search

daler / pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
http://daler.github.io/pybedtools
Other
297 stars 103 forks source link

pybedtools intersect error #389

Closed katelynmullen closed 1 year ago

katelynmullen commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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