Here, presented my PHG Scripts and required files. An error message appeared in the 6. imputation step.

ERROR net.maizegenetics.plugindef.AbstractPlugin - Index: 2, Size: 1

Sorry for the lengthy content. When I think about it, there seems to be a problem with the keyfile or vcf index file. Please point it out.

1. Create Default Directory

$ docker run --name create_directory --rm \
-v /hpvol/user/jysong/phg/:/phg/ \
-t maizegenetics/phg:latest \
/tassel-5-standalone/run_pipeline.pl -debug -MakeDefaultDirectoryPlugin -workingDir /phg/ -endPlugin

2. Create a bed file to define genome intervals

$ docker run --name test_assemblies --rm  \
-v /hpvol/user/jysong/phg/:/phg/ \
-t maizegenetics/phg \
/tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters /phg/configSQLite.txt \
-CreateValidIntervalsFilePlugin -intervalsFile /phg/Gmax_275_Wm82.a2.v1.gene.bed \
-referenceFasta /phg/inputDir/reference/Gmax_275_v2.0.fa.gz \
-mergeOverlaps true \
-generatedFile /phg/Gmax_validBedFile.bed -endPlugin

3. Create Initial DataBase

$ docker run --name create_initial_db --rm \ 
-v /hpvol/user/jysong/phg/:/phg/ \ 
-t maizegenetics/phg \ 
/tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters /phg/configSQLite.txt \ 
-MakeInitialPHGDBPipelinePlugin -endPlugin

(1). configSQLite.txt

host=localHost
user=sqlite
password=sqlite
DB=/phg/gvcf
DBtype=sqlite

# Load genome intervals parameters
referenceFasta=/phg/inputDir/reference/Gmax_275_v2.0.fa.gz
anchors=/phg/Gmax_validBedFile.bed
genomeData=/phg/inputDir/reference/load_genome_data.txt
refServerPath=/hpvol/user/jysong/phg/inputDir/assemblies
#liquibase results output directory, general output directory
outputDir=/phg/outputDir
liquibaseOutdir=/phg/outputDir
CreateIntervalBedFilesPlugin.refRangeMethods=FocusRegion,FocusComplement

(2) load_genome_data.txt

    Genotype    Hapnumber   Dataline    ploidy  genesPhased chromsPhased    confidence  Method  MethodDetails
Wm82    0   core_collection 1   true    true    1   Ref_Wm82_method corecoll_test version for a2

4. Create Haplotype From GVCF

$ docker run --name load_Haplotype --rm -v /hpvol/user/jysong/phg/:/phg/ -t maizegenetics/phg ./CreateHaplotypesFromGVCF.groovy -config /phg/LoadHaploconfig.txt

(3) LoadHaploconfig.txt

    #!

### config file. 
### Anything marked with UNASSIGNED needs to be set for at least one of the steps
### If it is marked as OPTIONAL, it will only need to be set if you want to run specific steps. 
host=localHost
user=sqlite
password=sqlite
DB=/phg/gvcf
DBtype=sqlite

# Load genome intervals parameters
referenceFasta=/phg/inputDir/reference/Gmax_275_v2.0.fa.gz
anchors=/phg/Gmax_validBedFile.bed
genomeData=/phg/inputDir/reference/load_genome_data.txt
refServerPath=/hpvol/user/jysong/phg/inputDir/assemblies
#liquibase results output directory, general output directory
outputDir=/phg/outputDir
liquibaseOutdir=/phg/outputDir


### Align WGS fastq files to reference genome parameters

# File Directories
gvcfFileDir=/phg/inputDir/loadDB/gvcf/
tempFileDir=/phg/inputDir/loadDB/temp/
filteredBamDir=/phg/inputDir/loadDB/bam/filteredBAMs/
dedupedBamDir=/phg/inputDir/loadDB/bam/DedupBAMs/

