I'm attempting to use Connor to deduplicate some bam files in my variant calling pipeline, but so far whenever I attempt to run Connor I get the following error message:
2017-07-17 10:32:28|ERROR|An unexpected error occurred 2017-07-17 10:32:28|ERROR|Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/connor/connor.py", line 498, in main command_validator.preflight(args, log) File "/usr/local/lib/python2.7/dist-packages/connor/command_validator.py", line 190, in preflight validate(args, log) File "/usr/local/lib/python2.7/dist-packages/connor/command_validator.py", line 76, in _check_input_bam_valid bamfile = samtools.alignment_file(args.input_bam, 'rb') File "/usr/local/lib/python2.7/dist-packages/connor/samtools.py", line 527, in alignment_file return pysam.AlignmentFile(filename, mode, template) AttributeError: 'module' object has no attribute 'AlignmentFile'
I installed Connor using pip, and have since tried updating pysam (which in turn required installation of liblzma-dev via apt-get), but I'm still getting the same error.
I've also tried using sorted, indexed bam files but that doesn't help either.
If anyone has any suggestions it would be much appreciated.