pybedtools intersect error

[katelynmullen]

Hi, I'm trying to intersect 2 bed files and getting the following error:

BEDToolsError:
Command was:

bedtools intersect -a /tmp/pybedtools.5zkx6wsw.tmp -loj -b /tmp/pybedtools.wfouqili.tmp

Error message was:
***** ERROR: illegal number ".". Exiting...

I checked both of my input files, and I do not see the string "." in either of my input files. Attaching both files for reference.
pybedtools_troubleshooting.txt
best.bbc.ucn.txt

[daler]

This looks like a BEDTools error rather than pybedtools, but do you get the same error if you remove the header from these files?

[katelynmullen]

I think the error was due to MT chromosome data being included.