User Error after running GATK BaseRecalibrator for WGS BAM file

Question

this is my first time write the pipeline using snakemake for converting WGS BAM file to VCF. I had the problem in the step of BaseRecalibrator.

The following is my code:

# Work Directory
DIR = config['workdir']

# Sample IDs
ID = [line.strip() for line in open(config["sampleID_file"], "r")]

# Date and time for logs
from datetime import datetime
date = datetime.now().strftime("%Y%m%d_%H%M%S")

# Memory parameter
MEMORY = "-Xmx32G"

rule all_bqsr:
   input:
       expand("{dir}/2.BQSR/1.BaseRecalibrator/{pID}/{pID}_BaseRecalibrator/{pID}.recal_data.table", pID=ID, dir=DIR)

rule calculate_bqsr:
   input:
       bam="{dir}/2.BQSR/0.add_read_group/{pID}/{pID}.rmdup.rg.bam",
       ref=config["reference_genome"],
       dbSNP_site=config["dbsnp_site"],
       mills_site=config["mills_site"],
       gatk=config["gatk"]
   output:
       table="{dir}/2.BQSR/1.BaseRecalibrator/{pID}/{pID}_BaseRecalibrator/{pID}.recal_data.table"
   params:
       memory=MEMORY
   log:
       calculate_bqsr_log="{dir}/2.BQSR/1.BaseRecalibrator/{pID}/{pID}_BaseRecalibrator/{pID}-BaseRecalibrator." + date + ".log"
   message:
       "\nStep 2-1: BaseRecalibrator: Calculate the distribution of systematic errors based on the base quality values."
   threads: 48
   shell:
       """
       {input.gatk} --java-options '{params.memory} -DGATK_STACKTRACE_ON_USER_EXCEPTION=true' BaseRecalibrator \
       -I {input.bam} \
       -R {input.ref} \
       --known-sites {input.dbSNP_site} \
       --known-sites {input.mills_site} \
       -O {output.table} 2>&1 | tee -a {log.calculate_bqsr_log}
       """ 

The reference_genome I download from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/**GCA_000001405.15_GRCh38_full_analysis_set.fna**, and converted it to fa format.

However I encountered errors are Contig chrUn_xxx not present in the sequence dictionary and MissingContigInSequenceDictionary.

