error in tools/generate_multihetsep.py

[cxue]

I got an error in tools/generate_multihetsep.py:
[cxue@sug-esxa-login1 msmc]$ python3 msmc-master/tools/generate_multihetsep.py --mask vcfs/9D4.outmask.2.txt.gz vcfs/final.9D4.2.vcf.gz
generating msmc input file with 2 haplotypes
adding mask: vcfs/9D4.outmask.2.txt.gz
Traceback (most recent call last):
File "msmc-master/tools/generate_multihetsep.py", line 159, in
maskIterators.append(MaskIterator(f))
File "msmc-master/tools/generate_multihetsep.py", line 19, in init
self.readLine()
File "msmc-master/tools/generate_multihetsep.py", line 23, in readLine
line = next(self.file)
File "/hgsc_software/python/python-3.4.0/lib/python3.4/codecs.py", line 313, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

Because mask file is a binary file, I don't know how to go on. Thanks.

[stschiff]

Hi,

are you sure the mask and the VCF really gzip-compressed? Which version of python are you using? You need python3.4 for this to work.

Stephan

Am 16.10.2014 um 14:36 schrieb cxue notifications@github.com:

I got an error in tools/generate_multihetsep.py:
[cxue@sug-esxa-login1 msmc]$ python3 msmc-master/tools/generate_multihetsep.py --mask vcfs/9D4.outmask.2.txt.gz vcfs/final.9D4.2.vcf.gz
generating msmc input file with 2 haplotypes
adding mask: vcfs/9D4.outmask.2.txt.gz
Traceback (most recent call last):
File "msmc-master/tools/generate_multihetsep.py", line 159, in
maskIterators.append(MaskIterator(f))
File "msmc-master/tools/generate_multihetsep.py", line 19, in init
self.readLine()
File "msmc-master/tools/generate_multihetsep.py", line 23, in readLine
line = next(self.file)
File "/hgsc_software/python/python-3.4.0/lib/python3.4/codecs.py", line 313, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

Because mask file is a binary file, I don't know how to go on. Thanks.

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