BEDOPS --sort-tmpdir bad substitution
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19 months 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.

software error snp GWAS rsID • 392 views
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Why are you using a full path as a variable? What happens if you just use --sort-tmpdir=/nird/projects/nird/NS9769K/GWAS_Summstats/

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Hi, thank you. Yes exactly I did, but another error is saying something like, cannot find 'convert2bed'. So I wrote as above, lol ...

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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 $PATH so the programs in that directory can be found. Something like export PATH=$PATH:/full_path_to_bin_in_above_command.

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