Hello again,
I was previously asking questions in this post Practical Haplotype Graph Paths.
Currently I am trying to impute our lines (-ImputePipelinePlugin -imputeTarget path -endPlugin) with our new pangenome_assembly_by_anchorwave.fa (we had to add a founder to our pre-consensus database and decided to try to impute without creating consensus haplotypes). When I created the new pangenome, I noticed I didn't get the pangenome_assembly_by_anchorwave_k21w11I90G.mmi file that I previously had. When I run the imputation on a test set of gbs fasq files, I get a .mmi file, but it has 0 bytes. The _pathKeyFile.txt & withMappingIds.txt that are returned also only have the headers, but looking at the output from running the command it looks like the lines specified in my keyfile are being used. Do you think I had an issue with the pangenome step or something in the imputation step? Here's an example:
In addition this is the config file I am working with:
host=localHost
user=sqlite
password=sqlite
DB=/scratch/pre_consensus_db1.db
DBtype=sqlite
liquibaseOutdir=Current_PHG/phg/outputDir
localGVCFFolder=Current_PHG/phg/inputDir/loadDB/gvcf/
HaplotypeGraphBuilderPlugin.localGVCFFolder=Current_PHG/phg/inputDir/loadDB/gvcf/
pangenomeHaplotypeMethod=assembly_by_anchorwave
pangenomeDir=Current_PHG/phg/outputDir/pangenome
indexKmerLength=21
indexWindowSize=11
indexNumberBases=90G
--- Used for mapping reads
inputType=fastq
readMethod=gbs_data
keyFile=Current_PHG/phg/testReadMapping_key_file.txt
fastqDir=Current_PHG/phg/inputDir/imputation/fastq/
samDir=Current_PHG/phg/inputDir/imputation/sam/
lowMemMode=true
maxRefRangeErr=0.25
outputSecondaryStats=false
maxSecondary=38
fParameter=f5000,6000
minimapLocation=minimap2
--- Used for path finding
pathHaplotypeMethod=assembly_by_anchorwave
pathMethod=assembly_by_anchorwave
overwrite=true
maxNodes=100000
maxReads=1000000
minReads=1
minTaxa=1
minTransitionProb=0.001
numThreads=15
probCorrect=0.99
removeEqual=true
splitNodes=true
splitProb=0.99
usebf=false
maxParents = 1000000
minCoverage = 1.0
parentOutputFile = optional
used by haploid path finding only
usebf=false
minP=0.8
--- Used to output a vcf file for pathMethod
outVcfFile=Current_PHG/phg/600k_ZeaSyn_output.vcf positions=Current_PHG/phg/Maize600k_v5_crossmapconverted_new.bed referenceFasta=Current_PHG/phg/inputDir/reference/Ref.fa