A USER ERROR has occurred: Contig chrUn_KN707606v1_decoy not present in the sequence dictionary [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270713v1_random, chr1_KI270714v1_random, chr2_KI270715v1_random, chr2_KI270716v1_random, chr3_GL000221v1_random, chr4_GL000008v2_random, chr5_GL000208v1_random, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr11_KI270721v1_random, chr14_GL000009v2_random, chr14_GL000225v1_random, chr14_KI270722v1_random, chr14_GL000194v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr15_KI270727v1_random, chr16_KI270728v1_random, chr17_GL000205v2_random, chr17_KI270729v1_random, chr17_KI270730v1_random, chr22_KI270731v1_random, chr22_KI270732v1_random, chr22_KI270733v1_random, chr22_KI270734v1_random, chr22_KI270735v1_random, chr22_KI270736v1_random, chr22_KI270737v1_random, chr22_KI270738v1_random, chr22_KI270739v1_random, chrY_KI270740v1_random, chrUn_KI270302v1, chrUn_KI270304v1, chrUn_KI270303v1, chrUn_KI270305v1, chrUn_KI270322v1, chrUn_KI270320v1, chrUn_KI270310v1, chrUn_KI270316v1, chrUn_KI270315v1, chrUn_KI270312v1, chrUn_KI270311v1, chrUn_KI270317v1, chrUn_KI270412v1, chrUn_KI270411v1, chrUn_KI270414v1, chrUn_KI270419v1, chrUn_KI270418v1, chrUn_KI270420v1, chrUn_KI270424v1, chrUn_KI270417v1, chrUn_KI270422v1, chrUn_KI270423v1, chrUn_KI270425v1, chrUn_KI270429v1, chrUn_KI270442v1, chrUn_KI270466v1, chrUn_KI270465v1, chrUn_KI270467v1, chrUn_KI270435v1, chrUn_KI270438v1, chrUn_KI270468v1, chrUn_KI270510v1, chrUn_KI270509v1, chrUn_KI270518v1, chrUn_KI270508v1, chrUn_KI270516v1, chrUn_KI270512v1, chrUn_KI270519v1, chrUn_KI270522v1, chrUn_KI270511v1, chrUn_KI270515v1, chrUn_KI270507v1, chrUn_KI270517v1, chrUn_KI270529v1, chrUn_KI270528v1, chrUn_KI270530v1, chrUn_KI270539v1, chrUn_KI270538v1, chrUn_KI270544v1, chrUn_KI270548v1, chrUn_KI270583v1, chrUn_KI270587v1, chrUn_KI270580v1, chrUn_KI270581v1, chrUn_KI270579v1, chrUn_KI270589v1, chrUn_KI270590v1, chrUn_KI270584v1, chrUn_KI270582v1, chrUn_KI270588v1, chrUn_KI270593v1, chrUn_KI270591v1, chrUn_KI270330v1, chrUn_KI270329v1, chrUn_KI270334v1, chrUn_KI270333v1, chrUn_KI270335v1, chrUn_KI270338v1, chrUn_KI270340v1, chrUn_KI270336v1, chrUn_KI270337v1, chrUn_KI270363v1, chrUn_KI270364v1, chrUn_KI270362v1, chrUn_KI270366v1, chrUn_KI270378v1, chrUn_KI270379v1, chrUn_KI270389v1, chrUn_KI270390v1, chrUn_KI270387v1, chrUn_KI270395v1, chrUn_KI270396v1, chrUn_KI270388v1, chrUn_KI270394v1, chrUn_KI270386v1, chrUn_KI270391v1, chrUn_KI270383v1, chrUn_KI270393v1, chrUn_KI270384v1, chrUn_KI270392v1, chrUn_KI270381v1, chrUn_KI270385v1, chrUn_KI270382v1, chrUn_KI270376v1, chrUn_KI270374v1, chrUn_KI270372v1, chrUn_KI270373v1, chrUn_KI270375v1, chrUn_KI270371v1, chrUn_KI270448v1, chrUn_KI270521v1, chrUn_GL000195v1, chrUn_GL000219v1, chrUn_GL000220v1, chrUn_GL000224v1, chrUn_KI270741v1, chrUn_GL000226v1, chrUn_GL000213v1, chrUn_KI270743v1, chrUn_KI270744v1, chrUn_KI270745v1, chrUn_KI270746v1, chrUn_KI270747v1, chrUn_KI270748v1, chrUn_KI270749v1, chrUn_KI270750v1, chrUn_KI270751v1, chrUn_KI270752v1, chrUn_KI270753v1, chrUn_KI270754v1, chrUn_KI270755v1, chrUn_KI270756v1, chrUn_KI270757v1, chrUn_GL000214v1, chrUn_KI270742v1, chrUn_GL000216v2, chrUn_GL000218v1, chr1_KI270762v1_alt, chr1_KI270766v1_alt, chr1_KI270760v1_alt, chr1_KI270765v1_alt, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270764v1_alt, chr1_KI270763v1_alt, chr1_KI270759v1_alt, chr1_KI270761v1_alt, chr2_KI270770v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270769v1_alt, chr2_GL383521v1_alt, chr2_KI270772v1_alt, chr2_KI270775v1_alt, chr2_KI270771v1_alt, chr2_KI270768v1_alt, chr2_GL582966v2_alt, chr2_GL383522v1_alt, chr2_KI270776v1_alt, chr2_KI270767v1_alt, chr3_JH636055v2_alt, chr3_KI270783v1_alt, chr3_KI270780v1_alt, chr3_GL383526v1_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270781v1_alt, chr3_KI270779v1_alt, chr3_KI270782v1_alt, chr3_KI270784v1_alt, chr4_KI270790v1_alt, chr4_GL383528v1_alt, chr4_KI270787v1_alt, chr4_GL000257v2_alt, chr4_KI270788v1_alt, chr4_GL383527v1_alt, chr4_KI270785v1_alt, chr4_KI270789v1_alt, chr4_KI270786v1_alt, chr5_KI270793v1_alt, chr5_KI270792v1_alt, chr5_KI270791v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270794v1_alt, chr5_GL339449v2_alt, chr5_GL383530v1_alt, chr5_KI270796v1_alt, chr5_GL383531v1_alt, chr5_KI270795v1_alt, chr6_GL000250v2_alt, chr6_KI270800v1_alt, chr6_KI270799v1_alt, chr6_GL383533v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KB021644v2_alt, chr6_KI270797v1_alt, chr6_KI270798v1_alt, chr7_KI270804v1_alt, chr7_KI270809v1_alt, chr7_KI270806v1_alt, chr7_GL383534v2_alt, chr7_KI270803v1_alt, chr7_KI270808v1_alt, chr7_KI270807v1_alt, chr7_KI270805v1_alt, chr8_KI270818v1_alt, chr8_KI270812v1_alt, chr8_KI270811v1_alt, chr8_KI270821v1_alt, chr8_KI270813v1_alt, chr8_KI270822v1_alt, chr8_KI270814v1_alt, chr8_KI270810v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270817v1_alt, chr8_KI270816v1_alt, chr8_KI270815v1_alt, chr9_GL383539v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270823v1_alt, chr10_GL383545v1_alt, chr10_KI270824v1_alt, chr10_GL383546v1_alt, chr10_KI270825v1_alt, chr11_KI270832v1_alt, chr11_KI270830v1_alt, chr11_KI270831v1_alt, chr11_KI270829v1_alt, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270827v1_alt, chr11_KI270826v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270837v1_alt, chr12_GL383549v1_alt, chr12_KI270835v1_alt, chr12_GL383550v2_alt, chr12_GL383552v1_alt, chr12_GL383553v2_alt, chr12_KI270834v1_alt, chr12_GL383551v1_alt, chr12_KI270833v1_alt, chr12_KI270836v1_alt, chr13_KI270840v1_alt, chr13_KI270839v1_alt, chr13_KI270843v1_alt, chr13_KI270841v1_alt, chr13_KI270838v1_alt, chr13_KI270842v1_alt, chr14_KI270844v1_alt, chr14_KI270847v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr15_KI270852v1_alt, chr15