# TASSEL parameters
Xmx=10G
tasselLocation=/tassel-5-standalone/run_pipeline.pl

# PHG CreateHaplotypes Parameters
referenceFasta=/phg/inputDir/reference/Gmax_275_v2.0.fa.gz
wgsKeyFile=/phg/load_wgs_genome_key_file.txt
LoadHaplotypesFromGVCFPlugin.gvcfDir=/phg/inputDir/loadDB/gvcf/
LoadHaplotypesFromGVCFPlugin.referenceFasta=/phg/inputDir/reference/Gmax_275_v2.0.fa.gz
CreateIntervalBedFilesPlugin.refRangeMethods=FocusRegion,FocusComplement
LoadHaplotypesFromGVCFPlugin.haplotypeMethodName=GATK_PIPELINE
LoadHaplotypesFromGVCFPlugin.haplotypeMethodDescription=”GATK_PIPELINE”
extendedWindowSize = 1000
mapQ = 48

# GATK and Sentieon Parameters
gatkPath = /gatk/gatk
numThreads=10
sentieon_license
sentieonPath=/sentieon/bin/sentieon

(4) load_wgs_genome_key_file.txt

sample_name sample_description  files   type    chrPhased   genePhased  phasingConf libraryID
CMJ001  CMJ001 Aligned using BWA    CMJ001_srt_dedup_mapQ_output.g.vcf  GVCF    true    true    .99 null
CMJ002  CMJ002 Aligned using BWA    CMJ002_srt_dedup_mapQ_output.g.vcf  GVCF    true    true    .99 null

5. Create consensus haplotypes

$ docker run --name phg_container_consensus --rm -v /hpvol/user/jysong/PHG_gvcf/:/phg/ -t maizegenetics/phg:latest /CreateConsensi.sh /phg/consensusconfig.txt Gmax_275_v2.0.fa.gz GATK_PIPELINE CONSENSUS -collapseMethod CONSENSUS

(5) consensusconfig.txt

    ##!

### config file. 
### Anything marked with UNASSIGNED needs to be set for at least one of the steps
### If it is marked as OPTIONAL, it will only need to be set if you want to run specific steps. 
host=localHost
user=sqlite
password=sqlite
DB=/phg/gvcf
DBtype=sqlite

# Load genome intervals parameters
referenceFasta=/phg/inputDir/reference/Gmax_275_v2.0.fa.gz
anchors=/phg/Gmax_validBedFile.bed
genomeData=/phg/inputDir/reference/load_genome_data.txt
refServerPath=/hpvol/user/jysong/phg/inputDir/assemblies
#liquibase results output directory, general output directory
outputDir=/phg/outputDir
liquibaseOutdir=/phg/outputDir


### Align WGS fastq files to reference genome parameters

# File Directories
gvcfFileDir=/phg/inputDir/loadDB/gvcf/
tempFileDir=/phg/inputDir/loadDB/temp/
filteredBamDir=/phg/inputDir/loadDB/bam/filteredBAMs/
dedupedBamDir=/phg/inputDir/loadDB/bam/DedupBAMs/

# TASSEL parameters
# Xmx=10G
tasselLocation=/tassel-5-standalone/run_pipeline.pl

# PHG CreateHaplotypes Parameters
referenceFasta=/phg/inputDir/reference/Gmax_275_v2.0.fa.gz
wgsKeyFile=/phg/load_wgs_genome_key_file.txt
LoadHaplotypesFromGVCFPlugin.gvcfDir=/phg/inputDir/loadDB/gvcf/
LoadHaplotypesFromGVCFPlugin.referenceFasta=/phg/inputDir/reference/Gmax_275_v2.0.fa.gz
LoadHaplotypesFromGVCFPlugin.haplotypeMethodName=GATK_PIPELINE
LoadHaplotypesFromGVCFPlugin.haplotypeMethodDescription=”GATK_PIPELINE”
extendedWindowSize = 1000
mapQ = 48

