Here, presented my PHG scripts, config, wgs_keyfile.
1. Create valid intervals
docker run --name test_assemblies --rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t maizegenetics/phg:1.0 /tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters /phg/Masterconfig.txt -CreateValidIntervalsFilePlugin -intervalsFile /phg/inputDir/reference/glyma.Wm82.gnm4.ann1.T8TQ.gene_models_main.bed -referenceFasta /phg/inputDir/reference/glyma.Wm82.gnm4.4PTR.genome_main.fixed.fna.gz -mergeOverlaps true -generatedFile /phg/validBedFile.bed -endPlugin &> Log/1.Create_validinterval.txt &
2. Create initial DB
docker run --name create_initial_db --rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t maizegenetics/phg:1.0 /tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters /phg/Masterconfig.txt -MakeInitialPHGDBPipelinePlugin -endPlugin &> Log/2.Create_InitialDB.txt &
3. check plugin update
docker run --name create_directory --rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t maizegenetics/phg:1.0 /tassel-5-standalone/run_pipeline.pl -debug -configParameters /phg/Masterconfig.txt -CheckDBVersionPlugin -outputDir /phg/outputDir -endPlugin -LiquibaseUpdatePlugin -outputDir /phg/outputDir -endPlugin &> Log/3.Check_Plugin.txt &
4. Load haplotype (In docker)
./CreateHaplotypesFromFastq.groovy -config phg/Masterconfig.txt &> phg/Log/4.CreateHAplotypeFromFastq.txt &
5. Create consensus (In docker)
/tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters Masterconfig.txt -HaplotypeGraphBuilderPlugin -configFile Masterconfig.txt -methods GATK_PIPELINE1:CONSENSUS -includeVariantContexts true -endPlugin -RunHapConsensusPipelinePlugin -referenceFasta /inputDir/reference/glyma.Wm82.gnm4.4PTR.genome_main.fixed.fna.gz -dbConfigFile Masterconfig.txt -collapseMethod CONSENSUS -collapseMethodDetails G.max_test -rankingFile rankingFile.txt -clusteringMode kmer_assembly -isTestMethod true -endPlugin &> phg/Log/5.Concensus.txt &
Config file
### 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/Gmax430 DBtype=sqlite
Load genome intervals parameters
referenceFasta=/phg/inputDir/reference/glyma.Wm82.gnm4.4PTR.genome_main.fna.gz anchors=/phg/validBedFile.bed genomeData=/phg/inputDir/reference/load_genome_data.txt refServerPath=localHost;/DATA/jysong/ver1.0_phg/ref
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=100G tasselLocation=/tassel-5-standalone/run_pipeline.pl
PHG CreateHaplotypes Parameters
wgsKeyFile=/phg/wgs_KeyFile.txt LoadHaplotypesFromGVCFPlugin.gvcfDir=/phg/inputDir/loadDB/gvcf/ LoadHaplotypesFromGVCFPlugin.referenceFasta=/phg/inputDir/reference/glyma.Wm82.gnm4.4PTR.genome_main.fna.gz LoadHaplotypesFromGVCFPlugin.haplotypeMethodName=GATK_PIPELINE LoadHaplotypesFromGVCFPlugin.haplotypeMethodDescription=GATK_PIPELINE extendedWindowSize = 1000 mapQ = 48
GATK and Sentieon Parameters
gatkPath = /gatk/gatk numThreads=35 sentieon_license sentieonPath=/sentieon/bin/sentieon
CreateConsensi parameters
haplotypeMethod = GARK_PIPELINE consensusMethod = CONSENSUS mxDiv = 0.005 seqErr = 0.02 minSites = 20 minTaxa = 2 maxThreads = 60
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=100
DP_max=UNASSIGNED
GQ_min=10
GQ_max=UNASSIGNED
QUAL_min=30
QUAL_max=UNASSIGNED
filterHets=UNASSIGNED
Imputation Pipeline parameters for VCF files
--- 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=GBD_readMethod 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=CONSENSUS pathMethod=GBD_pathMethod 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/
wgs_keyfile
The output file of the filtered gvcf file did not show any sequences. And in create consensus step, sever;/path/to/file error occurred.
After changing the colon of gvcfserverpath to a semicolon, executing CreateFromGVCF.groovy and proceeding with the create Consensus step, the same error occurred. Is there something wrong with the config file or keyfile?
