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| Key                 | Values                                                                                                                                                                             |
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| speciesTree         | example/data/Species.nwk                                                                                                                                                           |
| target              | A0                                                                                                                                                                                 |
| minimalWeight       | 1                                                                                                                                                                                  |
| anchorSize          | 2                                                                                                                                                                                  |
| minChromLength      | 2                                                                                                                                                                                  |
| nbThreads           | 1                                                                                                                                                                                  |
| extantSpeciesFilter |                                                                                                                                                                                    |
| IN.ancBlocks        | example/results/ancBlocks/denovo-size-1.0-1.0.fillin-size-0.9-1.1.fusion-size-0.9-1.1.insertion-size-0.9-1.1.fillin-size-0.77-1.33.fusion-size-0.77-1.33.insertion-size-0.77-1.33.fillin-all.fusion-all.insertion-all/blocks.%s.list.bz2 |
| LOG.ancGraph        | example/results/ancBlocks/denovo-size-1.0-1.0.fillin-size-0.9-1.1.fusion-size-0.9-1.1.insertion-size-0.9-1.1.fillin-size-0.77-1.33.fusion-size-0.77-1.33.insertion-size-0.77-1.33.fillin-all.fusion-all.insertion-all.scaffolds/graph.%s.txt.bz2 |
| OUT.ancBlocks       | example/results/ancBlocks/denovo-size-1.0-1.0.fillin-size-0.9-1.1.fusion-size-0.9-1.1.insertion-size-0.9-1.1.fillin-size-0.77-1.33.fusion-size-0.77-1.33.insertion-size-0.77-1.33.fillin-all.fusion-all.insertion-all.scaffolds/blocks.%s.list.bz2 |
| genesFiles          | example/data/genes/genes.%s.list.bz2                                                                                                                                               |
| ancGenesFiles       | example/results/ancGenes/all/ancGenes.%s.list.bz2                                                                                                                                  |
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Loading genome of example/results/ancGenes/all/ancGenes.A0.list.bz2 ... (ancestral genes) OK
Loading genome of example/results/ancGenes/all/ancGenes.A1.list.bz2 ... (ancestral genes) OK
Loading genome of example/results/ancGenes/all/ancGenes.A2.list.bz2 ... (ancestral genes) OK
Loading genome of example/results/ancGenes/all/ancGenes.A3.list.bz2 ... (ancestral genes) OK
Loading genome of example/data/genes/genes.M1.list.bz2 ... (Ensembl) OK
Loading genome of example/data/genes/genes.M2.list.bz2 ... (Ensembl) OK
Loading genome of example/data/genes/genes.M3.list.bz2 ... (Ensembl) OK
Loading genome of example/data/genes/genes.M4.list.bz2 ... (Ensembl) OK
Loading genome of example/data/genes/genes.M5.list.bz2 ... (Ensembl) OK
Elapsed time: 5.276693820953369
