Running MakePangenome.. Information about input data: Number of genomes: 3 Number of sequences: 3 Number of sequences per genome: 1 Total length of input (bp): 11404930 Minimum genome length (bp): 2530748 Median genome length (bp): 3615398 Average genome length (bp): 3801643 Maximum genome length (bp): 5258784 ============================ [2021-Dec-06 00:42:48 UTC+03:00] BeginIteration 1, AnchorJoinerFast Length of all major blocks of at least 2 fragments: 81088 Stable blocks (represented in all genomes once, but not minor): fragments: 0 blocks: 0 ============================ [2021-Dec-06 00:42:56 UTC+03:00] BeginIteration 2, AnchorJoinerFast Length of all major blocks of at least 2 fragments: 201787 Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 Block identity: 0.9038 Identity of joined blocks: 0.9038 Nucleotides in blocks: 312 The percentage of input length: 0% Distance from previous pre-pangenome (bp): 976692 The percentage of input length: 8.56% Distance is sufficient to carry on ============================ [2021-Dec-06 00:43:04 UTC+03:00] BeginIteration 3, AnchorJoinerFast Length of all major blocks of at least 2 fragments: 234357 Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 Block identity: 0.9038 Identity of joined blocks: 0.9038 Nucleotides in blocks: 312 The percentage of input length: 0% Distance from previous pre-pangenome (bp): 227040 The percentage of input length: 1.99% Distance is sufficient to carry on ============================ [2021-Dec-06 00:43:11 UTC+03:00] BeginIteration 4, AnchorJoinerFast Length of all major blocks of at least 2 fragments: 235861 Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 Block identity: 0.9038 Identity of joined blocks: 0.9038 Nucleotides in blocks: 312 The percentage of input length: 0% Distance from previous pre-pangenome (bp): 243086 The percentage of input length: 2.13% Distance is sufficient to carry on ============================ [2021-Dec-06 00:43:18 UTC+03:00] BeginIteration 5, AnchorJoiner Length of all major blocks of at least 2 fragments: 239815 Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 Block identity: 0.9038 Identity of joined blocks: 0.9038 Nucleotides in blocks: 312 The percentage of input length: 0% Distance from previous pre-pangenome (bp): 1031884 The percentage of input length: 9.05% Distance is sufficient to carry on ============================ [2021-Dec-06 00:43:27 UTC+03:00] BeginIteration 6, AnchorJoiner Length of all major blocks of at least 2 fragments: 240098 Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 Block identity: 0.9038 Identity of joined blocks: 0.9038 Nucleotides in blocks: 312 The percentage of input length: 0% Distance from previous pre-pangenome (bp): 286087 The percentage of input length: 2.51% Distance is sufficient to carry on ============================ [2021-Dec-06 00:43:35 UTC+03:00] BeginIteration 7, AnchorJoiner Length of all major blocks of at least 2 fragments: 240243 Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 Block identity: 0.9038 Identity of joined blocks: 0.9038 Nucleotides in blocks: 312 The percentage of input length: 0% Distance from previous pre-pangenome (bp): 10045 The percentage of input length: 0.09% Distance is too low => stopping this loop ============================ [2021-Dec-06 00:43:42 UTC+03:00] BeginIteration 8, AnchorBlastJoiner Length of all major blocks of at least 2 fragments: 247722 Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 Block identity: 0.9038 Identity of joined blocks: 0.9038 Nucleotides in blocks: 312 The percentage of input length: 0% Distance from previous pre-pangenome (bp): 1384056 The percentage of input length: 12.14% Distance is sufficient to carry on ============================ [2021-Dec-06 00:44:47 UTC+03:00] BeginIteration 9, AnchorBlastJoiner Length of all major blocks of at least 2 fragments: 248083 Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 Block identity: 0.9038 Identity of joined blocks: 0.9038 Nucleotides in blocks: 312 The percentage of input length: 0% Distance from previous pre-pangenome (bp): 7260 The percentage of input length: 0.06% Distance is too low => stopping this loop ============================ [2021-Dec-06 00:47:45 UTC+03:00] StopInfo The pangenome has been constructed. Blocks' lengths: 10864008 major: 10859407 minor: 4601 ============================ All major blocks of at least 2 fragments: fragments: 1210 blocks: 390 fragments / blocks: 3.1025 Block identity: min: 0.7885 median: 0.9261 avg: 0.9368 max: 1 Identity of joined blocks: 0.981138 Block sizes: min: 2 median: 2 avg: 3.10 max: 22 Fragment lengths: min: 80 median: 134 avg: 652.06 max: 55971 Fragment length spreading ((max - min) / avg) inside block: min: 0 median: 0 avg: 0.0092 max: 0.3367 GC content: min: 0.2157 median: 0.4099 avg: 0.4174 max: 0.6303 Nucleotides in blocks: 788998 The percentage of input length: 6.91% Total length of blocks: 249624 The percentage of total blocks' length: 2.29% ============================ Stable blocks (represented in all genomes once, but not minor): fragments: 3 blocks: 1 fragments / blocks: 3 Block identity: 0.9038 Identity of joined blocks: 0.9038 Block sizes: 3 Fragment lengths: 104 Fragment length spreading ((max - min) / avg) inside block: 0 GC content: 0.4839 Nucleotides in blocks: 312 The percentage of input length: 0% Total length of blocks: 104 The percentage of total blocks' length: 0% ============================ Partial blocks (represented once in subset of genomes): fragments: 98 blocks: 49 fragments / blocks: 2 Block identity: min: 0.8904 median: 0.9065 avg: 0.9083 max: 0.9423 Identity of joined blocks: 0.908906 Block sizes: 2 Fragment lengths: min: 99 median: 107 avg: 120.96 max: 303 Fragment length spreading ((max - min) / avg) inside block: min: 0 median: 0 avg: 0.001 max: 0.0185 GC content: min: 0.2157 median: 0.4257 avg: 0.4297 max: 0.5617 Nucleotides in blocks: 11854 The percentage of input length: 0.1% Total length of blocks: 5942 The percentage of total blocks' length: 0.05% ============================ Blocks with repeats (at least two copies in at least one genome): fragments: 1109 blocks: 340 fragments / blocks: 3.2617 Block identity: min: 0.7885 median: 0.9333 avg: 0.9411 max: 1 Identity of joined blocks: 0.982933 Block sizes: min: 2 median: 2 avg: 3.26 max: 22 Fragment lengths: min: 80 median: 138 avg: 700.48 max: 55971 Fragment length spreading ((max - min) / avg) inside block: min: 0 median: 0 avg: 0.0104 max: 0.3367 GC content: min: 0.2276 median: 0.4061 avg: 0.4154 max: 0.6303 Nucleotides in blocks: 776832 The percentage of input length: 6.81% Total length of blocks: 243578 The percentage of total blocks' length: 2.24% ============================ Unique (blocks of 1 fragment but not minor): fragments: 653 blocks: 653 Fragment lengths: min: 102 median: 6924 avg: 16247.75 max: 157324 GC content: min: 0.2333 median: 0.3712 avg: 0.3755 max: 0.5989 Nucleotides in blocks: 10609783 The percentage of input length: 93.02% Total length of blocks: 10609783 The percentage of total blocks' length: 97.65% ============================ Minor blocks (too short to say smth about): fragments: 237 blocks: 143 fragments / blocks: 1.6573 Block identity: min: 0 median: 1 avg: 0.9061 max: 1 Identity of joined blocks: 0.922726 Block sizes: min: 1 median: 1 avg: 1.66 max: 14 Fragment lengths: min: 1 median: 14 avg: 25.95 max: 99 Fragment length spreading ((max - min) / avg) inside block: min: 0 median: 0 avg: 0.0733 max: 1.9333 GC content: min: -1 median: 0.4142 avg: -135155.9751 max: 1 Nucleotides in blocks: 6149 The percentage of input length: 0.05% Total length of blocks: 4601 The percentage of total blocks' length: 0.04% The pangenome has been prepared for the next step: PostProcessing .. done