2026-07-03 20:39:22,210 - Reading Coords - INFO - syri:134 - Reading input from BAM file
2026-07-03 20:39:39,783 - Reading Coords - INFO - syri:134 - Filtering low-quality alignments (alignment quality < 90, alignment length < 100)
2026-07-03 20:39:52,597 - syri - INFO - syri:215 - starting
2026-07-03 20:39:52,607 - 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']
2026-07-03 20:39:52,944 - syri.NC_052307.1 - INFO - mapstar:48 - NC_052307.1 (686, 11)
2026-07-03 20:39:52,944 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052307.1
2026-07-03 20:39:52,962 - syri.NC_052308.1 - INFO - mapstar:48 - NC_052308.1 (906, 11)
2026-07-03 20:39:52,962 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052308.1
2026-07-03 20:39:52,982 - syri.NC_052309.1 - INFO - mapstar:48 - NC_052309.1 (809, 11)
2026-07-03 20:39:52,982 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052309.1
2026-07-03 20:39:53,006 - syri.NC_052310.1 - INFO - mapstar:48 - NC_052310.1 (624, 11)
2026-07-03 20:39:53,006 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052310.1
2026-07-03 20:39:53,032 - syri.NC_052311.1 - INFO - mapstar:48 - NC_052311.1 (772, 11)
2026-07-03 20:39:53,032 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052311.1
2026-07-03 20:39:53,048 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052307.1
2026-07-03 20:39:53,054 - syri.NC_052312.1 - INFO - mapstar:48 - NC_052312.1 (479, 11)
2026-07-03 20:39:53,054 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052312.1
2026-07-03 20:39:53,075 - syri.NC_052313.1 - INFO - mapstar:48 - NC_052313.1 (542, 11)
2026-07-03 20:39:53,075 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052313.1
2026-07-03 20:39:53,097 - syri.NC_052314.1 - INFO - mapstar:48 - NC_052314.1 (552, 11)
2026-07-03 20:39:53,097 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052314.1
2026-07-03 20:39:53,103 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052310.1
2026-07-03 20:39:53,107 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052309.1
2026-07-03 20:39:53,109 - syri.NC_052315.1 - INFO - mapstar:48 - NC_052315.1 (279, 11)
2026-07-03 20:39:53,110 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052315.1
2026-07-03 20:39:53,117 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052308.1
2026-07-03 20:39:53,130 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052312.1
2026-07-03 20:39:53,137 - syri.NC_052316.1 - INFO - mapstar:48 - NC_052316.1 (380, 11)
2026-07-03 20:39:53,137 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052316.1
2026-07-03 20:39:53,157 - syri.NC_052317.1 - INFO - mapstar:48 - NC_052317.1 (349, 11)
2026-07-03 20:39:53,158 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052317.1
2026-07-03 20:39:53,160 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052311.1
2026-07-03 20:39:53,164 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052313.1
2026-07-03 20:39:53,170 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052315.1
2026-07-03 20:39:53,186 - syri.NC_052318.1 - INFO - mapstar:48 - NC_052318.1 (276, 11)
2026-07-03 20:39:53,186 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052318.1
2026-07-03 20:39:53,192 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052314.1
2026-07-03 20:39:53,204 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052316.1
2026-07-03 20:39:53,208 - syri.NC_052319.1 - INFO - mapstar:48 - NC_052319.1 (280, 11)
2026-07-03 20:39:53,208 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052319.1
2026-07-03 20:39:53,219 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052317.1
2026-07-03 20:39:53,232 - syri.NC_052320.1 - INFO - mapstar:48 - NC_052320.1 (249, 11)
2026-07-03 20:39:53,232 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052320.1
2026-07-03 20:39:53,238 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052318.1
2026-07-03 20:39:53,255 - syri.NC_052321.1 - INFO - mapstar:48 - NC_052321.1 (264, 11)
2026-07-03 20:39:53,256 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052321.1
2026-07-03 20:39:53,261 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052319.1
2026-07-03 20:39:53,277 - syri.NC_052322.1 - INFO - mapstar:48 - NC_052322.1 (408, 11)
2026-07-03 20:39:53,277 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052322.1
2026-07-03 20:39:53,284 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052320.1
2026-07-03 20:39:53,298 - syri.NC_052323.1 - INFO - mapstar:48 - NC_052323.1 (382, 11)
2026-07-03 20:39:53,298 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052323.1
2026-07-03 20:39:53,310 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052321.1
2026-07-03 20:39:53,319 - syri.NC_052324.1 - INFO - mapstar:48 - NC_052324.1 (295, 11)
2026-07-03 20:39:53,319 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052324.1
2026-07-03 20:39:53,346 - syri.NC_052325.1 - INFO - mapstar:48 - NC_052325.1 (415, 11)
2026-07-03 20:39:53,347 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052325.1
2026-07-03 20:39:53,347 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052322.1
