Whenever I using bwa mem command:

bwa mem -t 10 -M ${classpath}/genome.fa 1.fastq > test.sam

or like that:

bwa mem -t 10  ${classpath}/genome.fa 1.fastq 2.fastq >test.sam

it just output the error message:

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[fread] Unexpected end of file

Is the problem of bwaIndex file ?

Thank you for your suggestion.