weng-lab/TEMP2

error on test

Closed this issue · 3 comments

piosierra commented

Hello,
running the initial test with TEMP2 I get the following 2 errors:

***** ERROR: Requested column 2, but database file - only has fields 1 - 0.
/home/pio/projects/TEMP2/bin/TEMP2_insertion.sh: line 354: intersectBed: command not found
/home/pio/projects/TEMP2/bin/TEMP2_insertion.sh: line 360: bedToBigBed: command not found

Initially it correctly detects bedtools Version: v2.29.2
Should those tools be included with that version?

tianxiongbb commented

Hi Pio,
Looks like the Bedtools integrated with TEMP2 is conflicted with your version. Re-install bedtools should be able to solve this problem. "bedToBigBed" will be integrated with the later version of TEMP2. but for now you can get it from kent tools.

jdaron commented

Got the same issue, you can a compiled version of bedToBigBed here which is much simpler to get than using kent tools.
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed

tianxiongbb commented

The compiled version v2.9 of bedToBigBed has been integrated into TEMP2.