BCF merge error

export THREADS=40
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR103/003/ERR1035223/ERR1035223_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR103/003/ERR1035223/ERR1035223_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_2.fastq.gz

wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz
gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz
mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa

bwa index H37Rv.fa

bwa mem -t $THREADS -R '@RG\tID:ERR1664619\tSM:ERR1664619\tPL:Illumina' H37Rv.fa ERR1664619_1.fastq.gz ERR1664619_2.fastq.gz | samtools view -b -@ $THREADS - | samtools sort -@ $THREADS -o ERR1664619.bam -
bwa mem -t $THREADS -R '@RG\tID:ERR1035223\tSM:ERR1035223\tPL:Illumina' H37Rv.fa ERR1035223_1.fastq.gz ERR1035223_2.fastq.gz | samtools view -b -@ $THREADS - | samtools sort -@ $THREADS -o ERR1035223.bam -

samtools mpileup -ugf H37Rv.fa ERR1664619.bam -t DP | bcftools call --threads $THREADS --ploidy 1 -g 10 -m -O b -o ERR1664619.bcf && bcftools index ERR1664619.bcf
samtools mpileup -ugf H37Rv.fa ERR1035223.bam -t DP | bcftools call --threads $THREADS --ploidy 1 -g 10 -m -O b -o ERR1035223.bcf && bcftools index ERR1035223.bcf

### Merging from BCF 
# check output
bcftools merge -g H37Rv.fa ERR1664619.bcf ERR1035223.bcf | awk '$2==1'

### Merging from VCF 
bcftools view ERR1664619.bcf -o ERR1664619.vcf.gz -O z && bcftools index ERR1664619.vcf.gz
bcftools view ERR1035223.bcf -o ERR1035223.vcf.gz -O z && bcftools index ERR1035223.vcf.gz

# check output
bcftools merge -g H37Rv.fa ERR1664619.vcf.gz ERR1035223.vcf.gz | awk '$2==1'

### Merging from back converted BCF 
bcftools view ERR1664619.bcf -o ERR1664619.vcf -O v && bcftools index -f ERR1664619.bcf
bcftools view ERR1035223.bcf -o ERR1035223.vcf -O v && bcftools index -f ERR1035223.bcf

# check output
bcftools merge -g H37Rv.fa ERR1664619.vcf.gz ERR1035223.vcf.gz | awk '$2==1'