BWA error [bwt_restore_sa]

Question

[sarahkhanishere]

Index FASTA genome:

bwa index hg19.fasta

hg19.fasta hg19.fasta.amb hg19.fasta.ann hg19.fasta.bwt hg19.fasta.pac

Aligning:

bwa mem hg19.fasta IonXpress_001.fastq > IonXpress_001.sam

[bwt_restore_sa] fail to open file 'reference/hg19.fasta.sa' : No such file or directory

Answer 1

[Arindam Ghosh]

Please recheck for the location of the file reference/hg19.fasta.sa.