Bedtools problem : It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited

Question

[Tomm]

I am trying to run bedtools on my tab-delimited file but it still show me an error : It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited?.

The command I run:

bedtools getfasta -fi fasta.fa -bed list.bed -fo results

my BED file looks like -->

scaffold_1000       9060  9912
scaffold_101084   600   2116
scaffold_101084   750   2330
scaffold_101084   800   2200
scaffold_101084   800   2300

What should I do next?

[michael.ante]

Hi Tomm,

Check your bed file with sed -n 'l' there you'll see all control characters.

Was the original file made in Windows? If so try dos2unix.

Cheers,

Michael

Answer 1

[rthapa]

You can try removing the extra space using;

sed 's/[[:space:]]*$//' input.bed > output.bed

[Tomm]

Thank you for commenting , it didn't work .. what else you think i should do ?

[rthapa]

Could you try converting your text file to bed file using,

awk -F"[:-]" 'BEGIN{ OFS="\t"; }{ print $1, $2, $3;}' bed.txt > bed.bed

and then removing the space,

sed 's/[[:space:]]*$//' input.bed > output.bed

[ATpoint]

How did you produce that BED (including code)?

Also try tr -d " " < your.bed > new.bed

[Tomm]

this command just smashing the three columns together , didn't work also. I just did it in vim , and then just used awk command .

[ATpoint]

There you have your problem. If your file was tab-delimited the result would be

tr -d " " < foo.bed 
chr1    1   10

as the command only removes whitespaces but not tabs. This means your file is whitespace- rather than tab-delimited.

What you can also try is:

awk 'OFS=" " {print $1"\t", $2"\t", $3}' your.bed | tr -d " "

This will first make sure that there are any tabs between the columns and then remove all whitespaces. If this does not work, tell how the BED was generated.

Answer 2

[Michael]

I ran into this issue. It was caused by the FASTA data being included in the GFF3 file I was working with. I truncated the file starting at the line that begun "##FASTA".

See: https://github.com/arq5x/bedtools2/issues/235