Hello,
I tried to execute the command line in putty (linux) as follows:
$ bwa mem -M -t 8 Homo_sapiens_assembly38.fasta SRR1517898_1.fastq SRR1517898_2.fastq > SRR1517898.sam
but this appears:
[E::bwa_idx_load_from_disk] fail to locate the index files
I already created the following files using bwa_index, samtools_faidx, and picard_createsequencedictionary without any error.
I have tried putting all my files (Homo_sapiens_assembly38.dict, Homo_sapiens_assembly38.fasta, Homo_sapiens_assembly38.fasta.amb, Homo_sapiens_assembly38.fasta.ann, Homo_sapiens_assembly38.fasta.pac, Homo_sapiens_assembly38.fasta.fai) all together in my home directory and also tried to put them inside the folder in which bwa-0.7.15 is installed (where bwa command resides), but still it doesn't work.
Is there something more than just putting them altogether in one directory...?
I'm new to the scene, and I don't understand why linux cannot find the index files.
And the manual says download hg38.fa too. Can you please tell me what use does this file have..? Is it the same file as Homo_sapiens_assembly38.fasta?
Thank you. Waiting for kind professionals that can give an advice..