A USER ERROR has occurred: Fasta index file
file:///home/ahmed/Desktop/assignment/ref/chr22_with_ERCC92.fa.fai for
reference file:///home/ahmed/Desktop/assignment/ref/chr22_with_ERCC92.fa does not exist.
Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference
for help creating it