empty output vcf file

[KamilSJaron]

Hello, I installed platypus according the README file, but when run it, it prints a lot of warrnings (pasted in the end of the issue) and what worse, it creates an empty vcf file.

I tried a test run with minimal number of arguments :

samtools faidx $REF
Platypus.py callVariants --bamFiles=$BAM --output=test.vcf --refFile=$REF

The reference is softmasked and it has many gaps (although I tried non-masked reference and it changes nothing). Have I done something wrong or the problem is not on my side? Notably variant 5_Tge_b3v06_scaf000001:36003 was also called by GATK, it seems that it is actually calling genotypes as it should, but instead of writing result to file it's complaining about unknown genome symbols.

2018-03-13 13:24:14,764 - INFO - Processing region 5_Tge_b3v06_scaf000001:0-100000. (Only printing this message every 10 regions of size 100000)
Traceback (most recent call last):
  File "cython/vcfutils.pyx", line 817, in vcfutils.trimLeftPadding
KeyError: 0
Exception KeyError: (0,) in 'vcfutils.outputCallToVCF' ignored
2018-03-13 13:24:14,812 - WARNING - Skipping output for call 5_Tge_b3v06_scaf000001:36003 {'GT': [['1', '/', '1']], 'GQ': [27], 'GOF': [3], 'NR': [10], 'GL': [-33.3, -2.71, 0.0],
Traceback (most recent call last):
  File "cython/vcfutils.pyx", line 817, in vcfutils.trimLeftPadding
KeyError: 0
Exception KeyError: (0,) in 'vcfutils.outputCallToVCF' ignored
2018-03-13 13:24:14,813 - WARNING - Skipping output for call 5_Tge_b3v06_scaf000001:61655 {'GT': [['0', '/', '1']], 'GQ': [47], 'GOF': [7], 'NR': [11], 'GL': [-4.69, 0.0, -21.89]
2018-03-13 13:24:14,813 - WARNING - Skipping output for call 5_Tge_b3v06_scaf000001:68829 {'GT': [['1', '/', '1']], 'GQ': [18], 'GOF': [3], 'NR': [7], 'GL': [-25.5, -1.81, 0.0], 
Traceback (most recent call last):
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