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==== Run 1 log ==== # This file contains all the commands and explanations for the commands\\ # used to run our SOAPdenovo2 assembly of the banana slug # Apr 28 2015\\ # run sparse pregraph for DBG assembly using config_file for 3 libraries\\ # SW018_S1_L001, SW018_S1_L007, SW019_S2_L008 SOAPdenovo2-63mer sparse_pregraph -s ../config_file -K 61 -g 15 -z 3000000000 -d 1 -e 1 -r 0 -p 20 -o soapdenovo2_sparseGraph # -s is the configuration file\\ # -K is the kmer size\\ # -g is the max kmer edge length, number of skipped intermediate kmers\\ # -z is the estimated genome size\\ # -d is the kmer frequency cutoff, kmers with freq no larger are deleted\\ # -e is the kmer edge ferquency cutoff, delete kmers' related edge smaller\\ # -r is to kead the available read\\ # -p is number of cpus for use\\ # -o is prefix of output graph\\ #\\ # 1st Run took about 9 hours and 28 minutes on 20 cores with 50 gb memory.\\ # Used a total of 136080.099 CPU seconds (~37.8 CPU hours) and 59.986 Gb of max virtual memory. SOAPdenovo2-63mer contig -p 20 -g soapdenovo2_sparseGraph # -p is number of cpus for use\\ # -g is prefix of output graph from sparse_pregraph output\\ #\\ # 1st Run took about 21 minutes on 20 cores with 50 gb memory.\\ # Used a total of 799.740 CPU seconds (~13 CPU minutes) and 5.780 Gb of\\ # max virtual memory. SOAPdenovo2-63mer map -p 20 -k 61 -s ../config_file -g soapdenovo2_sparseGraph # -p is number of cpus for use\\ # -k kmer size used for mapping read to contig\\ # -s is the configuration file\\ # -g is the prefix of output graph from sparse_pregraph output\\ #\\ # 1st Run took about 2 hours and 6 minutes on 20 cores with 50 gb memory.\\ # Used a total of 78902.546 CPU seconds (~21.9 CPU hours) and 66.103 Gb of\\ # max virtual memory. SOAPdenovo2-63mer scaff -F -p 20 -g soapdenovo2_sparseGraph # -F fill gaps in scaffold\\ # -p is number of cpus for use\\ # -g is prefix of output graph from sparse_pregraph output\\ #\\ # 1st Run took about 24 hours and 50 minutes running on 20 cores with 50 gb\\ # memory.\\ # Used a total of 333894.594 CPU seconds (~92.7 CPU hours) and 20.366 Gb of\\ # max virtual memory. ==== Run 2 log ==== # 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 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.
