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different line length in sequence

Error using samtools mpileup

samtools mpileup -uf REFERENCE.fasta SAMPLE_sorted.bam

  [fai_load] build FASTA index.
  [fai_build_core] different line length in sequence 'REFERENCE'.


Problem

The lines in the reference sequence fasta-file does not have all the same length.

Solutions


(1) Edit manually
Convert the reference sequence into a single line by removing all newlines "\n".

(2) Picard tool
# use Picard to normalize the reference fasta file
java -jar picard.jar NormalizeFasta  I=REFERENCE.fasta O=normalized_REFERENCE.fasta