ifishlin / hahap Goto Github PK

=== Start HAHap phasing ===
Parameters: Minimum mapping quality = 0
Parameters: Threshold of low coverage = Median
Parameters: Minimum junction number = 4
Parameters: Likelihood of P1 and P2 = 0.49

=== Read Heterozygous Data ===
Traceback (most recent call last):
File "./bin/HAHap", line 9, in
main()
File "/home/dhwani/Documents/softwares/HAHap/HAHap/main.py", line 73, in main
module.main(args)
File "/home/dhwani/Documents/softwares/HAHap/HAHap/phase.py", line 56, in main
var_chrom_dict = split_vcf_by_chrom(args.variant_file)
File "/home/dhwani/Documents/softwares/HAHap/HAHap/vcf.py", line 42, in split_vcf_by_chrom
for line in variants_vcf:
File "/home/dhwani/miniconda3/lib/python3.6/codecs.py", line 321, 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

This was the command line used for running the HAHap tool:-
python HAHap phase HG002_heter.vcf HG002.hs37d5.2x250.bam phased.vcf

This is the error i got
=== Build Connected Component ===
Traceback (most recent call last):
File "HAHap", line 9, in
main()
File "/home/dhwani/Documents/softwares/HAHap/HAHap/main.py", line 73, in main
module.main(args)
File "/home/dhwani/Documents/softwares/HAHap/HAHap/phase.py", line 63, in main
connected_component = blocks_main(args, str(chrom), var_loc, timer)
File "/home/dhwani/Documents/softwares/HAHap/HAHap/blocks.py", line 136, in main
samfile = pysam.AlignmentFile(args.bam_file, "rb")
File "pysam/libcalignmentfile.pyx", line 444, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 629, in pysam.libcalignmentfile.AlignmentFile._open
File "pysam/libchtslib.pyx", line 364, in pysam.libchtslib.HTSFile.check_truncation
OSError: no BGZF EOF marker; file may be truncated