I am attempting to liftover coordinates of several files in BigWig format from mm10 to mm9 using CrossMap. Below is an example of the output I am receiving with any of my files.
python ~/python-2.7.9/bin/CrossMap.py bigwig mm10ToMm9.over.chain.gz KO_merged.bw KO_mm9 @ 2017-03-13 15:16:16: Read chain_file: mm10ToMm9.over.chain.gz @ 2017-03-13 15:16:18: Liftover bigwig file: KO_merged.bw ==> KO_mm9.bgr @ 2017-03-13 15:16:18: Merging overlapped entries in bedGraph file ... @ 2017-03-13 15:16:18: Sorting bedGraph file:KO_mm9.bgr Traceback (most recent call last): File "/home/kasowitz/python-2.7.9/bin/CrossMap.py", line 1636, in <module> crossmap_wig_file(mapTree, in_file, out_file, sourceChromSizes, targetChromSizes, in_format = 'bigwig') File "/home/kasowitz/python-2.7.9/bin/CrossMap.py", line 1445, in crossmap_wig_file for (chr, start, end, score) in bgrMerge.merge(out_prefix + '.bgr'): File "/home/kasowitz/python-2.7.9/lib/python2.7/site-packages/cmmodule/bgrMerge.py", line 95, in merge (last_chr, last_start, last_end, last_score) = lines[-1].split() IndexError: list index out of range
The error looks like it is resulting from receiving an empty bgr file, but I am not sure whats happening to cause the liftover to fail before this step.
Thanks for any advice