# DATE: 02 Jun 21 02:36:18 # CMD LINE: mcl /work/yinlab/tangli/pan-genome_Escherichia_coli/random100/random_051/ori_data/pangenome/mcl-input.txt --abc -I 10.0 -o /work/yinlab/tangli/pan-genome_Escherichia_coli/random100/random_051/ori_data/pangenome/mcl-clusters.txt -te 32 .................................................. 1M .................................................. 2M .................................................. 3M .................................................. 4M .................................................. 5M .................................................. 6M .................................................. 7M .................................................. 8M .................................................. 9M .................................................. 10M .................................................. 11M .................................................. 12M .................................................. 13M .................................................. 14M .................................................. 15M .................................................. 16M .................................................. 17M .................................................. 18M .................................................. 19M .................................................. 20M .................................................. 21M .................................................. 22M .................................................. 23M .................................................. 24M .................................................. 25M .................................................. 26M .................................................. 27M .................................................. 28M .................................................. 29M .................................................. 30M .................................................. 31M .................................................. 32M .................................................. 33M .................................................. 34M .................................................. 35M .................................................. 36M .................................................. 37M .................................................. 38M .................................................. 39M .................................................. 40M .................................................. 41M .................................................. 42M .................................................. 43M .................................................. 44M ................................. [mcl] new tab created [mcl] pid 3724538 ite chaos time hom(avg,lo,hi) m-ie m-ex i-ex fmv 1 85.19 21.45 1.01/0.01/10.33 1.05 1.03 1.03 1 2 104.53 22.56 0.98/0.06/6.80 1.05 0.97 1.00 2 3 58.77 20.17 0.89/0.01/40.94 1.03 0.93 0.93 1 4 39.96 16.58 0.86/0.05/10.06 1.00 0.80 0.75 1 5 20.73 11.05 0.97/0.06/3.76 1.00 0.63 0.47 0 6 24.48 6.63 0.99/0.07/1.05 1.00 0.91 0.43 0 7 16.30 6.29 1.00/0.18/1.02 1.00 0.98 0.42 0 8 1.46 6.00 1.00/0.51/1.05 1.00 0.99 0.41 0 9 3.12 6.01 1.00/0.36/1.00 1.00 1.00 0.41 0 10 0.21 5.97 1.00/0.89/1.00 1.00 1.00 0.41 0 11 0.00 5.98 1.00/1.00/1.00 1.00 1.00 0.41 0 [mcl] jury pruning marks: <98,99,98>, out of 100 [mcl] jury pruning synopsis: <98.2 or marvelous> (cf -scheme, -do log) [mcl] output is in /work/yinlab/tangli/pan-genome_Escherichia_coli/random100/random_051/ori_data/pangenome/mcl-clusters.txt [mcl] 17421 clusters found [mcl] output is in /work/yinlab/tangli/pan-genome_Escherichia_coli/random100/random_051/ori_data/pangenome/mcl-clusters.txt Please cite: Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000. ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf or http://micans.org/mcl/lit/svdthesis.pdf.gz) OR Stijn van Dongen, A cluster algorithm for graphs. Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000. ( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z or http://micans.org/mcl/lit/INS-R0010.ps.Z) [02 Jun 21 02:41:41] MCL output ...................................: /work/yinlab/tangli/pan-genome_Escherichia_coli/random100/random_051/ori_data/pangenome/mcl-clusters.txt [02 Jun 21 02:41:41] Number of gene clusters ......................: 17,421 [02 Jun 21 04:12:27] gene clusters info ...........................: 17421 gene_clusters stored in the database [02 Jun 21 04:12:49] New items order ..............................: "presence-absence:euclidean:ward" (type newick) has been added to the database... [02 Jun 21 04:13:11] WARNING =============================================== Clustering for "presence-absence:euclidean:ward" is already in the database. It will be replaced with the new content. [02 Jun 21 04:13:11] New items order ..............................: "presence-absence:euclidean:ward" (type newick) has been added to the database... [02 Jun 21 04:13:27] New items order ..............................: "frequency:euclidean:ward" (type newick) has been added to the database... [02 Jun 21 04:13:28] New items order ..............................: "Forced synteny <> GCF_000010385:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:29] New items order ..............................: "Forced synteny <> GCF_000022225:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:29] New items order ..............................: "Forced synteny <> GCF_000025745:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:29] New items order ..............................: "Forced synteny <> GCF_000091005:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:29] New items order ..............................: "Forced synteny <> GCF_000258025:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:30] New items order ..............................: "Forced synteny <> GCF_000299475:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:30] New items order ..............................: "Forced synteny <> GCF_000800845:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:30] New items order ..............................: "Forced synteny <> GCF_000813165:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:30] New items order ..............................: "Forced synteny <> GCF_000829985:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:30] New items order ..............................: "Forced synteny <> GCF_000831565:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:31] New items order ..............................: "Forced synteny <> GCF_000967155:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:31] New items order ..............................: "Forced synteny <> GCF_000968515:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:31] New