2026-07-03 20:48:01,902 - Reading Coords - INFO - syri:134 - Reading input from BAM file
2026-07-03 20:48:24,955 - Reading Coords - INFO - syri:134 - Filtering low-quality alignments (alignment quality < 90, alignment length < 100)
2026-07-03 20:48:25,010 - Reading Coords - WARNING - syri:134 - Chromosomes IDs do not match.
2026-07-03 20:48:25,034 - Reading Coords - ERROR - syri:134 - Unequal number of chromosomes in the genomes. Exiting
2026-07-04 20:34:30,356 - Reading Coords - INFO - syri:134 - Reading input from BAM file
2026-07-04 20:34:52,124 - Reading Coords - INFO - syri:134 - Filtering low-quality alignments (alignment quality < 90, alignment length < 100)
2026-07-04 20:34:52,173 - Reading Coords - WARNING - syri:134 - Chromosomes IDs do not match.
2026-07-04 20:34:52,196 - Reading Coords - ERROR - syri:134 - Unequal number of chromosomes in the genomes. Exiting
2026-07-04 20:42:51,078 - Reading Coords - INFO - syri:134 - Reading input from BAM file
2026-07-04 20:43:12,864 - Reading Coords - INFO - syri:134 - Filtering low-quality alignments (alignment quality < 90, alignment length < 100)
2026-07-04 20:43:26,616 - syri - INFO - syri:215 - starting
2026-07-04 20:43:26,629 - syri - INFO - syri:215 - Analysing chromosomes: ['NC_052307.1', 'NC_052308.1', 'NC_052309.1', 'NC_052310.1', 'NC_052311.1', 'NC_052312.1', 'NC_052313.1', 'NC_052314.1', 'NC_052315.1', 'NC_052316.1', 'NC_052317.1', 'NC_052318.1', 'NC_052319.1', 'NC_052320.1', 'NC_052321.1', 'NC_052322.1', 'NC_052323.1', 'NC_052324.1', 'NC_052325.1', 'NC_052326.1', 'NC_052327.1', 'NC_052328.1', 'NC_052329.1', 'NC_052330.1', 'NC_052331.1', 'NC_052332.1', 'NC_052333.1', 'NC_052334.1', 'NC_052335.1', 'NC_052336.1', 'NC_052337.1', 'NC_052338.1', 'NC_052339.1', 'NC_052340.1', 'NC_052341.1', 'NC_052342.1', 'NC_052343.1', 'NC_052344.1', 'NC_052345.1', 'NC_052346.1', 'NC_052347.1', 'NC_052348.1']
2026-07-04 20:43:26,808 - syri.NC_052307.1 - INFO - mapstar:48 - NC_052307.1 (690, 11)
2026-07-04 20:43:26,808 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052307.1
2026-07-04 20:43:26,830 - syri.NC_052308.1 - INFO - mapstar:48 - NC_052308.1 (1049, 11)
2026-07-04 20:43:26,831 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052308.1
2026-07-04 20:43:26,859 - syri.NC_052309.1 - INFO - mapstar:48 - NC_052309.1 (775, 11)
2026-07-04 20:43:26,859 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052309.1
2026-07-04 20:43:26,888 - syri.NC_052310.1 - INFO - mapstar:48 - NC_052310.1 (946, 11)
2026-07-04 20:43:26,889 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052310.1
2026-07-04 20:43:26,913 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052307.1
2026-07-04 20:43:26,923 - syri.NC_052311.1 - INFO - mapstar:48 - NC_052311.1 (779, 11)
2026-07-04 20:43:26,923 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052311.1
2026-07-04 20:43:26,953 - syri.NC_052312.1 - INFO - mapstar:48 - NC_052312.1 (588, 11)
2026-07-04 20:43:26,953 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052312.1
2026-07-04 20:43:26,979 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052309.1
2026-07-04 20:43:26,985 - syri.NC_052313.1 - INFO - mapstar:48 - NC_052313.1 (632, 11)
2026-07-04 20:43:26,985 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052313.1
2026-07-04 20:43:27,018 - syri.NC_052314.1 - INFO - mapstar:48 - NC_052314.1 (683, 11)
2026-07-04 20:43:27,018 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052308.1
2026-07-04 20:43:27,019 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052314.1
2026-07-04 20:43:27,044 - syri.NC_052315.1 - INFO - mapstar:48 - NC_052315.1 (295, 11)
2026-07-04 20:43:27,044 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052315.1
2026-07-04 20:43:27,054 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052311.1
2026-07-04 20:43:27,058 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052312.1
2026-07-04 20:43:27,062 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052310.1
2026-07-04 20:43:27,074 - syri.NC_052316.1 - INFO - mapstar:48 - NC_052316.1 (431, 11)
2026-07-04 20:43:27,074 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052316.1
2026-07-04 20:43:27,103 - syri.NC_052317.1 - INFO - mapstar:48 - NC_052317.1 (338, 11)
2026-07-04 20:43:27,103 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052317.1
2026-07-04 20:43:27,107 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052315.1
2026-07-04 20:43:27,113 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052313.1
2026-07-04 20:43:27,131 - syri.NC_052318.1 - INFO - mapstar:48 - NC_052318.1 (340, 11)
2026-07-04 20:43:27,132 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052318.1
2026-07-04 20:43:27,137 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052314.1
2026-07-04 20:43:27,161 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052316.1
2026-07-04 20:43:27,163 - syri.NC_052319.1 - INFO - mapstar:48 - NC_052319.1 (313, 11)
2026-07-04 20:43:27,163 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052319.1
2026-07-04 20:43:27,166 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052317.1
2026-07-04 20:43:27,193 - syri.NC_052320.1 - INFO - mapstar:48 - NC_052320.1 (339, 11)
2026-07-04 20:43:27,194 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052320.1
