Question: 'Error: Unable to open file test1.bed. Exiting' , Bedtools help
0
gravatar for reece
7 months ago by
reece0
reece0 wrote:

Hi everyone,

I am very new to all of this so I apologise for any simple mistakes. Today I have been trying to merge 2 files at 500bp using Bedtools. I have both files in the format of:

chr1    812283  812293
chr1    812566  812576
chr1    811236  811246

As far as I'm aware each column is separated by tabs, and I have tried using test .bed files with only a few rows. When using: bedtools merge -i test1.bed test2.bed -d 500 < sorted.bed or even just trying to access the bed files using a different command (bedtools merge -i test1.bed), I am receiving 'Error: Unable to open the test1.bed. exiting.'

Does anyone know why this could be happening? Any help is greatly appreciated.

mergebed .bed bedtools • 538 views
ADD COMMENTlink modified 7 months ago by ATpoint19k • written 7 months ago by reece0
1
Bedtools merge -i test1.bed test2.bed -d 500 < sorted.bed

This cannot work as bedtools merge expect exact one bed file as input. You have three (test1.bed, test2.bed and as a stream from sorted.bed

'Error: Unable to open the test1.bed. exiting

This message appears also if bedtools cannot find the files. So check if you are in the correct folder from where you start bedtools merge. The correct syntax should be $ bedtools merge -i test1.bed -d 500.

fin swimmer

ADD REPLYlink written 7 months ago by finswimmer11k

I didn't realise this, I will give it a go. Thank you!

Edit - Unfortunately still no joy, grateful for the help though

ADD REPLYlink modified 7 months ago • written 7 months ago by reece0

Most likely either there's a typo in the command (you mistyped the file name) or the user you're running bedtools with doesn't have read permission.

ADD REPLYlink written 7 months ago by Devon Ryan91k

Hi, I've just checked and I believe the input to be correct and I am running as administrator. Do I need to store the .bed file anywhere specifically for it to work? Thank you for the feedback!

ADD REPLYlink written 7 months ago by reece0

Either you specify the full path to the bed file, or you make sure it's in your current working directory.

ADD REPLYlink written 7 months ago by WouterDeCoster40k
0
gravatar for ATpoint
7 months ago by
ATpoint19k
Germany
ATpoint19k wrote:

Bedtools complaining about files is 99.9% the case when the delimiter is not tab but something else like tab-whitespace, whitespace-tab or anything which is not exactly tab. Given your files were truely tab-delimited:

cat test1.bed test2.bed (...) testn.bed | sort k1,1 -k2,2n | bedtools merge -i - -d 500 > merged.bed
ADD COMMENTlink modified 7 months ago • written 7 months ago by ATpoint19k
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