Error: could not parse the input VCF

[wangzhx36]

Hi, Dr. Song
I successfully generated alignment.maf using AnchorWave and converted it into a BAM file using the provided script. However, when I attempted to convert the BAM file to a VCF file using bcftools, I noticed that the output VCF file only contains partial variant information from the first chromosome. Below are my scripts and error messages. I'm not sure what the reason is, and I hope to get your assistance.

script:
maf2bam=/data/software/AnchorWave-1.2.1/scripts/maf-convert
sP1=/data2/projects/zwang/macropodus_compare/synteny/pseudogenome/Anchorwave/MOP/
sP2=/data2/projects/zwang/macropodus_compare/synteny/pseudogenome/Anchorwave/MOP/Betta_splendens
python2 $maf2bam sam $sP2/alignment.maf | sed 's/[0-9]+H//g'
| samtools view -O BAM --reference $sP1/mopscf1-23.fa - | samtools sort - > ./Bspl.bam
samtools index $sP2/Bspl.bam
bcftools mpileup -Ou -q 30 -f $sP1/mopscf1-23.fa $sP2/Bspl.cram | bcftools call -m -Ou | bcftools norm -f $sP1/mopscf1-23.fa -Oz -o Bspl.g.vcf.gz

error:
[mpileup] 1 samples in 1 input files
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] maximum number of reads per input file set to -d 250
Error: could not parse the input VCF
Lines total/split/realigned/skipped: 11397420/0/0/0

[baoxingsong]

We never succeeded in calling variants from AnchorWave alignments using any short-reads mapping variant calling pipeline.
Please try this pipeline https://github.com/baoxingsong/AnchorWave/blob/master/doc/GATK.md