[phase_reads] opening alignment BAM file... done.
Traceback (most recent call last):
File "pr.py", line 364, in
output_main(args)
File "pr.py", line 334, in output_main
region=args.region)
File "pr.py", line 288, in phase_reads
hapcut_dict = HapCut(hapcut_file).to_dict()
File "/home/yuanwen/Tools/readphaser-master/hapcut.py", line 92, in to_dict
for phased_block in self.blocks():
File "/home/yuanwen/Tools/readphaser-master/hapcut.py", line 77, in blocks
block_line_dict = dict((k, block_entry_formattersk) for k, v in m.groupdict().items())
File "/home/yuanwen/Tools/readphaser-master/hapcut.py", line 77, in
block_line_dict = dict((k, block_entry_formattersk) for k, v in m.groupdict().items())
ValueError: invalid literal for float(): 2.0 MEC11 1.00 4.00 2.00
Hello!
I run into the error when I tried to use readphaser for sorting reads. Please see below for my script and error log information.
I will appreciate your help!
$ python pr.py -u unphased.fq -p phased.fq /home/yuanwen/Phylogeny_project/working_files/output/TA1851_output_haplotype_file /home/yuanwen/Phylogeny_project/working_files/output/TA1851_remove_duplicates_realigned.bam
[phase_reads] opening alignment BAM file... done. Traceback (most recent call last): File "pr.py", line 364, in
output_main(args)
File "pr.py", line 334, in output_main
region=args.region)
File "pr.py", line 288, in phase_reads
hapcut_dict = HapCut(hapcut_file).to_dict()
File "/home/yuanwen/Tools/readphaser-master/hapcut.py", line 92, in to_dict
for phased_block in self.blocks():
File "/home/yuanwen/Tools/readphaser-master/hapcut.py", line 77, in blocks
block_line_dict = dict((k, block_entry_formattersk) for k, v in m.groupdict().items())
File "/home/yuanwen/Tools/readphaser-master/hapcut.py", line 77, in
block_line_dict = dict((k, block_entry_formattersk) for k, v in m.groupdict().items())
ValueError: invalid literal for float(): 2.0 MEC11 1.00 4.00 2.00
Best, Yuanwen