CODEWITHSUNDEEP
bioinformaticssequence-alignment
Mirue Kang
Mirue Kang

Reputation: 23

BWA fail to locate the index files

I'm currently working on trying to analyze a dataset. I'm new to the field of bioinformatics and was trying to use BWA tools, however, as soon as I reach bwa mem, I keep running into the same error:

input --> mirues-macbook:sra ipmiruek$ bwa mem -t 8 Homo_sapiens.GRCh38.dna.chromosome.17.fa ERR3841737/ERR3841737_trimmed.fq.gz > ERR3841737/ERR3841737_mapped.sam

output --> [E::bwa_idx_load_from_disk] fail to locate the index files

I've already indexed the reference chromosome as such:

bwa index Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz

Is there anything I could do to fix this problem? Thank you.

I tried changing the dataset that I was using along with the corresponding reference chromosome but it still yielded the same result. Is this an issue with the code or with the dataset I'm working with?

Upvotes: 2

Views: 2404

Answers (1)

Steve
Steve

Reputation: 54562

It looks like you indexed a gzip-compressed FASTA file, but are supplying an index base (idxbase) without the .gz extenstion. What you want is:

$ bwa mem \
    -t 8 \
    Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz \ 
    ERR3841737/ERR3841737_trimmed.fq.gz \
    > ERR3841737/ERR3841737_mapped.sam

Alternatively, gunzip the reference FASTA file and index it. For example:

$ gunzip Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz
$ bwa index Homo_sapiens.GRCh38.dna.chromosome.17.fa

Note that BWA packs the reference sequences (into the .pac file), so you don't even need the FASTA file to run BWA MEM after it's been indexed.

Upvotes: 2

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