When creating consensus haplotypes script fails to find reference line PHG

Question

[nicohlara]

I am trying to run Step 2 of the PHG creation pipeline, and after successfully loading my intervals and creating haplotypes from BAMs cannot make the RunHapConsensusPipelinePlugin work.

After mounting the phg directory to docker and running CreateHaplotypesFromBAM.groovy, I tried:

singularity exec $DOCKER /tassel-5-standalone/run_pipeline.pl -configParameters $CONFIG_FILE \
     -HaplotypeGraphBuilderPlugin -configFile $CONFIG_FILE -methods method1:method2 -endPlugin \
     -RunHapConsensusPipelinePlugin -dbConfigFile $CONFIG_FILE \
             -referenceFasta /phg/inputDir/reference/iwgsc_refseqv2.1_assembly.fa \
         -rankingFile phg/ranking_file.txt -mxDiv 0.0001 \
         -endPlugin

While running the HaplotypeGraphBuilderPlugin step I get the following error:

[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = phg/srww_phg_v2dot1.db host: localHost user: sqlite type: sqlite
[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:phg/srww_phg_v2dot1.db
[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:  

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 
Usage:
HaplotypeGraphBuilderPlugin <options>
-configFile <Config File> : Database configuration file (required)
-methods <Methods> : Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by colon. The range group is optional 
Usage: <haplotype method name1>,<range group name1>:<haplotype method name2>,<range group name2>:<haplotype method name3>
-includeSequences <true | false> : Whether to include sequences in haplotype nodes. (Default: true)
-includeVariantContexts <true | false> : Whether to include variant contexts in haplotype nodes. (Default: false)
-haplotypeIds <Haplotype Ids> : List of haplotype ids to include in the graph. If not specified, all ids are included.
-chromosomes <Chromosomes> : List of chromosomes to include in graph.  Default is to include all chromosomes.  (i.e. -chromosomes 1,3)
-taxa <Taxa> : Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
-localGVCFFolder <Local GVCF Folder> : Folder where ref/assembly gvcfs are stored.  Only required if includeVariantContexts is true

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - processData: Problem creating graph: CreateGraphUtils: getRelLineName: db failure getting reference line name CreateGraphUtils: getRefLineName: genotypes table has no line marked as reference

I've tried adding a '-referenceFasta' flag both at the docker mounted location and at the current location and got an error that it wasn't a recognized option for the plugin. I also have added a line to my ranking file for 'Ref,' ranked at both 1 and 0. Any help understanding how to fix this error would be appreciated!