Running MakePangenome.. Information about input data: Number of genomes: 4 Number of sequences: 4 Number of sequences per genome: 1 Total length of input (bp): 21041543 Minimum genome length (bp): 5251490 Median genome length (bp): 5258747 Average genome length (bp): 5260385 Maximum genome length (bp): 5272559 ============================ [2021-Nov-15 20:27:18 UTC+03:00] BeginIteration 1, AnchorJoinerFast Length of all major blocks of at least 2 fragments: 75764 Stable blocks (represented in all genomes once, but not minor): fragments: 0 blocks: 0 ============================ [2021-Nov-15 20:27:39 UTC+03:00] BeginIteration 2, AnchorJoinerFast Length of all major blocks of at least 2 fragments: 3832162 Stable blocks (represented in all genomes once, but not minor): fragments: 656 blocks: 164 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999951 Nucleotides in blocks: 14875756 The percentage of input length: 70.69% Distance from previous pre-pangenome (bp): 11735184 The percentage of input length: 55.77% Distance is sufficient to carry on ============================ [2021-Nov-15 20:28:48 UTC+03:00] BeginIteration 3, AnchorJoinerFast Length of all major blocks of at least 2 fragments: 4689064 Stable blocks (represented in all genomes once, but not minor): fragments: 828 blocks: 207 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999953 Nucleotides in blocks: 18300334 The percentage of input length: 86.97% Distance from previous pre-pangenome (bp): 2730900 The percentage of input length: 12.98% Distance is sufficient to carry on ============================ [2021-Nov-15 20:29:55 UTC+03:00] BeginIteration 4, AnchorJoinerFast Length of all major blocks of at least 2 fragments: 4842473 Stable blocks (represented in all genomes once, but not minor): fragments: 844 blocks: 211 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999952 Nucleotides in blocks: 18913463 The percentage of input length: 89.88% Distance from previous pre-pangenome (bp): 679333 The percentage of input length: 3.23% Distance is sufficient to carry on ============================ [2021-Nov-15 20:30:56 UTC+03:00] BeginIteration 5, AnchorJoiner Length of all major blocks of at least 2 fragments: 5145609 Stable blocks (represented in all genomes once, but not minor): fragments: 872 blocks: 218 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999951 Nucleotides in blocks: 20123026 The percentage of input length: 95.63% Distance from previous pre-pangenome (bp): 1558275 The percentage of input length: 7.41% Distance is sufficient to carry on ============================ [2021-Nov-15 20:34:31 UTC+03:00] BeginIteration 6, AnchorJoiner Length of all major blocks of at least 2 fragments: 5145448 Stable blocks (represented in all genomes once, but not minor): fragments: 876 blocks: 219 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999951 Nucleotides in blocks: 20121882 The percentage of input length: 95.62% Distance from previous pre-pangenome (bp): 255111 The percentage of input length: 1.21% Distance is sufficient to carry on ============================ [2021-Nov-15 20:36:42 UTC+03:00] BeginIteration 7, AnchorJoiner Length of all major blocks of at least 2 fragments: 5145448 Stable blocks (represented in all genomes once, but not minor): fragments: 876 blocks: 219 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999951 Nucleotides in blocks: 20121882 The percentage of input length: 95.62% Distance from previous pre-pangenome (bp): 0 The percentage of input length: 0.00% Distance is too low => stopping this loop ============================ [2021-Nov-15 20:37:41 UTC+03:00] BeginIteration 8, AnchorBlastJoiner Length of all major blocks of at least 2 fragments: 5144235 Stable blocks (represented in all genomes once, but not minor): fragments: 900 blocks: 225 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999951 Nucleotides in blocks: 20116098 The