Alignment Error in BWA: The sequence "lcl|" was not found

Question

[gt]

I have aligned DNA-seq data to the following reference genome: https://www.ncbi.nlm.nih.gov/nuccore/U00096 I keep getting the following output in my error file when I try to run the bcftools mpileup command for variant calling:

[E::faidx_adjust_position] The sequence "lcl|" was not found
[E::faidx_adjust_position] The sequence "lcl|" was not found
[E::faidx_adjust_position] The sequence "lcl|" was not found
[E::faidx_adjust_position] The sequence "lcl|" was not found
[E::faidx_adjust_position] The sequence "lcl|" was not found
[E::faidx_adjust_position] The sequence "lcl|" was not found
[E::faidx_adjust_position] The sequence "lcl|" was not found
[E::faidx_adjust_position] The sequence "lcl|" was not found
[E::faidx_adjust_position] The sequence "lcl|" was not found

I have these same error lines for tons of rows. I know in my .fa file which I downloaded I have the following first line

>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome

Do I have a missing string here or something at the beginning? I did not touch the file when I downloaded it so I just assumed the alignment would work. This is the command I am using to align:

bwa mem -t 180 ecoli R1_001.fastq R2_001.fastq > sample.sam

This is the command I am using to find the variants:

bcftools mpileup -d 500 -Ou -f GCF_000005845.2_ASM584v2_genomic.fa sample.bam | bcftools call -mv -Ob -o sample_calls.bcf

which I took directly from the Github page.

"ecoli" is the index I built using the .fa and .gtf files from the same website. Any help appreciated here! Important note: I have not included my file paths here for privacy reasons.

[GenoMax]

Just to be sure you downloaded fasta format of the genome sequence correct? Do you just see only one line when you do grep "^>" your_fasta_file or additional lines?