SAM Tools version 0.1.18 loaded.
OpenMPI libraries (GNU) version 1.6.3 loaded.
GMP arithmetic library version 5.1.1 loaded.
MPFR version 3.1.1 loaded.
Mpc version 1.0.1 loaded.
gcc version 4.9.2 loaded.
R version 3.1.1 loaded
Boost version 1.52.0 loaded.
Sun/Oracle Java SE Development Kit version 1.7.0_51 loaded.
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
[samopen] SAM header is present: 2 sequences.
Read 41120392 spots for /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-only/29CHIP_Input-GSM1035301.sra
Written 41120392 spots for /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-only/29CHIP_Input-GSM1035301.sra
End-to-end 2/3-mismatch full-index search: 00:11:45
# reads processed: 41120392
# reads with at least one reported alignment: 3974276 (9.66%)
# reads that failed to align: 36902862 (89.74%)
# reads with alignments suppressed due to -m: 243254 (0.59%)
Reported 5364874 alignments to 1 output stream(s)
Time searching: 00:11:45
Overall time: 00:11:46
[bam_sort_core] merging from 15 files...