2026-07-04 20:43:27,195 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052318.1
2026-07-04 20:43:27,230 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052319.1
2026-07-04 20:43:27,238 - syri.NC_052321.1 - INFO - mapstar:48 - NC_052321.1 (286, 11)
2026-07-04 20:43:27,238 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052321.1
2026-07-04 20:43:27,268 - syri.NC_052322.1 - INFO - mapstar:48 - NC_052322.1 (431, 11)
2026-07-04 20:43:27,269 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052322.1
2026-07-04 20:43:27,269 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052320.1
2026-07-04 20:43:27,298 - syri.NC_052323.1 - INFO - mapstar:48 - NC_052323.1 (605, 11)
2026-07-04 20:43:27,298 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052323.1
2026-07-04 20:43:27,303 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052321.1
2026-07-04 20:43:27,328 - syri.NC_052324.1 - INFO - mapstar:48 - NC_052324.1 (366, 11)
2026-07-04 20:43:27,329 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052324.1
2026-07-04 20:43:27,351 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052322.1
2026-07-04 20:43:27,358 - syri.NC_052325.1 - INFO - mapstar:48 - NC_052325.1 (419, 11)
2026-07-04 20:43:27,358 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052325.1
2026-07-04 20:43:27,382 - syri.NC_052326.1 - INFO - mapstar:48 - NC_052326.1 (338, 11)
2026-07-04 20:43:27,382 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052326.1
2026-07-04 20:43:27,390 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052307.1
2026-07-04 20:43:27,403 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052324.1
2026-07-04 20:43:27,414 - syri.NC_052327.1 - INFO - mapstar:48 - NC_052327.1 (412, 11)
2026-07-04 20:43:27,414 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052327.1
2026-07-04 20:43:27,420 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052323.1
2026-07-04 20:43:27,441 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052325.1
2026-07-04 20:43:27,448 - syri.NC_052328.1 - INFO - mapstar:48 - NC_052328.1 (309, 11)
2026-07-04 20:43:27,448 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052328.1
2026-07-04 20:43:27,451 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052326.1
2026-07-04 20:43:27,474 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052309.1
2026-07-04 20:43:27,478 - syri.NC_052329.1 - INFO - mapstar:48 - NC_052329.1 (355, 11)
2026-07-04 20:43:27,478 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052329.1
2026-07-04 20:43:27,498 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052327.1
2026-07-04 20:43:27,500 - syri.NC_052330.1 - INFO - mapstar:48 - NC_052330.1 (279, 11)
2026-07-04 20:43:27,501 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052330.1
2026-07-04 20:43:27,536 - syri.NC_052331.1 - INFO - mapstar:48 - NC_052331.1 (242, 11)
2026-07-04 20:43:27,536 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052331.1
2026-07-04 20:43:27,538 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052310.1
2026-07-04 20:43:27,540 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052311.1
2026-07-04 20:43:27,561 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052328.1
2026-07-04 20:43:27,564 - syri.NC_052332.1 - INFO - mapstar:48 - NC_052332.1 (337, 11)
2026-07-04 20:43:27,564 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052332.1
2026-07-04 20:43:27,565 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052330.1
2026-07-04 20:43:27,569 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052312.1
2026-07-04 20:43:27,591 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052315.1
2026-07-04 20:43:27,593 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052329.1
2026-07-04 20:43:27,593 - syri.NC_052333.1 - INFO - mapstar:48 - NC_052333.1 (622, 11)
2026-07-04 20:43:27,594 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052333.1
2026-07-04 20:43:27,612 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052313.1
2026-07-04 20:43:27,620 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052308.1
2026-07-04 20:43:27,623 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052331.1
2026-07-04 20:43:27,627 - syri.NC_052334.1 - INFO - mapstar:48 - NC_052334.1 (356, 11)
2026-07-04 20:43:27,627 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052334.1
2026-07-04 20:43:27,653 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052314.1
2026-07-04 20:43:27,654 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052317.1
2026-07-04 20:43:27,659 - syri.NC_052335.1 - INFO - mapstar:48 - NC_052335.1 (224, 11)
2026-07-04 20:43:27,659 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052335.1
2026-07-04 20:43:27,665 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052316.1
2026-07-04 20:43:27,676 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052332.1
2026-07-04 20:43:27,686 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052318.1
2026-07-04 20:43:27,687 - syri.NC_052336.1 - INFO - mapstar:48 - NC_052336.1 (320, 11)
2026-07-04 20:43:27,688 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052336.1
2026-07-04 20:43:27,715 - syri.NC_052337.1 - INFO - mapstar:48 - NC_052337.1 (293, 11)
2026-07-04 20:43:27,716 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052337.1
