100/10,000 1,000/10,000 100/100,000 FABIA 12s 1m 46s 1m 9s FABIA & 21s 2m 2s 3m 55s IBD extract BEAGLE 52s 43 m57s 8m2s PLINK 1m 47s 2h 59m 10s 18m 12s GERMLINE 5s 8m 17s 52s DASH 22s 52m 32s 44m 17s RELATE 53m 2s 89h 11m 33s 10h 43m 22s (3d 17h) MCMC >564h (23d 12h) LD PLINK 24s 2m 27s 3m 59s ######################################## system("date") res <- ttspfabia(paste("dataSim",run,"fabia",sep=""),p=SS,alpha=0.035,cyc=50,spl=0,non_negative=1,write_file=0,norm=0,lap=1.0,samples=(1:haploN),iter=A,quant=0.001,lowerB=1.1,upperB=1000) system("date") FABIA: ------ ####100 samples, 10000 snps: run <- 1 system("date") source("run_fabia.R") system("date") fabia only: Mon Dec 19 07:59:49 CET 2011 Mon Dec 19 08:00:01 CET 2011 12s fabia + IBD extract: Wed Jan 4 23:05:40 2012 Wed Jan 4 23:06:01 2012 21s ####1000 samples, 10000 snps: run <- 5 system("date") source("run_fabia.R") system("date") fabia only: Mon Dec 19 08:51:23 CET 2011 Mon Dec 19 08:53:09 CET 2011 1m 46s fabia + IBD extract: Wed Jan 4 23:23:28 2012 Wed Jan 4 23:25:30 2012 2m 2s ####100 samples, 100000 snps: run <- 6 system("date") source("run_fabia.R") system("date") fabiy only: Mon Dec 19 08:15:59 CET 2011 Mon Dec 19 08:18:08 CET 2011 1m 9s fabia + IBD extract: Mon Dec 19 10:49:02 CET 2011 Mon Dec 19 10:52:57 CET 2011 3m 55s ######################################## BEAGLE: ------- date time(java -jar /system/user/hochreit/bin/beagle.jar unphased=dataSim1beagle.txt fastibd=true missing=N out=beagleres.txt) date ####100 samples, 10000 snps: Sun Dec 18 10:54:01 CET 2011 Elapsed time for fastIBD detection: 11 seconds Running time for phasing: 41 seconds real 0m41.433s user 0m42.712s sys 0m1.327s Sun Dec 18 10:54:53 CET 2011 52s ####1000 samples, 10000 snps: date time(java -jar /system/user/hochreit/bin/beagle.jar unphased=dataSim5beagle.txt fastibd=true missing=N out=beagleres.txt) date Sun Dec 18 12:53:37 CET 2011 Start time: 12:53 PM CET on 18 Dec 2011 Elapsed time for fastIBD detection: 34 minutes 27 seconds Running time for phasing: 43 minutes 53 seconds Beagle version 3.3.2 (31 Oct 2011) finished real 43m56.748s user 43m59.360s sys 0m38.757s Sun Dec 18 13:37:34 CET 2011 43m57s ####100 samples, 100000 snps: date time(java -jar /system/user/hochreit/bin/beagle.jar unphased=dataSim6beagle.txt fastibd=true missing=N out=beagleres.txt) date Sun Dec 18 20:19:07 CET 2011 Elapsed time for fastIBD detection: 1 minutes 44 seconds Running time for phasing: 7 minutes 59 seconds Beagle version 3.3.2 (31 Oct 2011) finished real 8m2.884s user 8m12.303s sys 0m19.232s Sun Dec 18 20:27:10 CET 2011 8m2s ######################################## PLINK: ------ date time(plink --file dataSim1plink --genome --allow-no-sex) time(plink --file dataSim1plink --read-genome plink.genome --segment --all-pairs --segment-length 0.1 --segment-snp 2) date ####100 samples, 10000 snps: Sun Dec 18 11:00:27 CET 2011 Analysis started: Sun Dec 18 11:00:27 2011 Analysis finished: Sun Dec 18 11:00:28 2011 real 0m1.720s user 0m1.706s sys 0m0.011s Analysis started: Sun Dec 18 11:00:28 2011 Analysis finished: Sun Dec 18 11:02:14 2011 real 1m45.616s user 1m45.489s sys 0m0.105s Sun Dec 18 11:02:14 CET 2011 1m47s ####1000 samples, 10000 snps: date time(plink --file dataSim5plink --genome --allow-no-sex) time(plink --file dataSim5plink --read-genome plink.genome --segment --all-pairs --segment-length 0.1 --segment-snp 2) date Sun Dec 18 15:34:20 CET 2011 Analysis started: Sun Dec 18 15:34:20 2011 Analysis finished: Sun Dec 18 15:36:21 2011 real 2m1.059s user 2m0.808s sys 0m0.222s Analysis started: Sun Dec 18 15:36:21 2011 Analysis finished: Sun Dec 18 18:33:10 2011 real 176m48.918s user 176m41.994s sys 0m3.621s Sun Dec 18 18:33:10 CET 2011 179m10s ####100 samples, 100000 snps: date time(plink --file dataSim6plink --genome --allow-no-sex) time(plink --file dataSim6plink --read-genome plink.genome --segment --all-pairs --segment-length 0.1 --segment-snp 2) date Sun Dec 18 20:28:37 CET 2011 Analysis started: Sun Dec 18 20:28:37 2011 Analysis finished: Sun Dec 18 20:28:53 2011 real 0m15.840s user 0m15.756s sys 0m0.068s Analysis started: Sun Dec 18 20:28:53 2011 Analysis finished: Sun Dec 18 20:46:49 2011 real 17m55.599s user 17m55.138s sys 0m0.191s Sun Dec 18 20:46:49 CET 2011 18m12s ######################################## GERMLINE: --------- echo '1' > germin echo 'dataSim1plink.map' >> germin echo 'dataSim1plink.ped' >> germin echo 'germline_output.txt' >> germin date time(germline -haploid -min_m 0.001 -err_hom 1 -err_het 1 -bits 30 < germin) date rm germin ##: -bits !!! 20 or 30 etc. ####100 samples, 10000 snps: Sun Dec 18 11:04:46 CET 2011 real 0m4.930s user 0m3.069s sys 0m1.857s Sun Dec 18 11:04:51 CET 2011 5s ####1000 samples, 10000 snps: echo '1' > germin echo 'dataSim5plink.map' >> germin echo 'dataSim5plink.ped' >> germin echo 'germline_output.txt' >> germin date time(germline -haploid -min_m 0.001 -err_hom 1 -err_het 1 -bits 30 < germin) date Sun Dec 18 18:51:41 CET 2011 real 8m16.787s user 5m29.298s sys 2m44.932s Sun Dec 18 18:59:58 CET 2011 8m17s ####100 samples, 100000 snps: echo '1' > germin echo 'dataSim6plink.map' >> germin echo 'dataSim6plink.ped' >> germin echo 'germline_output.txt' >> germin date time(germline -haploid -min_m 0.001 -err_hom 1 -err_het 1 -bits 30 < germin) date Sun Dec 18 20:48:04 CET 2011 real 0m51.470s user 0m32.707s sys 0m16.820s Sun Dec 18 20:48:56 CET 2011 52s ######################################## DASH: ----- echo '1' > germin echo 'dataSim1plink.map' >> germin echo 'dataSim1plink.ped' >> germin echo 'germline_output.txt' >> germin date time(germline -haploid -bin_out -min_m 0.001 -err_hom 1 -err_het 1 -bits 30 < germin) time(/system/user/hochreit/bin/parse_bmatch germline_output.txt.bmatch germline_output.txt.bsid germline_output.txt.bmid | cut -f 1,2,4 | dash_cc dataSim1plink.fam dash_output -min 2) date ####100 samples, 10000 snps: Sun Dec 18 11:05:44 CET 2011 real 0m1.942s user 0m1.832s sys 0m0.110s real 0m19.891s user 0m21.689s sys 0m1.809s Sun Dec 18 11:06:06 CET 2011 22s ####1000 samples, 10000 snps: echo '1' > germin echo 'dataSim5plink.map' >> germin echo 'dataSim5plink.ped' >> germin echo 'germline_output.txt' >> germin date time(germline -haploid -bin_out -min_m 0.001 -err_hom 1 -err_het 1 -bits 30 < germin) time(/system/user/hochreit/bin/parse_bmatch germline_output.txt.bmatch germline_output.txt.bsid germline_output.txt.bmid | cut -f 1,2,4 | dash_cc dataSim5plink.fam dash_output -min 2) date Sun Dec 18 19:05:06 CET 2011 real 3m24.877s user 3m11.740s sys 0m3.476s real 49m6.356s user 52m44.211s sys 3m8.504s Sun Dec 18 19:57:38 CET 2011 52m32s ####100 samples, 100000 snps: echo '1' > germin echo 'dataSim6plink.map' >> germin echo 'dataSim6plink.ped' >> germin echo 