Entering edit mode
3.5 years ago
panmy2015
•
0
I have a error report like this, --sort-tmpdir bad substitution, not quite sure why. And my code line is ./bin/vcf2bed --sort-tmpdir=${/nird/projects/nird/NS9769K/GWAS_Summstats/} --max-mem=2G All_20170710.vcf > hg19.dbSNP150.bed
, I guess there should be problem at 'sort-tmpdir' part, but I have no idea how to correct it.
Why are you using a full path as a variable? What happens if you just use
--sort-tmpdir=/nird/projects/nird/NS9769K/GWAS_Summstats/
Hi, thank you. Yes exactly I did, but another error is saying something like, cannot find 'convert2bed'. So I wrote as above, lol ...
That is because the program likely needs and can't find
convert2bed
. You will need to add the./bin
whatever directory that is to your$PATH
so the programs in that directory can be found. Something likeexport PATH=$PATH:/full_path_to_bin_in_above_command
.