_KI270851v1_alt, chr15_KI270848v1_alt, chr15_GL383554v1_alt, chr15_KI270849v1_alt, chr15_GL383555v2_alt, chr15_KI270850v1_alt, chr16_KI270854v1_alt, chr16_KI270856v1_alt, chr16_KI270855v1_alt, chr16_KI270853v1_alt, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr17_GL383563v3_alt, chr17_KI270862v1_alt, chr17_KI270861v1_alt, chr17_KI270857v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_GL383564v2_alt, chr17_GL000258v2_alt, chr17_GL383565v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_GL383566v1_alt, chr17_KI270860v1_alt, chr18_KI270864v1_alt, chr18_GL383567v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr19_KI270868v1_alt, chr19_KI270865v1_alt, chr19_GL383573v1_alt, chr19_GL383575v2_alt, chr19_GL383576v1_alt, chr19_GL383574v1_alt, chr19_KI270866v1_alt, chr19_KI270867v1_alt, chr19_GL949746v1_alt, chr20_GL383577v2_alt, chr20_KI270869v1_alt, chr20_KI270871v1_alt, chr20_KI270870v1_alt, chr21_GL383578v2_alt, chr21_KI270874v1_alt, chr21_KI270873v1_alt, chr21_GL383579v2_alt, chr21_GL383580v2_alt, chr21_GL383581v2_alt, chr21_KI270872v1_alt, chr22_KI270875v1_alt, chr22_KI270878v1_alt, chr22_KI270879v1_alt, chr22_KI270876v1_alt, chr22_KI270877v1_alt, chr22_GL383583v2_alt, chr22_GL383582v2_alt, chrX_KI270880v1_alt, chrX_KI270881v1_alt, chr19_KI270882v1_alt, chr19_KI270883v1_alt, chr19_KI270884v1_alt, chr19_KI270885v1_alt, chr19_KI270886v1_alt, chr19_KI270887v1_alt, chr19_KI270888v1_alt, chr19_KI270889v1_alt, chr19_KI270890v1_alt, chr19_KI270891v1_alt, chr1_KI270892v1_alt, chr2_KI270894v1_alt, chr2_KI270893v1_alt, chr3_KI270895v1_alt, chr4_KI270896v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr6_GL000251v2_alt, chr7_KI270899v1_alt, chr8_KI270901v1_alt, chr8_KI270900v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr12_KI270904v1_alt, chr15_KI270906v1_alt, chr15_KI270905v1_alt, chr17_KI270907v1_alt, chr17_KI270910v1_alt, chr17_KI270909v1_alt, chr17_JH159148v1_alt, chr17_KI270908v1_alt, chr18_KI270912v1_alt, chr18_KI270911v1_alt, chr19_GL949747v2_alt, chr22_KB663609v1_alt, chrX_KI270913v1_alt, chr19_KI270914v1_alt, chr19_KI270915v1_alt, chr19_KI270916v1_alt, chr19_KI270917v1_alt, chr19_KI270918v1_alt, chr19_KI270919v1_alt, chr19_KI270920v1_alt, chr19_KI270921v1_alt, chr19_KI270922v1_alt, chr19_KI270923v1_alt, chr3_KI270924v1_alt, chr4_KI270925v1_alt, chr6_GL000252v2_alt, chr8_KI270926v1_alt, chr11_KI270927v1_alt, chr19_GL949748v2_alt, chr22_KI270928v1_alt, chr19_KI270929v1_alt, chr19_KI270930v1_alt, chr19_KI270931v1_alt, chr19_KI270932v1_alt, chr19_KI270933v1_alt, chr19_GL000209v2_alt, chr3_KI270934v1_alt, chr6_GL000253v2_alt, chr19_GL949749v2_alt, chr3_KI270935v1_alt, chr6_GL000254v2_alt, chr19_GL949750v2_alt, chr3_KI270936v1_alt, chr6_GL000255v2_alt, chr19_GL949751v2_alt, chr3_KI270937v1_alt, chr6_GL000256v2_alt, chr19_GL949752v1_alt, chr6_KI270758v1_alt, chr19_GL949753v2_alt, chr19_KI270938v1_alt, chrEBV]