percentage of input length: 95.6% Distance from previous pre-pangenome (bp): 399304 The percentage of input length: 1.90% Distance is sufficient to carry on ============================ [2021-Nov-15 20:39:49 UTC+03:00] BeginIteration 9, AnchorBlastJoiner Length of all major blocks of at least 2 fragments: 5144233 Stable blocks (represented in all genomes once, but not minor): fragments: 900 blocks: 225 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999951 Nucleotides in blocks: 20116122 The percentage of input length: 95.6% Distance from previous pre-pangenome (bp): 229 The percentage of input length: 0.00% Distance is too low => stopping this loop ============================ [2021-Nov-15 20:42:33 UTC+03:00] StopInfo The pangenome has been constructed. Blocks' lengths: 5147599 major: 5146146 minor: 1453 ============================ All major blocks of at least 2 fragments: fragments: 2121 blocks: 362 fragments / blocks: 5.8591 Block identity: min: 0.8628 median: 1 avg: 0.9749 max: 1 Identity of joined blocks: 0.999518 Block sizes: min: 4 median: 4 avg: 5.86 max: 44 Fragment lengths: min: 98 median: 299 avg: 9916.59 max: 325176 Fragment length spreading ((max - min) / avg) inside block: min: 0 median: 0 avg: 0.0012 max: 0.0548 GC content: min: 0.2546 median: 0.3528 avg: 0.3634 max: 0.6165 Nucleotides in blocks: 21033080 The percentage of input length: 99.95% Total length of blocks: 5145410 The percentage of total blocks' length: 99.95% ============================ Stable blocks (represented in all genomes once, but not minor): fragments: 900 blocks: 225 fragments / blocks: 4 Block identity: min: 0.999 median: 1 avg: 0.9999 max: 1 Identity of joined blocks: 0.999951 Block sizes: 4 Fragment lengths: min: 101 median: 7690 avg: 22351.25 max: 325176 Fragment length spreading ((max - min) / avg) inside block: min: 0 median: 0 avg: 0 max: 0.0002 GC content: min: 0.256 median: 0.3497 avg: 0.3528 max: 0.5454 Nucleotides in blocks: 20116122 The percentage of input length: 95.6% Total length of blocks: 5029057 The percentage of total blocks' length: 97.69% ============================ Partial blocks (represented once in subset of genomes): fragments: 0 blocks: 0 ============================ Blocks with repeats (at least two copies in at least one genome): fragments: 1221 blocks: 137 fragments / blocks: 8.9124 Block identity: min: 0.8628 median: 0.9215 avg: 0.9338 max: 1 Identity of joined blocks: 0.980799 Block sizes: min: 5 median: 8 avg: 8.91 max: 44 Fragment lengths: min: 98 median: 147 avg: 750.99 max: 18899 Fragment length spreading ((max - min) / avg) inside block: min: 0 median: 0 avg: 0.0031 max: 0.0548 GC content: min: 0.2546 median: 0.3656 avg: 0.3809 max: 0.6165 Nucleotides in blocks: 916958 The percentage of input length: 4.35% Total length of blocks: 116353 The percentage of total blocks' length: 2.26% ============================ Unique (blocks of 1 fragment but not minor): fragments: 5 blocks: 5 Fragment lengths: min: 100 median: 100 avg: 147.20 max: 336 GC content: min: -1 median: -1 avg: -85900.0823 max: 0.3184 Nucleotides in blocks: 736 The percentage of input length: 0% Total length of blocks: 736 The percentage of total blocks' length: 0.01% ============================ Minor blocks (too short to say smth about): fragments: 192 blocks: 32 fragments / blocks: 6 Block identity: min: 0 median: 1 avg: 0.918 max: 1 Identity of joined blocks: 0.959044 Block sizes: min: 4 median: 4 avg: 6.00 max: 36 Fragment lengths: min: 1 median: 26 avg: 40.24 max: 98 Fragment length spreading ((max - min) / avg) inside block: min: 0 median: 0 avg: 0.0521 max: 1.4693 GC content: min: 0.0909 median: 0.3912 avg: 0.3611 max: 0.6641 Nucleotides in blocks: 7727 The percentage of input length: 0.03% Total length of blocks: 1453 The percentage of total blocks' length: 0.02% The pangenome has been prepared for the next step: PostProcessing .. done