BEDOPS sort-bed Unable to access --tempdir error

Question

[eford.dna]

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.

Answer 1

[Alex Reynolds]

Use --tmpdir, not --tempdir, i.e.:

[ethanf@cpebrazor mClevels]$ sort-bed --tmpdir /home/ethanf/temp test.bed > test_sorted.bed

[eford.dna]

opps. O.k. I'm a little stupid. Thanks!!

[panmy2015]

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