items order ..............................: "Forced synteny <> GCF_000974465:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:31] New items order ..............................: "Forced synteny <> GCF_000974575:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:32] New items order ..............................: "Forced synteny <> GCF_000974825:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:32] New items order ..............................: "Forced synteny <> GCF_001021595:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:32] New items order ..............................: "Forced synteny <> GCF_001021635:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:32] New items order ..............................: "Forced synteny <> GCF_001183665:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:33] New items order ..............................: "Forced synteny <> GCF_001183685:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:33] New items order ..............................: "Forced synteny <> GCF_001420955:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:33] New items order ..............................: "Forced synteny <> GCF_001612495:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:33] New items order ..............................: "Forced synteny <> GCF_001618325:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:33] New items order ..............................: "Forced synteny <> GCF_001663075:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:34] New items order ..............................: "Forced synteny <> GCF_001675145:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:34] New items order ..............................: "Forced synteny <> GCF_001721525:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:34] New items order ..............................: "Forced synteny <> GCF_001753545:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:34] New items order ..............................: "Forced synteny <> GCF_001886555:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:35] New items order ..............................: "Forced synteny <> GCF_001900555:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:35] New items order ..............................: "Forced synteny <> GCF_001900635:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:35] New items order ..............................: "Forced synteny <> GCF_001900695:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:35] New items order ..............................: "Forced synteny <> GCF_001900815:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:36] New items order ..............................: "Forced synteny <> GCF_001900885:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:36] New items order ..............................: "Forced synteny <> GCF_001901145:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:36] New items order ..............................: "Forced synteny <> GCF_001901165:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:36] New items order ..............................: "Forced synteny <> GCF_001901185:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:37] New items order ..............................: "Forced synteny <> GCF_001901365:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:37] New items order ..............................: "Forced synteny <> GCF_001901405:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:37] New items order ..............................: "Forced synteny <> GCF_002012045:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:37] New items order ..............................: "Forced synteny <> GCF_002012065:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:37] New items order ..............................: "Forced synteny <> GCF_002012205:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:38] New items order ..............................: "Forced synteny <> GCF_002012225:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:38] New items order ..............................: "Forced synteny <> GCF_002024865:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:38] New items order ..............................: "Forced synteny <> GCF_002058765:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:39] New items order ..............................: "Forced synteny <> GCF_002142695:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:39] New items order ..............................: "Forced synteny <> GCF_002142715:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:39] New items order ..............................: "Forced synteny <> GCF_002163935:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:39] New items order ..............................: "Forced synteny <> GCF_002180055:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:39] New items order ..............................: "Forced synteny <> GCF_002192275:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:40] New items order ..............................: "Forced synteny <> GCF_002192295:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:40] New items order ..............................: "Forced synteny <> GCF_002201835:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:40] New items order ..............................: "Forced synteny <> GCF_002208865:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:40] New items order ..............................: "Forced synteny <> GCF_002278115:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:41] New items order ..............................: "Forced synteny <> GCF_002741255:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:41] New items order ..............................: "Forced synteny <> GCF_002787935:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:41] New items order ..............................: "Forced synteny <> GCF_002788295:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:41] New items order ..............................: "Forced synteny <> GCF_002853655:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:41] New items order ..............................: "Forced synteny <> GCF_002853715:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:42] New items order ..............................: "Forced synteny <> GCF_002860085:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:42] New items order ..............................: "Forced synteny <> GCF_002903125:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:42] New items order ..............................: "Forced synteny <> GCF_002925525:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:42] New items order ..............................: "Forced synteny <> GCF_002946715:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:43] New items order ..............................: "Forced synteny <> GCF_002953895:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:43] New items order ..............................: "Forced synteny <> GCF_003017455:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:43] New items order ..............................: "Forced synteny <> GCF_003018355:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:43] New items order ..............................: "Forced synteny <> GCF_003018915:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:44] New items order ..............................: "Forced synteny <> GCF_003018995:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:44] New items order ..............................: "Forced synteny <> GCF_003051985:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:44] New items order ..............................: "Forced synteny <> GCF_003073875:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:44] New items order ..............................: "Forced synteny <> GCF_003570765:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:45] New items order ..............................: "Forced synteny <> GCF_003586045:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:45] New items order ..............................: "Forced synteny <> GCF_003586065:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:45] New items order ..............................: "Forced synteny <> GCF_003591595:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:45] New items order ..............................: "Forced synteny <> GCF_003856575:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:46] New items order ..............................: "Forced synteny <> GCF_003956325:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:46] New items order ..............................: "Forced synteny <> GCF_003956485:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:46] New items order ..............................: "Forced synteny <> GCF_003966425:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:46] New items order ..............................: "Forced synteny <> GCF_004006545:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:46] New items order ..............................: "Forced synteny <> GCF_004135165:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:47] New items order ..............................: "Forced synteny <> GCF_004355105:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:47] New items order ..............................: "Forced synteny <> GCF_004358405:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:47] New items order ..............................: "Forced synteny <> GCF_004358965:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:48] New items order ..............................: "Forced synteny <> GCF_004368015:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:48] New items order ..............................: "Forced synteny <> GCF_004526255:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:48] New items order ..............................: "Forced synteny <> GCF_004924355:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:48] New items order ..............................: "Forced synteny <> GCF_005037805:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:49] New items order ..............................: "Forced synteny <> GCF_005221745:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:49] New items order ..............................: "Forced synteny <> GCF_007833255:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:49] New items order ..............................: "Forced synteny <> GCF_007990655:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:49] New items order ..............................: "Forced synteny <> GCF_008124145:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:50] New items order ..............................: "Forced synteny <> GCF_008462425:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:50] New items order ..............................: "Forced synteny <> GCF_008807655:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:50] New items order ..............................: "Forced synteny <> GCF_900149875:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:50] New items order ..............................: "Forced synteny <> GCF_900497455:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:50] New items order ..............................: "Forced synteny <> GCF_900635145:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:51] New items order ..............................: "Forced synteny <> GCF_900635185:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:51] New items order ..............................: "Forced synteny <> GCF_900635195:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:51] New items order ..............................: "Forced synteny <> GCF_900635325:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:51] New items order ..............................: "Forced synteny <> GCF_900636175:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:52] New items order ..............................: "Forced synteny <> GCF_900699165:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:52] New items order ..............................: "Forced synteny <> GCF_900747785:NA:NA" (type basic) has been added to the database... [02 Jun 21 04:13:59] Pan database ................................................: An existing database, /work/yinlab/tangli/pan-genome_Escherichia_coli/random100/random_051/ori_data/pangenome/ECtest-PAN.db, has been initiated. [02 Jun 21 04:13:59] Genomes .....................................................: 101 found [02 Jun 21 04:14:13] Genomes storage .............................................: Initialized (storage hash: hash700fce72) [02 Jun 21 04:14:13] Num genomes in storage ......................................: 100 [02 Jun 21 04:14:13] Num genomes will be used ....................................: 100 [02 Jun 21 04:14:14] Pan DB ......................................................: Initialized: /work/yinlab/tangli/pan-genome_Escherichia_coli/random100/random_051/ori_data/pangenome/ECtest-PAN.db (v. 14) [02 Jun 21 04:14:14] Gene cluster homogeneity estimates ..........................: Functional: [NO]; Geometric: [NO]; Combined: [NO] [02 Jun 21 04:14:18] * Gene clusters are initialized for all 17421 gene clusters in the database. [02 Jun 21 05:06:19] log file ....................................................: /work/yinlab/tangli/pan-genome_Escherichia_coli/random100/random_051/ori_data/pangenome/log.txt [02 Jun 21 05:06:19] Bye.