2026-07-04 20:43:27,722 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052333.1
2026-07-04 20:43:27,740 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052334.1
2026-07-04 20:43:27,748 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052320.1
2026-07-04 20:43:27,751 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052335.1
2026-07-04 20:43:27,755 - syri.NC_052338.1 - INFO - mapstar:48 - NC_052338.1 (482, 11)
2026-07-04 20:43:27,756 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052338.1
2026-07-04 20:43:27,780 - syri.NC_052339.1 - INFO - mapstar:48 - NC_052339.1 (351, 11)
2026-07-04 20:43:27,780 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052339.1
2026-07-04 20:43:27,782 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052321.1
2026-07-04 20:43:27,806 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052336.1
2026-07-04 20:43:27,808 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052319.1
2026-07-04 20:43:27,811 - syri.NC_052340.1 - INFO - mapstar:48 - NC_052340.1 (414, 11)
2026-07-04 20:43:27,811 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052340.1
2026-07-04 20:43:27,814 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052337.1
2026-07-04 20:43:27,842 - syri.NC_052341.1 - INFO - mapstar:48 - NC_052341.1 (268, 11)
2026-07-04 20:43:27,842 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052341.1
2026-07-04 20:43:27,852 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.506111145019531e-05. iterations remaining 37
2026-07-04 20:43:27,868 - syri.NC_052342.1 - INFO - mapstar:48 - NC_052342.1 (365, 11)
2026-07-04 20:43:27,868 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052342.1
2026-07-04 20:43:27,897 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052322.1
2026-07-04 20:43:27,901 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052324.1
2026-07-04 20:43:27,905 - syri.NC_052343.1 - INFO - mapstar:48 - NC_052343.1 (226, 11)
2026-07-04 20:43:27,905 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052343.1
2026-07-04 20:43:27,907 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052339.1
2026-07-04 20:43:27,915 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052338.1
2026-07-04 20:43:27,937 - syri.NC_052344.1 - INFO - mapstar:48 - NC_052344.1 (288, 11)
2026-07-04 20:43:27,938 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052344.1
2026-07-04 20:43:27,943 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052341.1
2026-07-04 20:43:27,945 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052325.1
2026-07-04 20:43:27,951 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052326.1
2026-07-04 20:43:27,959 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052340.1
2026-07-04 20:43:27,966 - syri.NC_052345.1 - INFO - mapstar:48 - NC_052345.1 (341, 11)
2026-07-04 20:43:27,966 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052345.1
2026-07-04 20:43:27,990 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052327.1
2026-07-04 20:43:27,990 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052342.1
2026-07-04 20:43:27,993 - syri.NC_052346.1 - INFO - mapstar:48 - NC_052346.1 (267, 11)
2026-07-04 20:43:27,993 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052346.1
2026-07-04 20:43:27,999 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052343.1
2026-07-04 20:43:28,029 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 3.314018249511719e-05. iterations remaining 36
2026-07-04 20:43:28,035 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052344.1
2026-07-04 20:43:28,069 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052323.1
2026-07-04 20:43:28,093 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052345.1
2026-07-04 20:43:28,095 - syri.NC_052347.1 - INFO - mapstar:48 - NC_052347.1 (178, 11)
2026-07-04 20:43:28,095 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052347.1
2026-07-04 20:43:28,102 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052346.1
2026-07-04 20:43:28,182 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052347.1
2026-07-04 20:43:28,197 - syri.NC_052348.1 - INFO - mapstar:48 - NC_052348.1 (299, 11)
2026-07-04 20:43:28,197 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052348.1
2026-07-04 20:43:28,269 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052347.1
2026-07-04 20:43:28,281 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052348.1
2026-07-04 20:43:28,294 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 6.818771362304688e-05. iterations remaining 36
2026-07-04 20:43:28,318 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052330.1
2026-07-04 20:43:28,356 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052348.1
2026-07-04 20:43:28,402 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052328.1
2026-07-04 20:43:28,407 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.459785461425781e-05. iterations remaining 42
2026-07-04 20:43:28,414 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 8.702278137207031e-05. iterations remaining 36
2026-07-04 20:43:28,458 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052329.1
2026-07-04 20:43:28,485 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052331.1
2026-07-04 20:43:28,500 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0003714561462402344. iterations remaining 33
