[E::bwa_idx_load_from_disk] fail to locate the index files

[Mohajertabassom]

I used bwa mem for alignment and got this error, although I index the reference in this directory and all of my data are in one directory which I run the command in it.
What is your suggestion?

[jts]

There's really no explanation other than the index files are missing. Can you show me an ls of the directory and what command you tried to run?

[Mohajertabassom]

I just want to do the whole process for only 2 data sets to know more about the procedure but actually faced to lots of problem. one of them was about bwa. the command which I write is
bwa mem -x ont2d -t 4 Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.29.dna.genome.fa 1.fasta > alignment1.sam

[timp0]

Before you run that command, did you run bwa index Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.29.dna.genome.fa

That's needed first to generate the index for use with bwa mem, as detailed here: https://github.com/lh3/bwa

[cement-head]

Yeah, the instructions aren't perfectly clear for new users.

1. run the indexing command and choose a prefix, in this case, we'll use goober

$ bwa index -p goober reference.fasta

This will generate five files.

2. In the same directory, then run bwa mem using the prefix and map the Illumina reads to the original genome, making use of the index files (goober) that you just generated.

$ bwa mem -t 124 -P goober read1.fastq read2.fastq > output-pe-aln.sam