
[root@7f6d1fb335c2 10:36:17 /work/desaturase/01.data_prepare]# gff=Homo_sapiens.GRCh38.112.chr.gff3.gz
[root@7f6d1fb335c2 10:36:31 /work/desaturase/01.data_prepare]# species=Homo_sapiens
[root@7f6d1fb335c2 10:36:39 /work/desaturase/01.data_prepare]# agat_sp_filter_feature_by_attribute_value.pl --gff $gff --attribute biotype --value protein_coding -t '!' -o $species.protein_coding.gff3
Using standard /share/work/biosoft/perl/perl-5.22.1/lib/site_perl/5.22.1/auto/share/dist/AGAT/config.yaml file
08/01/2024 at 10h36m50s
usage: /share/work/biosoft/perl/latest/bin/agat_sp_filter_feature_by_attribute_value.pl --gff Homo_sapiens.GRCh38.112.chr.gff3.gz --attribute biotype --value protein_coding -t ! -o Homo_sapiens.protein_coding.gff3
We will discard all features that have the attribute biotype with the value ne protein_coding.
********************************************************************************
* - Start parsing - *
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-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /share/work/biosoft/perl/perl-5.22.1/lib/site_perl/5.22.1/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 v5.22.1
Bioperl location being used: /share/work/biosoft/perl/perl-5.22.1/lib/site_perl/5.22.1/Bio/
Operating system being used: linux
=> Accessing Ontology
No ontology accessible from the gff file header!
We use the SOFA ontology distributed with AGAT:
/share/work/biosoft/perl/perl-5.22.1/lib/site_perl/5.22.1/auto/share/dist/AGAT/so.obo
Read ontology /share/work/biosoft/perl/perl-5.22.1/lib/site_perl/5.22.1/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: 3516552
=> Number of comment lines: 63142
=> Fasta included: No
=> Number of features lines: 3453410
=> Number of feature type (3rd column): 25
* Level1: 5 => gene chromosome biological_region pseudogene ncRNA_gene
* level2: 16 => rRNA pseudogenic_transcript D_gene_segment J_gene_segment mRNA snoRNA lnc_RNA unconfirmed_transcript transcript scRNA tRNA miRNA processed_transcript C_gene_segment V_gene_segment snRNA
* level3: 4 => CDS three_prime_UTR exon five_prime_UTR
* unknown: 0 =>
=> Version of the Bioperl GFF parser selected by AGAT: 3
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10469 11240 1.3e+03 .. external_name "oe = 0.79" ; logic_name cpg
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10650 10657 0.999 +. logic_name eponine
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10655 10657 0.999 -. logic_name eponine
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10678 10687 0.999 +. logic_name eponine
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10681 10688 0.999 -. logic_name eponine
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10707 10716 0.999 +. logic_name eponine
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10708 10718 0.999 -. logic_name eponine
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10735 10747 0.999 -. logic_name eponine
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10737 10744 0.999 +. logic_name eponine
gff3 reader error level1: No ID attribute found @ for the feature: 1 . biological_region 10766 10773 0.999 +. logic_name eponine
gff3 reader error level1: No ID attribute found ************** Too much WARNING message we skip the next **************