'germline_output.txt' >> germin date time(germline -haploid -bin_out -min_m 0.001 -err_hom 1 -err_het 1 -bits 30 < germin) time(/system/user/hochreit/bin/parse_bmatch germline_output.txt.bmatch germline_output.txt.bsid germline_output.txt.bmid | cut -f 1,2,4 | dash_cc dataSim6plink.fam dash_output -min 2) date Sun Dec 18 20:55:07 CET 2011 real 0m21.438s user 0m19.801s sys 0m1.444s real 43m56.635s user 42m8.146s sys 0m18.805s Sun Dec 18 21:39:25 CET 2011 44m17s ######################################## MCMC: ----- MCMC_IBDfinder -h MCMC_IBDfinder -g dataSim1mcmc.genotype -p dataSim1mcmc.posmaf -z dataSim1mcmc.initz ####100 samples, 10000 snps: Fri Dec 16 20:13:43 CET 2011 Mon Jan 9 08:52:28 CET 2012 23 days 12h 48m >564 h ######################################## Relate: ------- echo '1 #1=allpairs 0=normal run' > relate_options echo '8 #pair[0]' >> relate_options echo '9 #pair[1]' >> relate_options echo '0 #double recombination' >> relate_options echo '0 #LD=0=rsq2 LD=1=D' >> relate_options echo '0.001 #min default: 0.025' >> relate_options echo '0.001 # alim[0]' >> relate_options echo '5.0 # alim[1]' >> relate_options echo '0 #doParameter calculation (pars)' >> relate_options echo '0.3 # par[0] = a this is only used if doParameter is set to 1' >> relate_options echo '0.25 # par[1] = k2 this is only used if doParameter is set to 1' >> relate_options echo '0.5 # par[2] = k1 this is only used if doParameter is set to 1' >> relate_options echo '1 #ld_adj' >> relate_options echo '0.01 #epsilon' >> relate_options echo '5 #back default 50' >> relate_options echo '0 #doPrune' >> relate_options echo '0.1 #prune_value' >> relate_options echo '0 #fixA' >> relate_options echo '0.0 #fixA_value' >> relate_options echo '1 #fixK2' >> relate_options echo '0.0 #fixk2_value' >> relate_options echo '1 #calculateA' >> relate_options echo '0.013 #phi_value' >> relate_options echo '0.1 #convergence_tolerance' >> relate_options echo '3 #times_to_converge' >> relate_options echo '8 #times_to_run' >> relate_options echo '100 #back2' >> relate_options relateHMM -o relate_options -g dataSim1relate.geno -c dataSim1relate.chr -p dataSim1relate.pos -post relate_post.txt -k relate_stat.txt ld_adj = 0 -> segmentation fault ####100 samples 10,000 snps: date relateHMM -o relate_options -g dataSim5relate.geno -c dataSim1relate.chr -p dataSim5relate.pos -post relate_post.txt -k relate_stat.txt date Tue Dec 13 07:06:42 2011 Tue Dec 13 07:59:44 2011 53m2s ####1000 samples 10,000 snps: date relateHMM -o relate_options -g dataSim5relate.geno -c dataSim5relate.chr -p dataSim5relate.pos -post relate_post.txt -k relate_stat.txt date ####100 samples 100,000 snps: date relateHMM -o relate_options -g dataSim6relate.geno -c dataSim6relate.chr -p dataSim6relate.pos -post relate_post.txt -k relate_stat.txt date Sun Dec 18 21:42:39 CET 2011 Mon Dec 19 08:26:01 CET 2011 10h 43m 22s ################################################################### ################################################################### ################################################################### LD computation date plink --file dataSim1plink --r --ld-window 500 --out plink date A100: Thu Jan 19 18:58:11 2012 Thu Jan 19 18:58:35 2012 24s A1000: Fri Jan 20 03:45:54 2012 Fri Jan 20 03:48:21 2012 2m 27s A100 with 100,000 SNPS: Mon Feb 13 17:43:39 2012 Mon Feb 13 17:47:38 2012 3m 59s