Hi,

I'm trying to get a mappability wig file by running generateMap.pl from hmmcopy_utils. However, I'm getting a message which states that,

Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.

What I did,

HMMCOPY_DIR=~/mysofts/hmmcopy_utils-master
REF=~/RefHu/btindx/GRCh38_chr.fa
index=~/RefHu/btindx

First, I created an index file using Bowtie,

time srun bowtie-build --threads 8 -f $REF $index/GRCh38_chr

time srun $HMMCOPY_DIR/util/mappability/generateMap.pl -w 10000 ${REF} --index $index/GRCh38_chr -o $index/GRCh38_chr.fa.map.bw  

Again I used -b for creating index

time srun $HMMCOPY_DIR/util/mappability/generateMap.pl  -b ${REF}  -o $index/GRCh38_chr.fa.map.bw

time srun $HMMCOPY_DIR/util/mappability/generateMap.pl  ${REF}  -o $index/GRCh38_chr.fa.map.bw

I also tried using -i and -x for index files but not getting the desired output.

It will be a great help if someone please correct me.