Loading genome of example/results/ancBlocks/denovo-size-1.0-1.0.fillin-size-0.9-1.1.fusion-size-0.9-1.1.insertion-size-0.9-1.1.fillin-size-0.77-1.33.fusion-size-0.77-1.33.insertion-size-0.77-1.33.fillin-all.fusion-all.insertion-all/blocks.A0.list.bz2 ... (ancestral genome: diags) OK
Gene order comparison between A0 and M1 ... 2 [2/5/12] [9/18/33] 107 [9.84/11.58-1377] 746 adjacencies / 883 blocks
Gene order comparison between A0 and M2 ... 2 [2/5/12] [8/16/30] 87 [9.17/10.38-1464] 735 adjacencies / 875 blocks
Gene order comparison between A0 and M3 ... 2 [2/5/12] [8/18/31] 83 [9.07/10.81-1400] 749 adjacencies / 871 blocks
Gene order comparison between A0 and M4 ... 2 [2/5/15] [12/25/44] 149 [11.71/15.17-1021] 784 adjacencies / 836 blocks
Gene order comparison between A0 and M5 ... 2 [2/4/7] [4/8/13] 49 [5.57/4.85-2179] 409 adjacencies / 858 blocks
Output blocks of A0 2 [4/10/27] [20/39/65] 176 [19.18/22.49-741] + 2064 singletons
Loading genome of example/results/ancBlocks/denovo-size-1.0-1.0.fillin-size-0.9-1.1.fusion-size-0.9-1.1.insertion-size-0.9-1.1.fillin-size-0.77-1.33.fusion-size-0.77-1.33.insertion-size-0.77-1.33.fillin-all.fusion-all.insertion-all/blocks.A1.list.bz2 ... (ancestral genome: diags) OK
Gene order comparison between A1 and M1 ... 2 [2/6/17] [14/30/55] 131 [13.96/18.13-1099] 452 adjacencies / 581 blocks
Gene order comparison between A1 and M2 ... 2 [2/6/17] [13/26/44] 124 [12.63/15.46-1211] 436 adjacencies / 587 blocks
Gene order comparison between A1 and M3 ... 2 [2/4/15] [16/36/65] 153 [13.13/19.82-1129] 463 adjacencies / 589 blocks
Gene order comparison between A1 and M4 ... 2 [2/5/13] [10/20/34] 109 [10.02/11.89-1210] 372 adjacencies / 485 blocks
Gene order comparison between A1 and M5 ... 2 [2/4/7] [4/7/12] 32 [5.26/4.38-2329] 199 adjacencies / 485 blocks
Output blocks of A1 2 [3/11/78] [93/173/315] 531 [56.87/92.63-284] + 1188 singletons
Loading genome of example/results/ancBlocks/denovo-size-1.0-1.0.fillin-size-0.9-1.1.fusion-size-0.9-1.1.insertion-size-0.9-1.1.fillin-size-0.77-1.33.fusion-size-0.77-1.33.insertion-size-0.77-1.33.fillin-all.fusion-all.insertion-all/blocks.A2.list.bz2 ... (ancestral genome: diags) OK
Gene order comparison between A2 and M1 ... 2 [2/5/11] [7/14/27] 107 [8.57/9.70-1580] 506 adjacencies / 699 blocks
Gene order comparison between A2 and M2 ... 2 [2/5/10] [7/13/23] 87 [8.10/8.64-1654] 508 adjacencies / 700 blocks
Gene order comparison between A2 and M3 ... 2 [2/5/11] [7/14/25] 83 [8.24/9.46-1534] 491 adjacencies / 683 blocks
Gene order comparison between A2 and M4 ... 2 [2/6/17] [15/35/57] 162 [13.68/19.27-902] 653 adjacencies / 699 blocks
Gene order comparison between A2 and M5 ... 2 [2/4/8] [5/10/17] 54 [6.55/6.32-1932] 93 adjacencies / 722 blocks
Output blocks of A2 2 [3/12/52] [57/110/201] 483 [39.84/62.54-365] + 1029 singletons
Loading genome of example/results/ancBlocks/denovo-size-1.0-1.0.fillin-size-0.9-1.1.fusion-size-0.9-1.1.insertion-size-0.9-1.1.fillin-size-0.77-1.33.fusion-size-0.77-1.33.insertion-size-0.77-1.33.fillin-all.fusion-all.insertion-all/blocks.A3.list.bz2 ... (ancestral genome: diags) OK
Gene order comparison between A3 and M1 ... 2 [2/7/28] [30/65/122] 227 [22.77/35.44-730] 213 adjacencies / 309 blocks
Gene order comparison between A3 and M2 ... 2 [2/6/25] [28/53/88] 235 [19.39/29.02-856] 174 adjacencies / 321 blocks
Gene order comparison between A3 and M3 ... 2 [2/5/14] [12/28/50] 147 [11.66/16.13-1249] 183 adjacencies / 285 blocks
Gene order comparison between A3 and M4 ... 2 [2/5/13] [10/19/32] 75 [9.76/11.24-1228] 121 adjacencies / 215 blocks
Gene order comparison between A3 and M5 ... 2 [2/4/6] [4/7/11] 48 [5.10/4.32-2395] 69 adjacencies / 216 blocks
Output blocks of A3 2 [2/10/113] [161/276/454] 661 [82.38/134.97-208] + 983 singletons
