bcftools mipileup error: format error, unexpected A at line 1

Question

[jiyoung]

I had a problem using bcftools. After using the command line(below): there is some error in my results. The error message stated: "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid

[E::fai_build_core] Format error, unexpected "A" at line 4 

Failed to read from standard input: unknown file type"

 bcftools mpileup -f A.fasta out.bam | bcftools call -mv -Ob -o out.bcf

there is problem in my index file? i using bwa tool to make index file.

bwa index A.fasta

This is my index file (A.fasta)

Thank you in advance for your help.

[Pierre Lindenbaum]

i using bwa tool to make index file.

bcftools wants an index created with samtools faidx (describe the number of chromosomes and the lengths of the fasta lines) , not bwa index (index for mapping with bwa)

[Pierre Lindenbaum]

Format error, unexpected "A" at line 4

i suspect your fasta file is a windows file with CRLF lines. https://en.wikipedia.org/wiki/Newline#Issues_with_different_newline_formats ? if true: https://www.cyberciti.biz/faq/how-to-remove-carriage-return-in-linux-or-unix/

[jiyoung]

My FASTA file was not downloaded from a database. My fasta file was created by converting a txt file to FASTA format. How can I resolve these problems?

[Pierre Lindenbaum]

My fasta file was created by converting a txt file to FASTA format.

what does that mean ?

How can I resolve these problems?

see the second link

[Jautis]

You can usually fix it with the dos2unix command