I'd like to phase the SNPs in a vcf file and output consensus files for each haplotype, as suggested in this post:

https://www.biostars.org/p/298635/

I've managed to install beagle in a conda environment:

conda create -n beagle -c conda-forge -c bioconda beagle
conda activate beagle

When I run beagle using this command:

java -Xmx2g -jar "/Users/michaelflower/opt/anaconda3/envs/beagle/share/beagle-5.2_21Apr21.304-0/beagle.jar" gt="$VCF" out="$DIR"/beagle/phased_beagle

I get the error message:

No genetic map is specified: using 1 cM = 1 Mb

The full output of beagle is below. Also the vcf file produced contains no SNPs.

So as suggested here, I downloaded the plink.GRCh37.map.zip map file from here:

wget -qO- http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh37.map.zip | bsdtar -xvf- -C ~/refs/hap/hg19/

The SNPs I'm interested in phasing are on chr4, so I set the map shortcut as follows:

MAP=~/refs/hap/hg19/plink.chr4.GRCh37.map

But when I try and run beagle like this:

java -Xmx2g -jar "/Users/michaelflower/opt/anaconda3/envs/beagle/share/beagle-5.2_21Apr21.304-0/beagle.jar" gt="$VCF" map="$MAP" out="$DIR"/beagle/phased_beagle

I get this error (see full error 2 below):

java.lang.IllegalArgumentException: missing genetic map for chromosome chr4

Ful beagle error 1:

$ java -Xmx2g -jar "/Users/michaelflower/opt/anaconda3/envs/beagle/share/beagle-5.2_21Apr21.304-0/beagle.jar" gt="$VCF" out="$DIR"/beagle/phased_beagle
beagle.21Apr21.304.jar (version 5.2)
Copyright (C) 2014-2021 Brian L. Browning
Enter "java -jar beagle.21Apr21.304.jar" to list command line argument
Start time: 04:44 PM GMT on 21 Nov 2021

Command line: java -Xmx2048m -jar beagle.21Apr21.304.jar
  gt=/Users/michaelflower/Documents/ACL/Research/Projects/HTT ASO/2021.11.20 125Q SNP phasing/gatk/125QiPSC_chr4_HaplotypeCallerPGT.vcf
  out=/Users/michaelflower/Documents/ACL/Research/Projects/HTT ASO/2021.11.20 125Q SNP phasing/beagle/phased_beagle

No genetic map is specified: using 1 cM = 1 Mb

Reference samples:                    0
Study     samples:                    1

Window 1 [chr4:1-39999997]
Reference markers:            2,463,043
Study     markers:            2,463,043
Exception in thread "main" java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: bound must be positive
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:600)
    at java.base/java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:678)
    at java.base/java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:737)
    at java.base/java.util.stream.Nodes.collect(Nodes.java:333)
    at java.base/java.util.stream.ReferencePipeline.evaluateToNode(ReferencePipeline.java:109)
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:545)
    at java.base/java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
    at java.base/java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:517)
    at phase.PbwtPhaser.pbwtPhasers(PbwtPhaser.java:183)
    at phase.PbwtPhaser.initPhase(PbwtPhaser.java:72)
    at phase.EstPhase.<init>(EstPhase.java:46)
    at phase.PhaseData.<init>(PhaseData.java:52)
    at main.Main.phaseStage1Variants(Main.java:188)
    at main.Main.phaseTarg(Main.java:181)
    at main.Main.phaseAndImpute(Main.java:171)
    at main.Main.main(Main.java:126)
Caused by: java.lang.IllegalArgumentException: bound must be positive
    at java.base/java.util.Random.nextInt(Random.java:388)
    at phase.RevPbwtPhaser.imputeAllele(RevPbwtPhaser.java:128)
    at phase.RevPbwtPhaser.finishPhasing(RevPbwtPhaser.java:118)
    at phase.RevPbwtPhaser.phase(RevPbwtPhaser.java:94)
    at phase.RevPbwtPhaser.<init>(RevPbwtPhaser.java:75)
    at phase.FwdPbwtPhaser.phase(FwdPbwtPhaser.java:86)
    at phase.FwdPbwtPhaser.<init>(FwdPbwtPhaser.java:79)
    at phase.PbwtPhaser.<init>(PbwtPhaser.java:59)
    at phase.PbwtPhaser.lambda$pbwtPhasers$1(PbwtPhaser.java:181)
    at java.base/java.util.stream.IntPipeline$1$1.accept(IntPipeline.java:180)
    at java.base/java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:104)
    at java.base/java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:699)
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
    at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
    at java.base/java.util.stream.Nodes$SizedCollectorTask.compute(Nodes.java:1886)
    at java.base/java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:746)
    at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290)
    at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020)
    at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656)
    at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594)
    at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183)

Full beagle error 2:

$ java -Xmx2g -jar "/Users/michaelflower/opt/anaconda3/envs/beagle/share/beagle-5.2_21Apr21.304-0/beagle.jar" gt="$VCF" map="$MAP" out="$DIR"/beagle/phased_beagle
beagle.21Apr21.304.jar (version 5.2)
Copyright (C) 2014-2021 Brian L. Browning
Enter "java -jar beagle.21Apr21.304.jar" to list command line argument
Start time: 04:49 PM GMT on 21 Nov 2021

Command line: java -Xmx2048m -jar beagle.21Apr21.304.jar
  gt=/Users/michaelflower/Documents/ACL/Research/Projects/HTT ASO/2021.11.20 125Q SNP phasing/gatk/125QiPSC_chr4_HaplotypeCallerPGT.vcf
  map=/Users/michaelflower/refs/hap/hg19/plink.chr4.GRCh37.map
  out=/Users/michaelflower/Documents/ACL/Research/Projects/HTT ASO/2021.11.20 125Q SNP phasing/beagle/phased_beagle
java.lang.IllegalArgumentException: missing genetic map for chromosome chr4
    at vcf.PlinkGenMap.checkChromIndex(PlinkGenMap.java:213)
    at vcf.PlinkGenMap.genPos(PlinkGenMap.java:311)
    at vcf.PlinkGenMap.genPos(PlinkGenMap.java:306)
    at vcf.WindowIt$Reader.run(WindowIt.java:255)
    at java.base/java.lang.Thread.run(Thread.java:834)