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org.broadinstitute.hellbender.exceptions.UserException$MissingContigInSequenceDictionary: Contig chrUn_KN707606v1_decoy not present in the sequence dictionary [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270713v1_random, chr1_KI270714v1_random, chr2_KI270715v1_random, chr2_KI270716v1_random, chr3_GL000221v1_random, chr4_GL000008v2_random, chr5_GL000208v1_random, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr11_KI270721v1_random, chr14_GL000009v2_random, chr14_GL000225v1_random, chr14_KI270722v1_random, chr14_GL000194v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr15_KI270727v1_random, chr16_KI270728v1_random, chr17_GL000205v2_random, chr17_KI270729v1_random, chr17_KI270730v1_random, chr22_KI270731v1_random, chr22_KI270732v1_random, chr22_KI270733v1_random, chr22_KI270734v1_random, chr22_KI270735v1_random, chr22_KI270736v1_random, chr22_KI270737v1_random, chr22_KI270738v1_random, chr22_KI270739v1_random, chrY_KI270740v1_random, chrUn_KI270302v1, chrUn_KI270304v1, chrUn_KI270303v1, chrUn_KI270305v1, chrUn_KI270322v1, chrUn_KI270320v1, chrUn_KI270310v1, chrUn_KI270316v1, chrUn_KI270315v1, chrUn_KI270312v1, chrUn_KI270311v1, chrUn_KI270317v1, chrUn_KI270412v1, chrUn_KI270411v1, chrUn_KI270414v1, chrUn_KI270419v1, chrUn_KI270418v1, chrUn_KI270420v1, chrUn_KI270424v1, chrUn_KI270417v1, chrUn_KI270422v1, chrUn_KI270423v1, chrUn_KI270425v1, chrUn_KI270429v1, chrUn_KI270442v1, chrUn_KI270466v1, chrUn_KI270465v1, chrUn_KI270467v1, chrUn_KI270435v1, chrUn_KI270438v1, chrUn_KI270468v1, chrUn_KI270510v1, chrUn_KI270509v1, chrUn_KI270518v1, chrUn_KI270508v1, chrUn_KI270516v1, chrUn_KI270512v1, chrUn_KI270519v1, chrUn_KI270522v1, chrUn_KI270511v1, chrUn_KI270515v1, chrUn_KI270507v1, chrUn_KI270517v1, chrUn_KI270529v1, chrUn_KI270528v1, chrUn_KI270530v1, chrUn_KI270539v1, chrUn_KI270538v1, chrUn_KI270544v1, chrUn_KI270548v1, chrUn_KI270583v1, chrUn_KI270587v1, chrUn_KI270580v1, chrUn_KI270581v1, chrUn_KI270579v1, chrUn_KI270589v1, chrUn_KI270590v1, chrUn_KI270584v1, chrUn_KI270582v1, chrUn_KI270588v1, chrUn_KI270593v1, chrUn_KI270591v1, chrUn_KI270330v1, chrUn_KI270329v1, chrUn_KI270334v1, chrUn_KI270333v1, chrUn_KI270335v1, chrUn_KI270338v1, chrUn_KI270340v1, chrUn_KI270336v1, chrUn_KI270337v1, chrUn_KI270363v1, chrUn_KI270364v1, chrUn_KI270362v1, chrUn_KI270366v1, chrUn_KI270378v1, chrUn_KI270379v1, chrUn_KI270389v1, chrUn_KI270390v1, chrUn_KI270387v1, chrUn_KI270395v1, chrUn_KI270396v1, chrUn_KI270388v1, chrUn_KI270394v1, chrUn_KI270386v1, chrUn_KI270391v1, chrUn_KI270383v1, chrUn_KI270393v1, chrUn_KI270384v1, chrUn_KI270392v1, chrUn_KI270381v1, chrUn_KI270385v1, chrUn_KI270382v1, chrUn_KI270376v1, chrUn_KI270374v1, chrUn_KI270372v1, chrUn_KI270373v1, chrUn_KI270375v1, chrUn_KI270371v1, chrUn_KI270448v1, chrUn_KI270521v1, chrUn_GL000195v1, chrUn_GL000219v1, chrUn_GL000220v1, chrUn_GL000224v1, chrUn_KI270741v1, chrUn_GL000226v1, chrUn_GL000213v1, chrUn_KI270743v1, chrUn_KI270744v1, chrUn_KI270745v1, chrUn_KI270746v1, chrUn_KI