'Chromosome was not found in the FASTA file' error

[Artem Nemudryi]

Hey all,

I am trying to use getfasta (bedtools v2.30.0) to extract sequences from my reference using the .bed file and getting the error:

WARNING. chromosome (ref105621_1k) was not found in the FASTA file. Skipping.

I know that this error pops up if the header in the .FASTA file does not match the chromosome name in the .BED file. But mine do match. I would even copy chromosome name from .bed and paste it into .fasta. Still get the error.

My .fasta file:

>ref105621_1k

gtaactgtcagaccaagtttactcatatatactttagattgatttaaaacttcatttttaatttaaaaggatctaggtgaagatcctttttga......

My .bed file:

ref105621_1k 11 169 6ea6475a-cf32-4b20-b6e6-3ce7c2db9d8d 0 -

ref105621_1k 11 499 6317c1cd-323b-4e2a-b4e3-3aabfd85347e 0 -

ref105621_1k 13 351 7a883b22-ad17-4944-a880-ac02c7905f6d 0 -

........

Any thoughts on how to get this working? Thanks in advance!