# May 10 2015
# 2nd assembly run. Lucigen mate-pair data is the only new addition to this
# assembly.
#
# run sparse pregraph for DBG assembly using config_file for 4 libraries
# SW018_S1_L001, SW018_S1_L007, SW019_S2_L008, and R1_IJS8_mates_ICC5_SW023_S60

SOAPdenovo2-63mer sparse_pregraph -s ../config_file -K 61 -g 15 -z 2500000000 -d 1 -e 1 -r 0 -p 20 -o soapdenovo2_sparseGraph_2

# 2nd Run took about 4 hours and 45 minutes on 12 cores with 60 gb memory.
# Used a total of 127383.665 CPU seconds (~35.4 CPU hours) and 58.941 Gb of
# max virtual memory.

SOAPdenovo2-63mer contig -s ../config_file -p 12 -g soapdenovo2_sparseGraph_2

# 2nd Run took about 18 minutes on 12 cores with 10 gb memory.
# Used a total of 856.445 CPU seconds (~14.3 CPU minutes) and 5.781 Gb of
# max virtual memory.

SOAPdenovo2-63mer map -p 12 -k 61 -s ../config_file -g soap_denovo2_mapStep_2

# 2nd Run took about 2 hours and 55 minutes on 12 cores with 30 gb memory.
# Used a total of 53220.443 CPU seconds (~14.78 CPU hours) and 78.048 Gb of
# max virtual memory.

SOAPdenovo2-63mer scaff -F -p 12 -g soap_denovo2_scaffStep_2

# 2nd Run took about 31 hours and 10 minutes on 30 cores with 50 gb memory (requires at least 50 gb, otherwise job will fail).
# Used a total of 390771.403 CPU seconds (~108.55 CPU hours) and 21.282 Gb
# of max virtual memory.