Second BEDOPS sort-bed question of the morning.
I'm getting the below error when trying to sort a bed file with sort-bed:
[ethanf@cpebrazor mClevels]$ sort-bed --tempdir /home/ethanf/temp test.bed > test_sorted.bed
Unable to access --tempdir
[ethanf@cpebrazor mClevels]$ sort-bed --tempdir $PWD test.bed > test_sorted.bed
Unable to access --tempdir
[ethanf@cpebrazor mClevels]$ sort-bed test.bed > test_sorted.bed
[ethanf@cpebrazor mClevels]$ export TMPDIR=/home/ethanf/temp
[ethanf@cpebrazor mClevels]$ sort-bed test.bed > test_sorted.bed
[ethanf@cpebrazor mClevels]$
Could it be a permissions problem? I have full access to the directories I tried.
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written
by
eford.dna •
Use --tmpdir, not --tempdir, i.e.:
[ethanf@cpebrazor mClevels]$ sort-bed --tmpdir /home/ethanf/temp test.bed > test_sorted.bed
opps. O.k. I'm a little stupid. Thanks!!
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written
by
eford.dna •
Hi,dear Alex. I met a same problem, and when I wrote as .
/bin/vcf2bed \
--sort-tmpdir=${/nird/projects/nird/NS9769K/GWAS_Summstats/} --max-mem=2G All_20170710.vcf > hg19.dbSNP150.bed
the error is saying --sort-tmpdir bad substitution, but if I change to --sort-tmpdir=/nird/projects/nird/NS9769K/GWAS_Summstats/, another error will be cannot find 'convert2bed', could you help me ... many thanks
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written
by
panmy2015 •
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