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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
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Access file within container - docker - agat_convert_sp_gxf2gxf.pl GFF file doesn't exist when it does? #321

Closed Floyd1229 closed 1 year ago

Floyd1229 commented 1 year ago

Hello,

I'm trying to convert my GFF file to a GTF file using agat_convert_sp_gxf2gxf.pl. When running my command, I'm getting the following error:

**myname@company.vm**:~$ docker run quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0 agat_convert_sp_gxf2gxf.pl --gff test_file.gff --output test_file.gtf
_Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/config.yaml file_
********************************************************************************
*                              - 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 ---------------------------------
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!test_file.gff does not exist. Please verify the input fi!
!                                 le name/path                                 !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!_

My GFF file absolutely exists and has the GFF header as the 1st line:

**myname@company.vm**:~$ head -n 10 test_file.gff
_##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build GRCm39
#!genome-build-accession NCBI_Assembly:GCF_000001635.27
#!annotation-source NCBI Mus musculus Annotation Release 109
##sequence-region NC_000067.7 1 195154279
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090
NC_000067.7 RefSeq  region  1   195154279   .   +   .   ID=NC_000067.7:1..195154279;Dbxref=taxon:10090;Name=1;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=C57BL/6J
NC_000067.7 cmsearch    gene    3172239 3172348 .   +   .   ID=gene-Gm26206;Dbxref=GeneID:115487594,MGI:MGI:5455983;Name=Gm26206;gbkey=Gene;gene=Gm26206;gene_biotype=snRNA_

It seems as if agat_convert_sp_gxf2gxf.pl can't find my perl? Here's where my perl is located and the files within the directory:

myname@company.vm:/usr/local/lib/x86_64-linux-gnu/perl/5.26.1$ ls _Bundle DBD DBI DBI.pm List Math Win32 auto dbixsrev.pl perllocal.pod

Any help would be appreciated: thank you.

General Info

Juke34 commented 1 year ago

Thank you for using AGAT. Using containers work slightly differently. When using docker you must load/mount the data within the container, otherwise it is not accessible.

You can do something like that:

docker run -v ${PWD}:/agat quay.io/biocontainers/agat:0.8.0--pl5262hdfd78af_0 agat_convert_sp_gxf2gxf.pl --gff /agat/path/to/my/folder/test.gff -o /agat/test.gtf
Juke34 commented 1 year ago

I hope you found your way.