bdg2bw

#!/bin/bash

# check commands: slopBed, bedGraphToBigWig and bedClip

which slopBed &>/dev/null || which bedtools &>/dev/null || { echo "slopBed/bedtools not found! Download bedTools: <http://code.google.com/p/bedtools/>"; exit 1; }
which bedGraphToBigWig &>/dev/null || { echo "bedGraphToBigWig not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }
which bedClip &>/dev/null || { echo "bedClip not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }

# end of checking

if [ $# -lt 2 ];then
    echo "Need 2 parameters! <bedgraph> <chrom info>"
    exit
fi

F=$1
G=$2

slopBed -i ${F} -g ${G} -b 0 | bedClip stdin ${G} ${F}.clip

bedGraphToBigWig ${F}.clip ${G} ${F/bdg/bw}

rm -f ${F}.clip

Hi, I'm using bdg2bw and I'm getting this error:

* Input error: Chromosome chrX doesn't present in the .genome file. *
needLargeMem: trying to allocate 0 bytes (limit: 17179869184)

Previously the error was for chrY. I removed all of the chrY entries in the bdg file and go this. I presume if I remove chrX the error will be a different chromosome. If the notion is that there are no chrY or X or whichever chromosome is not present in my genome file is ridiculous. Of course they are (or I couldn't have removed them!) I've used bdg2bw countless times and never had an error. I get no unusual errors after alignment (either bowtie or bowtie2) or after peak calling (either MACS or MACS2). I'm at my wits end. Any suggestions?