...taint levels were done in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using...
.... 0.06 sec[bwa_aln_core] 70989574 sequences have been processed.[main] Version: 0.7.15-r1140[main] CMD: bwa...oldSeq.fasta scaffoldSeq.fasta
To resolve this, try downloading blasr version 1.3 above and re-run :)