samblaster: Version 0.1.22
samblaster: Inputting from stdin
samblaster: Outputting to stdout
samblaster: Opening /vagrant/test-out6/virtual-normal-samblaster-markdups.txt for write.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
samblaster: Loaded 86 header sequence entries.
samblaster: Removed 1 of 78 (1.28%) read ids as duplicates using 1724k memory in 0.000S CPU seconds and 31S wall time.
[main] Version: 0.7.7-r441
[main] CMD:[samopen] SAM header is present: 86 sequences.
 bwa mem -M -v 1 -R @RG\tID:virtual-normal\tSM:virtual-normal\tLB:virtual-normal\tPL:ILLUMINA -t 2 /proj/b2010040/private/nobackup/autoseq-genome/bwa/human_g1k_v37_decoy.fasta /vagrant/test-out6/skewer/virtual-normal_1.fastq.gz /vagrant/test-out6/skewer/virtual-normal_2.fastq.gz
[main] Real time: 30.780 sec; CPU: 13.292 sec