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ccgd-profile / BreaKmer

A method to identify structural variation from sequencing data in target regions
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Issue using BreaKmer #3

Closed vonholdt closed 9 years ago

vonholdt commented 9 years ago

Hi-

I mapped my paired end data with BWA and now would like to use BreaKmer, here is the command I'm running:

$ python <path/to/BreaKmer-master/>breakmer.py <path/to/configure/>breakmer.cfg

Traceback (most recent call last): File "<path/to/>BreaKmer-master/breakmer.py", line 103, in r = runner(config_d) File "<path/to/>BreaKmer-master/sv_processor.py", line 100, in init self.params = params(config_d) File "<path/to/>BreaKmer-master/utils.py", line 705, in init self.set_params() File "<path/to/>BreaKmer-master/utils.py", line 792, in set_params self.set_targets(self.opts['gene_list']) File "<path/to/>BreaKmer-master/utils.py", line 769, in set_targets self.targets[name.upper()].append((chrm,int(bp1),int(bp2),name,feature)) ValueError: invalid literal for int() with base 10: 'M\xa5^\xb9\x97\xa8q\xd7]v1\x9a\xb7\x98\xf7>\xbd'

Can you provide advice for how I should proceed? Thank you!

ryanabo commented 9 years ago

This was an issue with specifying the bam file as the bed file in the configuration. This has been resolved.