container problem - cannot open file

[shhayat]

Hello,

I am using docker image to run agat_convert_sp_gxf2gxf.pl and I get following error message.

Info: Cannot count total line number with builtin wc. Consequently progress bar unavailable. cannot open file /path/to/my/folder/test.gffDied at /usr/local/lib/site_perl/5.26.2/AGAT/OmniscientI.pm line 3243.

I used following command to run the script docker run quay.io/biocontainers/agat:0.8.0--pl5262hdfd78af_0 agat_convert_sp_gxf2gxf.pl --gff /path/to/my/folder/test.gff -o test.gtf

I also added file path to docker under Preferences/Resources/File Sharing but the file is still not accessible. I could not figure out the issue.

[Juke34]

can you use agat:0.9.1 successfully?

[shhayat]

I used agat:0.9.1 and I am getting same error.

--------------------------------- parsing file --------------------------------- !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! test.gff does not exist. Please verify the input file name/path ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

[Juke34]

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

[shhayat]

Thanks for your suggestion.

I managed to load the data and used function agat_convert_sp_gtf2gff.pl with agat:0.9.1. But after parsing 59% of the file the command crashes.

The warning messages which I get are as following

WARNING l2 and l1 features not on same seq_id @ nbis-srp_rna-2 level2 feature is on 10 sequence while gene-RN7SL1 level1 feature is on 1
WARNING l2 and l1 features not on same seq_id @ nbis-srp_rna-3 level2 feature is on 10 sequence while gene-RN7SL1 level1 feature is on 1
WARNING l2 and l1 features not on same seq_id @ nbis-srp_rna-4 level2 feature is on 10 sequence while gene-RN7SL1 level1 feature is on 1
WARNING l2 and l1 features not on same seq_id @ nbis-trna-2 level2 feature is on 10 sequence while gene-TRNAC-ACA-29 level1 feature is on 1
WARNING l2 and l1 features not on same seq_id @ nbis-snrna-1 level2 feature is on 12 sequence while gene-LOC112448637 level1 feature is on 10
WARNING l2 and l1 features not on same seq_id @ nbis-snorna-1 level2 feature is on 12 sequence while gene-LOC112449172 level1 feature is on 11
WARNING l2 and l1 features not on same seq_id @ nbis-trna-3 level2 feature is on 12 sequence while gene-TRNAC-ACA-29 level1 feature is on 1
WARNING l2 and l1 features not on same seq_id @ nbis-mrna-48 level2 feature is on 12 sequence while gene-LOC525863 level1 feature is on 1
WARNING l2 and l1 features not on same seq_id @ nbis-mrna-54 level2 feature is on 13 sequence while gene-LOC525863 level1 feature is on 1
WARNING l2 and l1 features not on same seq_id @ nbis-mrna-55 level2 feature is on 13 sequence while gene-LOC100848353 level1 feature is on 12
WARNING l2 and l1 features not on same seq_id  ************** Too much WARNING message we skip the next **************

[Juke34]

These are just warning but it shows that you have a poorly formated files. Indeed chuncks of a single feature is spread over several sequences. That often arise with results from liftover tools.

But for the crash it is probably not related. I guess the memory needed to handle this file is larger than what is provided. Check the image or/and the machine to verify the memory available and the memory used by AGAT while running.

[Juke34]

Please feel free to re-open the issue if you still need help for this issue.

[claumer]

Hi there,

I'm trying to use agat within a docker container in a similar way as explained in this issue, but the suggested -v flag you've offered doesn't seem to be helping:

sudo docker run -v ${PWD}:/agat quay.io/biocontainers/agat:0.9.2--pl5321hdfd78af_1 agat_convert_sp_gxf2gxf.pl -g braker.gtf -o braker.gff

---

• • Start parsing - *

    ---

    -------------------------- parse options and metadata -------------------------- => Accessing the feature level json files Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/features_level1.json file Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/features_level2.json file Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/features_level3.json file Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/features_spread.json 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 --------------------------------- !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! braker.gtf does not exist. Please verify the input file name/path ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Do you know what could be going wrong?

Regards, Chris L

[Juke34]

Thank you for using AGAT @claumer. Sorry there is an error in the command, you should type: docker run -v ${PWD}:/agat quay.io/biocontainers/agat:0.9.2--pl5321hdfd78af_1 agat_convert_sp_gxf2gxf.pl -g /agat/braker.gtf -o /agat/braker.gff