Closed yjx1217 closed 3 years ago
Dear @yjx1217,
Thanks for using Circle-Map. I have never seen that error. Based on the traceback, it seems to be on the bedtools/pybedtools side. Which version of bedtools/pybedtools are you using?
best,
Inigo
Dear @iprada
I figured out the problem. It was caused by the fact that the bedtools binaries were not in my $PATH. Only install bedtools with conda is not enough.
Best, Jia-Xing
Dear Jia-Xing,
Great to hear! Happy circle hunting
I am closing this issue. Feel free to open a new one if you have more questions
best,
Inigo
Hello,
I installed Circle-Map via conda and encountered the following problem:
I checked the file "
/public/jxyue/Projects/ecDNA/build/circlemap_conda_env/lib/python3.7/site-packages/pybedtools/bedtool.py
" and clearlysortBed
has been defined in it. So I don't know why this problem occurs. Also, this problem persists even after I explicitly installed latest version of bedtools and pybedtools via conda.Thanks in advance.
Best, Jia-Xing