AssertionError while using generate_multihetsep.py

[Luker121]

Hi, I am trying to try following code:

python3 generate_multihetsep.py --mask=final.mask.bed.gz \
  final.vcf.gz > final.msmc

My both files only contain one individual with several chromosomes. And obviously it stops directly when the first chromosome ends. It stops with this error:

Traceback (most recent call last):
  File "/mnt/nvme1n1p1/Arabis_data/VCF/msmc-tools-master/generate_multihetsep.py", line 226, in <module>
    if mergedMask.getVal(snp_pos):
  File "/mnt/nvme1n1p1/Arabis_data/VCF/msmc-tools-master/generate_multihetsep.py", line 51, in getVal
    return all((m.getVal(pos) for m in self.maskIterators))
  File "/mnt/nvme1n1p1/Arabis_data/VCF/msmc-tools-master/generate_multihetsep.py", line 51, in <genexpr>
    return all((m.getVal(pos) for m in self.maskIterators))
  File "/mnt/nvme1n1p1/Arabis_data/VCF/msmc-tools-master/generate_multihetsep.py", line 35, in getVal
    assert pos >= self.lastPos
AssertionError

Do you know what happened here?

[stschiff]

I think you need to run every chromosome separately.