bwa index error with hg19

[cmccabe]

I indexed the ucsc.hg19.fasta for bwa using:

bwa index -p hg19bwaidx -a bwtsw /home/cmccabe/Desktop/NGS/bwa-0.7.12/ucsc.hg19.fasta

However, I am getting:

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ bwa mem -M -t 16 /home/cmccabe/Desktop/NGS/bwa-0.7.12/ucsc.hg19.fasta /home/cmccabe/IDP/NA12878-NextSeq-S1_R1.fastq.gz /home/cmccabe/IDP/NA12878-NextSeq-S1_R2.fastq.gz > /home/cmccabe/IDP/bwa_reads.sam 
[B][E::bwa_idx_load_from_disk] fail to locate the index files[/B]

Why the error? The path to the index files is there. Thank you

Index files:

hg19bwaidx.ann hg19bwaidx.bwt hg19bwaidx.amb hg19bwaidx.pac hg19bwaidx.sa

[GenoMax]

bwa indexes are included in the iGenomes bundle in /path_to/Sequence/BWAIndex. You did not need to make your own.

Since you gave a prefix name for your index try this

$ ~/Desktop/NGS$ bwa mem -M -t 16 /path_to/hg19bwaidx /home/cmccabe/IDP/NA12878-NextSeq-S1_R1.fastq.gz /home/cmccabe/IDP/NA12878-NextSeq-S1_R2.fastq.gz > /home/cmccabe/IDP/bwa_reads.sam