How to run QFO benchmarks

First clone the QFO benchmark https://github.com/qfo/benchmark-webservice and download the reference data.

git clone git@github.com:qfo/benchmark-webservice.git
python fetch_reference_data.py  2020.2
mv reference_data/2020.2/ reference_data/2020

(for group-based benchmarks at the level of Bilateria add -b group-based-benchmarks)

The QFO results are also available on the newest fastoma zenodo here.

Then consider you have the output of fastOMA with case.orthoxml, run this

module purge               # depending on your HPC
module load singularityce


id="case"
NXF_VER=21.10.6 nextflow run main.nf -profile singularity --results_dir out_${id} --goldstandard_dir reference_data/2020 --event_year 2020  --participant_id ${id} --input ${id}.orthoxml

Alternatively, you can create submit your orthoxml or orthologous pairs to the QFO website at QFO benchmark service or directly on openebench

How to Run FastOMA?

With FastOMA's last step in nextflow you need to activate an option to convert protein ID --id-transform UniProt

fastoma-collect-subhogs --pickle-folder pickle_folders/   --roothogs-folder omamer_rhogs/      --gene-id-pickle-file gene_id_dic_xml.pickle   --out FastOMA_HOGs.orthoxml     --marker-groups-fasta OrthologousGroups.tsv    --roothog-tsv RootHOGs.tsv                                 --species-tree species_tree_checked.nwk     -vv --id-transform UniProt

the output would be like this

  <species name="ANOGA" taxonId="107" NCBITaxId="0">
    <database name="database" version="2023">
      <genes>
        <gene id="1000000001" protId="A0A1S4GMD5" />
        <gene id="1000000001" protId="A0A1S4GMD5" />
        <gene id="1000000002" protId="A0A1S4GN31" />
        <gene id="1000000003" protId="A0A1S4GYH6" />
        <gene id="1000000004" protId="A0A1S4H2E2" />

Otherwise you might get this error with benchmarking:

  Compile failed for sources FixedSetSources[name='/groovy/script//_nf_config_436f7c40']. Cau
se: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:                                                
  General error during conversion: Unsupported class file major version 65                                                         
                                                                                                                                   
  java.lang.IllegalArgumentException: Unsupported class file major version 65                                                      
        at groovyjarjarasm.asm.ClassReader.<init>(ClassReader.java:199)