# GATK and Sentieon Parameters
gatkPath = /gatk/gatk
numThreads=10
sentieon_license
sentieonPath=/sentieon/bin/sentieon


# CreateConsensi parameters
haplotypeMethod = GARK_PIPELINE
consensusMethod = CONSENSUS
mxDiv = 0.005
seqErr = 0.02
minSites = 20
minTaxa = 2
#rankingFile = null
clusteringMode = upgma


# Graph Building Parameters
includeVariants = true

#FilterGVCF Parameters.  Adding any of these will add more filters.#exclusionString=**UNASSIGNED**
#DP_poisson_min=0.0
#DP_poisson_max=1.0
#DP_min=**UNASSIGNED**
#DP_max=**UNASSIGNED**
#GQ_min=**UNASSIGNED**
#GQ_max=**UNASSIGNED**
#QUAL_min=**UNASSIGNED**
#QUAL_max=**UNASSIGNED**
#filterHets=**UNASSIGNED**

exportMergedVCF=/tempFileDir/data/outputs/mergedVCFs/

6. Imputation

$ docker run --name pipeline_container --rm -v /hpvol/user/jysong/phg_test/:/phg/ -t maizegenetics/phg /tassel-5-standalone/run_pipeline.pl -Xmx10G -debug -configParameters /phg/imputevcfconfig.txt -ImputePipelinePlugin -imputeTarget pathToVCF -endPlugin

(6) imputevcfconfig.txt

    # Imputation Pipeline parameters for VCF files

#!!! Required Parameters !!!
#--- Database ---
host=localHost
user=sqlite
password=sqlite
DB=/phg/gvcf
DBtype=sqlite

#--- Used by liquibase to check DB version ---
liquibaseOutdir=/phg/outputDir

#--- Used for indexing SNP positions ---
#   pangenomeHaplotypeMethod is the database method or methods for the haplotypes to which SNPs will be indexed
#   the index file lists the SNP allele to haplotype mapping and is used for mapping reads
 pangenomeHaplotypeMethod=CONSENSUS
 pangenomeDir=/phg/outputDir/pangenome
 indexFile=/phg/outputDir/vcfIndexfile
 vcfFile=/phg/inputDir/imputation/vcf/SoyHapMap.SNP.GT.fixed.vcf.414accession.KASP.gz

#--- Used for mapping reads
#   readMethod is the method name for storing the resulting read mappings
#   countAlleleDepths=true means allele depths will be used for haplotype counts, which is almost always a good choice
inputType=vcf
keyFile=/phg/readMapping_key_file.txt
readMethod=GATK_PIPELINE
vcfDir=/phg/inputDir/loadDB/gvcf/
countAlleleDepths=true

#--- Used for path finding
#   pathHaplotypeMethod determines which haplotypes will be consider for path finding
#   pathHaplotypeMethod should be the same as pangenomeHaplotypeMethod, but could be a subset
#   pathMethod is the method name used for storing the paths
pathHaplotypeMethod=GATK_PIPELINE
pathMethod=GATK_PIPELINE
maxNodes=1000
maxReads=10000
minReads=1
minTaxa=20
minTransitionProb=0.001
numThreads=3
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 - if true use Forward-Backward algorithm, other Viterbi
usebf=false
minP=0.8

#--- used by diploid path finding only
maxHap=11
maxReadsKB=100
algorithmType=efficient

#--- Used to output a vcf file for pathMethod
outVcfFile=/phg/outputDir/Result.vcf

#~~~ Optional Parameters ~~~
#readMethodDescription=**OPTIONAL**
#pathMethodDescription=**OPTIONAL**
#bfInfoFile=**OPTIONAL**
#~~~ providing a value for outputDir will write read mappings to file rather than the PHG db ~~~
outputDir=/phg/

(7) readMapping_key_file.txt

    cultivar    flowcell_lane   filename    PlateID
CMJ001  wgsFlowcell CMJ001_srt_dedup_mapQ_output.g.vcf  wgs
CMJ002  wgsFlowcell  CMJ002_srt_dedup_mapQ_output.g.vcf  wgs

Thank you for your time.