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custom microbe reference files for use with PathSeq


im trying to use PathSeq for pathogen discovery in my species of interest and im having issue on preparing my microbe reference files. As microbe reference i have a metagenome characterized by several strains of the pathogen im interested in and I was able to create the fasta.img, fasta.fai, .dict, but when im running PathSeqBuildReferenceTaxonomy i get the issue that it is not in the "--refseq-catalog $microbe/RefSeq-release95.catalog.gz". The catalogue contains just one complete genome of the pathogen but i really would like to use all the strains available, is there a way to go around it?

Thanks for your time and support,


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @lbuggiotti

    Would you please post the exact command, version of GATK and the entire error log.

  • lbuggiottilbuggiotti Member
    Hi, here are the details:

    $gatk4/gatk PathSeqBuildReferenceTaxonomy \
    -R $microbe/BVDV_207_strains_genome.fasta \
    -O $microbe/BVDV_genome_207.db \
    --refseq-catalog $microbe/RefSeq-release95.catalog.gz \
    --tax-dump $microbe/taxdump.tar.gz \

    version of GATK: gatk-

    log error:

    A USER ERROR has occurred: Bad input: Did not find any taxa corresponding to reference sequence names.

    Check that reference names follow one of the required formats:


    I cannot copy paste the entire log file, is there a way of uploading as a file?
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @lbuggiotti

    As mentioned in the docs here, The reference should only contain sequences from NCBI RefSeq and/or Genbank databases. which does not seem to be the case with your data. This is a requirement of this tool.

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