bedtools getfasta chromosome not found

Question

[from the mountains]

I am getting a curious error when using bedtools to extract sequences from a reference fasta and a gff3 file.

I enter: /gpfs/gwngs/tools/bedtools2/bin/bedtools getfasta -s -fullHeader -fi ref.fa -bed ref.gff3

And I get a million lines saying, for example:

WARNING. chromosome (CP014594) was not found in the FASTA file. Skipping.

The thing is I grepped the fasta header for this chromosome and got:

>CP014594

There are no white spaces in the line. what's going on? i have tried inserting the prefix 'chr' into both files, and inserting a space between > and the chromosome name for the fasta file.

[Pierre Lindenbaum]

what is the output of

file ref.fa

?

[from the mountains]

ref.fa: ASCII text, with CRLF line terminators

[from the mountains]

00000000 54 47 47 54 47 47 41 54 47 43 54 47 0a 3e 43 50 |TGGTGGATGCTG.>CP| 00000010 30 31 34 35 39 34 0a 41 43 41 47 43 43 47 41 43 |014594.ACAGCCGAC| 00000020 41 41 43 43 43 41 41 43 41 54 47 43 43 41 41 41 |AACCCAACATGCCAAA| 00000030 43 54 43 43 41 47 41 43 54 43 47 41 41 43 43 54 |CTCCAGACTCGAACCT| 00000040 47 47 47 41 43 54 43 43 41 41 47 41 41 54 43 41 |GGGACTCCAAGAATCA| 00000050 41 41 43 0a |AAC.| 00000054

and

00000000 43 50 30 31 34 35 39 34 09 2e 09 67 65 6e 65 09 |CP014594...gene.| 00000010 31 30 34 36 31 09 31 34 36 35 38 09 2e 09 2b 09 |10461.14658...+.| 00000020 2e 09 4e 61 6d 65 3d 41 54 59 34 30 5f 72 52 4e |..Name=ATY40_rRN| 00000030 41 63 53 43 37 73 31 30 34 36 31 65 31 34 36 35 |AcSC7s10461e1465| 00000040 38 3b 6c 6f 63 75 73 5f 74 61 67 3d 22 41 54 59 |8;locus_tag="ATY| 00000050 34 30 5f 72 52 4e 41 63 53 43 37 73 31 30 34 36 |40_rRNAcSC7s1046| 00000060 31 65 31 34 36 35 38 22 0a |1e14658".| 00000069

Answer 1

[Pierre Lindenbaum]

your fasta is a windows file . https://en.wikipedia.org/wiki/Newline#Frequent_issues

remove the invisible '\r' with

tr -d '\r' < ref.fa > tmp.fa
mv tmp.fa ref.fa

and try again.

[cmdcolin]

alternative command line fix: use the dos2unix command (dos2unix yourfile.fa)

[from the mountains]

good catch! unfortunately, it still doesn't work, in spite of both files now being ASCII text with no \r .

[Pierre Lindenbaum]

hum... output of

grep CP014594 -B 1 -A 1 ref.fa | hexdump -C ?

and

grep -w CP014594 ref.gff3 | tail -1  | hexdump -C ?

[from the mountains]

for some reason my answer posted above, i'm not sure how to move it:

00000000 54 47 47 54 47 47 41 54 47 43 54 47 0a 3e 43 50 |TGGTGGATGCTG.>CP| 00000010 30 31 34 35 39 34 0a 41 43 41 47 43 43 47 41 43 |014594.ACAGCCGAC| 00000020 41 41 43 43 43 41 41 43 41 54 47 43 43 41 41 41 |AACCCAACATGCCAAA| 00000030 43 54 43 43 41 47 41 43 54 43 47 41 41 43 43 54 |CTCCAGACTCGAACCT| 00000040 47 47 47 41 43 54 43 43 41 41 47 41 41 54 43 41 |GGGACTCCAAGAATCA| 00000050 41 41 43 0a

and

00000000 43 50 30 31 34 35 39 34 09 2e 09 67 65 6e 65 09 |CP014594...gene.| 00000010 31 30 34 36 31 09 31 34 36 35 38 09 2e 09 2b 09 |10461.14658...+.| 00000020 2e 09 4e 61 6d 65 3d 41 54 59 34 30 5f 72 52 4e |..Name=ATY40_rRN| 00000030 41 63 53 43 37 73 31 30 34 36 31 65 31 34 36 35 |AcSC7s10461e1465| 00000040 38 3b 6c 6f 63 75 73 5f 74 61 67 3d 22 41 54 59 |8;locus_tag="ATY| 00000050 34 30 5f 72 52 4e 41 63 53 43 37 73 31 30 34 36 |40_rRNAcSC7s1046| 00000060 31 65 31 34 36 35 38 22 0a |1e14658".| 00000069

it looks like the characters are the same. i tried downloading another copy of bedtools (didn't work), but new copies of the ref.fa and ref.gff have worked. not sure why...maybe the error is misleading? thank you for your help.