270747v1, chrUn_KI270748v1, chrUn_KI270749v1, chrUn_KI270750v1, chrUn_KI270751v1, chrUn_KI270752v1, chrUn_KI270753v1, chrUn_KI270754v1, chrUn_KI270755v1, chrUn_KI270756v1, chrUn_KI270757v1, chrUn_GL000214v1, chrUn_KI270742v1, chrUn_GL000216v2, chrUn_GL000218v1, chr1_KI270762v1_alt, chr1_KI270766v1_alt, chr1_KI270760v1_alt, chr1_KI270765v1_alt, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270764v1_alt, chr1_KI270763v1_alt, chr1_KI270759v1_alt, chr1_KI270761v1_alt, chr2_KI270770v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270769v1_alt, chr2_GL383521v1_alt, chr2_KI270772v1_alt, chr2_KI270775v1_alt, chr2_KI270771v1_alt, chr2_KI270768v1_alt, chr2_GL582966v2_alt, chr2_GL383522v1_alt, chr2_KI270776v1_alt, chr2_KI270767v1_alt, chr3_JH636055v2_alt, chr3_KI270783v1_alt, chr3_KI270780v1_alt, chr3_GL383526v1_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270781v1_alt, chr3_KI270779v1_alt, chr3_KI270782v1_alt, chr3_KI270784v1_alt, chr4_KI270790v1_alt, chr4_GL383528v1_alt, chr4_KI270787v1_alt, chr4_GL000257v2_alt, chr4_KI270788v1_alt, chr4_GL383527v1_alt, chr4_KI270785v1_alt, chr4_KI270789v1_alt, chr4_KI270786v1_alt, chr5_KI270793v1_alt, chr5_KI270792v1_alt, chr5_KI270791v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270794v1_alt, chr5_GL339449v2_alt, chr5_GL383530v1_alt, chr5_KI270796v1_alt, chr5_GL383531v1_alt, chr5_KI270795v1_alt, chr6_GL000250v2_alt, chr6_KI270800v1_alt, chr6_KI270799v1_alt, chr6_GL383533v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KB021644v2_alt, chr6_KI270797v1_alt, chr6_KI270798v1_alt, chr7_KI270804v1_alt, chr7_KI270809v1_alt, chr7_KI270806v1_alt, chr7_GL383534v2_alt, chr7_KI270803v1_alt, chr7_KI270808v1_alt, chr7_KI270807v1_alt, chr7_KI270805v1_alt, chr8_KI270818v1_alt, chr8_KI270812v1_alt, chr8_KI270811v1_alt, chr8_KI270821v1_alt, chr8_KI270813v1_alt, chr8_KI270822v1_alt, chr8_KI270814v1_alt, chr8_KI270810v1_alt, chr8_KI270819v1_alt, chr8_KI270820v1_alt, chr8_KI270817v1_alt, chr8_KI270816v1_alt, chr8_KI270815v1_alt, chr9_GL383539v1_alt, chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr9_GL383542v1_alt, chr9_KI270823v1_alt, chr10_GL383545v1_alt, chr10_KI270824v1_alt, chr10_GL383546v1_alt, chr10_KI270825v1_alt, chr11_KI270832v1_alt, chr11_KI270830v1_alt, chr11_KI270831v1_alt, chr11_KI270829v1_alt, chr11_GL383547v1_alt, chr11_JH159136v1_alt, chr11_JH159137v1_alt, chr11_KI270827v1_alt, chr11_KI270826v1_alt, chr12_GL877875v1_alt, chr12_GL877876v1_alt, chr12_KI270837v1_alt, chr12_GL383549v1_alt, chr12_KI270835v1_alt, chr12_GL383550v2_alt, chr12_GL383552v1_alt, chr12_GL383553v2_alt, chr12_KI270834v1_alt, chr12_GL383551v1_alt, chr12_KI270833v1_alt, chr12_KI270836v1_alt, chr13_KI270840v1_alt, chr13_KI270839v1_alt, chr13_KI270843v1_alt, chr13_KI270841v1_alt, chr13_KI270838v1_alt, chr13_KI270842v1_alt, chr14_KI270844v1_alt, chr14_KI270847v1_alt, chr14_KI270845v1_alt, chr14_KI270846v1_alt, chr15_KI270852v1_alt, chr15_KI270851v1_alt, chr15_KI270848v1_alt, chr15_GL383554v1_alt, chr15_KI270849v1_alt, chr15_GL383555v2_alt, chr15_KI270850v1_alt, chr16_KI270854v1_alt, chr16_KI270856v1_alt, chr16_KI270855v1_alt, chr16_KI270853v1_alt, chr16_GL383556v1_alt, chr16_GL383557v1_alt, chr17_GL383563v3_alt, chr17_KI270862v1_alt, chr17_KI270861v1_alt, chr17_KI270857v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_GL383564v2_alt, chr17_GL000258v2_alt, chr17_GL383565v1_alt, chr17_KI270858v1_alt, chr17_KI270859v1_alt, chr17_GL383566v1_alt, chr17_KI270860v1_alt, chr18_KI270864v1_alt, chr18_GL383567v1_alt, chr18_GL383570v1_alt, chr18_GL383571v1_alt, chr18_GL383568v1_alt, chr18_GL383569v1_alt, chr18_GL383572v1_alt, chr18_KI270863v1_alt, chr19_KI270868v1_alt, chr19_KI270865v1_alt, chr19_GL383573v1_alt, chr19_GL383575v2_alt, chr19_GL383576v1_alt, chr19_GL383574v1_alt, chr19_KI270866v1_alt, chr19_KI270867v1_alt, chr19_GL949746v1_alt, chr20_GL383577v2_alt, chr20_KI270869v1_alt, chr20_KI270871v1_alt, chr20_KI270870v1_alt, chr21_GL383578v2_alt, chr21_KI270874v1_alt, chr21_KI270873v1_alt, chr21_GL383579v2_alt, chr21_GL383580v2_alt, chr21_GL383581v2_alt, chr21_KI270872v1_alt, chr22_KI270875v1_alt, chr22_KI270878v1_alt, chr22_KI270879v1_alt, chr22_KI270876v1_alt, chr22_KI270877v1_alt, chr22_GL383583v2_alt, chr22_GL383582v2_alt, chrX_KI270880v1_alt, chrX_KI270881v1_alt, chr19_KI270882v1_alt, chr19_KI270883v1_alt, chr19_KI270884v1_alt, chr19_KI270885v1_alt, chr19_KI270886v1_alt, chr19_KI270887v1_alt, chr19_KI270888v1_alt, chr19_KI270889v1_alt, chr19_KI270890v1_alt, chr19_KI270891v1_alt, chr1_KI270892v1_alt, chr2_KI270894v1_alt, chr2_KI270893v1_alt, chr3_KI270895v1_alt, chr4_KI270896v1_alt, chr5_KI270897v1_alt, chr5_KI270898v1_alt, chr6_GL000251v2_alt, chr7_KI270899v1_alt, chr8_KI270901v1_alt, chr8_KI270900v1_alt, chr11_KI270902v1_alt, chr11_KI270903v1_alt, chr12_KI270904v1_alt, chr15_KI270906v1_alt, chr15_KI270905v1_alt, chr17_KI270907v1_alt, chr17_KI270910v1_alt, chr17_KI270909v1_alt, chr17_JH159148v1_alt, chr17_KI270908v1_alt, chr18_KI270912v1_alt, chr18_KI270911v1_alt, chr19_GL949747v2_alt, chr22_KB663609v1_alt, chrX_KI270913v1_alt, chr19_KI270914v1_alt, chr19_KI270915v1_alt, chr19_KI270916v1_alt, chr19_KI270917v1_alt, chr19_KI270918v1_alt, chr19_KI270919v1_alt, chr19_KI270920v1_alt, chr19_KI270921v1_alt, chr19_KI270922v1_alt, chr19_KI270923v1_alt, chr3_KI270924v1_alt, chr4_KI270925v1_alt, chr6_GL000252v2_alt, chr8_KI270926v1_alt, chr11_KI270927v1_alt, chr19_GL949748v2_alt, chr22_KI270928v1_alt, chr19_KI270929v1_alt, chr19_KI270930v1_alt, chr19_KI270931v1_alt, chr19_KI270932v1_alt, chr19_KI270933v1_alt, chr19_GL000209v2_alt, chr3_KI270934v1_alt, chr6_GL000253v2_alt, chr19_GL949749v2_alt, chr3_KI270935v1_alt, chr6_GL000254v2_alt, chr19_GL949750v2_alt, chr3_KI270936v1_alt, chr6_GL000255v2_alt, chr19_GL949751v2_alt, chr3_KI270937v1_alt, chr6_GL000256v2_alt, chr19_GL949752v1_alt, chr6_KI270758v1_alt, chr19_GL949753v2_alt, chr19_KI270938v1_alt, chrEBV]

Did anyone encounter this issue before and solve it ? Or which reference genome you recommend using in BaseRecalibrator for WGS ? Or should I make own Contig file ? If so, how to do ?

Thank you so much !