QTLplots have missing chromosomes

[StephenSiazon]

Hello! I am having problems with generating my QTLplot.
 
I have run QTLseq for my sequences and the initial QTLplot from this run has does not have a smooth red line. So I decided to run QTLplot using the vcf file from my QTLseq run using the code below:
 
qtlplot -v qtlseq.vcf.gz
        -o bsa_plot
        -n1 10
        -n2 10
        -w 2000
        -s 100

Here’s the picture:

I tried changing the -w to 1000 and the chromosomes are okay. But running the same -w 1000 for the second time, chromosomes 1-5 are lost (picture below). Same with when I run -w 3000, first one is okay and the rerun has missing chromosomes.

-w 1000 rerun

-w 3000 rerun

I don't understand why. Hope you could help. Thank you very much! :)

[YuSugihara]

Thank you very much for reporting this error.

I have never seen this kind of error before.

I will leave this thread open so that other people can add more information.

If someone faces the same error, please provide the VCF with me.