I'm trying to use bedtools to extract regions of a genome based on coordinates in an annotation file. I keep getting error messages that Line 15 of my BED file has a start/end position where start > end,
Error: malformed GFF entry at line 15. Coordinate detected that is < 1. Exiting. srun: error: cn68: task 0: Exited with exit code 1
but the file looks like this (line 15):
JAJFZI010040149.1 Complete 1671.3 0 4952 - 2371at8457 1421 https://www.orthodb.org/v10?query=2371at8457 Upstream transcription factor family member 3
BED files are zero-based I believe, but it's reading it as a GFF file. It has a .BED file extension so I'm not sure why it's detecting a GFF...