2026-07-04 20:43:28,503 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052333.1
2026-07-04 20:43:28,530 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052332.1
2026-07-04 20:43:28,535 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052334.1
2026-07-04 20:43:28,565 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052335.1
2026-07-04 20:43:28,596 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052341.1
2026-07-04 20:43:28,625 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052337.1
2026-07-04 20:43:28,638 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0008001327514648438. iterations remaining 28
2026-07-04 20:43:28,646 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052336.1
2026-07-04 20:43:28,751 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052338.1
2026-07-04 20:43:28,753 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052339.1
2026-07-04 20:43:28,780 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052340.1
2026-07-04 20:43:28,802 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052343.1
2026-07-04 20:43:28,851 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.029273986816406e-05. iterations remaining 43
2026-07-04 20:43:28,852 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052344.1
2026-07-04 20:43:28,858 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052342.1
2026-07-04 20:43:28,919 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052345.1
2026-07-04 20:43:28,921 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052346.1
2026-07-04 20:43:29,185 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 6.341934204101562e-05. iterations remaining 38
2026-07-04 20:43:29,185 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.458427429199219e-05. iterations remaining 37
2026-07-04 20:43:29,383 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 7.176399230957031e-05. iterations remaining 35
2026-07-04 20:43:29,443 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 6.771087646484375e-05. iterations remaining 35
2026-07-04 20:43:29,518 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.00019931793212890625. iterations remaining 34
2026-07-04 20:43:29,682 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.984306335449219e-05. iterations remaining 47
2026-07-04 20:43:29,827 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.002716064453125e-05. iterations remaining 38
2026-07-04 20:43:29,914 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.02797102928161621. iterations remaining 19
2026-07-04 20:43:35,897 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.00010180473327636719. iterations remaining 43
2026-07-04 20:43:35,944 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.09808349609375e-05. iterations remaining 40
2026-07-04 20:43:44,603 - getCTX - INFO - syri:215 - Identifying cross-chromosomal translocation and duplication for chromosome2026-07-04 20:43:44.603653
2026-07-04 20:43:52,803 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 6.4373016357421875e-06. iterations remaining 47
2026-07-04 20:43:53,507 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.935264587402344e-05. iterations remaining 49
2026-07-04 20:43:53,623 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.3365020751953125e-05. iterations remaining 40
2026-07-04 20:43:53,715 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.0067901611328125e-06. iterations remaining 49
2026-07-04 20:43:53,747 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 1.2636184692382812e-05. iterations remaining 42
2026-07-04 20:43:54,536 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.935264587402344e-05. iterations remaining 36
2026-07-04 20:43:55,420 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.3126602172851562e-05. iterations remaining 37
2026-07-04 20:43:56,104 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 9.274482727050781e-05. iterations remaining 33
2026-07-04 20:43:56,350 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 3.337860107421875e-05. iterations remaining 37
2026-07-04 20:43:58,426 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.459785461425781e-05. iterations remaining 44
2026-07-04 20:44:00,287 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.384185791015625e-05. iterations remaining 45
2026-07-04 20:44:01,131 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 7.82012939453125e-05. iterations remaining 43
2026-07-04 20:44:01,755 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.459785461425781e-05. iterations remaining 36
2026-07-04 20:44:01,871 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.2928924560546875e-05. iterations remaining 37
2026-07-04 20:44:31,703 - local_variation - INFO - syri:226 - Finding SVs in synOut.txt, invOut.txt, TLOut.txt, invTLOut.txt, ctxOut.txt
2026-07-04 20:45:12,338 - local_variation - INFO - syri:246 - Finding SNPs and small indels
2026-07-04 20:48:14,026 - local_variation - INFO - syri:258 - Combining outputs
2026-07-04 20:48:14,027 - local_variation - INFO - syri:263 - Generating table output
2026-07-04 20:52:58,509 - local_variation - INFO - syri:268 - Generating VCF
2026-07-04 20:53:13,253 - local_variation - INFO - syri:276 - Finished syri