2026-07-03 20:39:53,367 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052323.1
2026-07-03 20:39:53,367 - syri.NC_052326.1 - INFO - mapstar:48 - NC_052326.1 (318, 11)
2026-07-03 20:39:53,367 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052326.1
2026-07-03 20:39:53,377 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052324.1
2026-07-03 20:39:53,389 - syri.NC_052327.1 - INFO - mapstar:48 - NC_052327.1 (340, 11)
2026-07-03 20:39:53,389 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052327.1
2026-07-03 20:39:53,411 - syri.NC_052328.1 - INFO - mapstar:48 - NC_052328.1 (279, 11)
2026-07-03 20:39:53,411 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052328.1
2026-07-03 20:39:53,424 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052326.1
2026-07-03 20:39:53,433 - syri.NC_052329.1 - INFO - mapstar:48 - NC_052329.1 (302, 11)
2026-07-03 20:39:53,433 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052329.1
2026-07-03 20:39:53,437 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052325.1
2026-07-03 20:39:53,445 - syri.NC_052330.1 - INFO - mapstar:48 - NC_052330.1 (267, 11)
2026-07-03 20:39:53,446 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052330.1
2026-07-03 20:39:53,456 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052327.1
2026-07-03 20:39:53,467 - syri.NC_052331.1 - INFO - mapstar:48 - NC_052331.1 (235, 11)
2026-07-03 20:39:53,467 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052331.1
2026-07-03 20:39:53,469 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052328.1
2026-07-03 20:39:53,490 - syri.NC_052332.1 - INFO - mapstar:48 - NC_052332.1 (339, 11)
2026-07-03 20:39:53,490 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052332.1
2026-07-03 20:39:53,498 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052329.1
2026-07-03 20:39:53,507 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052330.1
2026-07-03 20:39:53,511 - syri.NC_052333.1 - INFO - mapstar:48 - NC_052333.1 (670, 11)
2026-07-03 20:39:53,511 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052333.1
2026-07-03 20:39:53,523 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052331.1
2026-07-03 20:39:53,534 - syri.NC_052334.1 - INFO - mapstar:48 - NC_052334.1 (304, 11)
2026-07-03 20:39:53,535 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052334.1
2026-07-03 20:39:53,550 - syri.NC_052335.1 - INFO - mapstar:48 - NC_052335.1 (197, 11)
2026-07-03 20:39:53,551 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052335.1
2026-07-03 20:39:53,570 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052332.1
2026-07-03 20:39:53,572 - syri.NC_052336.1 - INFO - mapstar:48 - NC_052336.1 (333, 11)
2026-07-03 20:39:53,573 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052336.1
2026-07-03 20:39:53,595 - syri.NC_052337.1 - INFO - mapstar:48 - NC_052337.1 (820, 11)
2026-07-03 20:39:53,596 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052337.1
2026-07-03 20:39:53,596 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052334.1
2026-07-03 20:39:53,614 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052335.1
2026-07-03 20:39:53,615 - syri.NC_052338.1 - INFO - mapstar:48 - NC_052338.1 (363, 11)
2026-07-03 20:39:53,616 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052338.1
2026-07-03 20:39:53,627 - syri.NC_052339.1 - INFO - mapstar:48 - NC_052339.1 (294, 11)
2026-07-03 20:39:53,627 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052339.1
2026-07-03 20:39:53,634 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052336.1
2026-07-03 20:39:53,634 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052333.1
2026-07-03 20:39:53,655 - syri.NC_052340.1 - INFO - mapstar:48 - NC_052340.1 (280, 11)
2026-07-03 20:39:53,655 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052340.1
2026-07-03 20:39:53,676 - syri.NC_052341.1 - INFO - mapstar:48 - NC_052341.1 (203, 11)
2026-07-03 20:39:53,676 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052341.1
2026-07-03 20:39:53,684 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052338.1
2026-07-03 20:39:53,697 - syri.NC_052342.1 - INFO - mapstar:48 - NC_052342.1 (303, 11)
2026-07-03 20:39:53,697 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052342.1
2026-07-03 20:39:53,709 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052339.1
2026-07-03 20:39:53,718 - syri.NC_052343.1 - INFO - mapstar:48 - NC_052343.1 (193, 11)
2026-07-03 20:39:53,719 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052343.1
2026-07-03 20:39:53,719 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052340.1
2026-07-03 20:39:53,723 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052337.1
2026-07-03 20:39:53,729 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052341.1
2026-07-03 20:39:53,737 - syri.NC_052344.1 - INFO - mapstar:48 - NC_052344.1 (378, 11)
2026-07-03 20:39:53,738 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052344.1
2026-07-03 20:39:53,759 - syri.NC_052345.1 - INFO - mapstar:48 - NC_052345.1 (332, 11)
2026-07-03 20:39:53,759 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052345.1
2026-07-03 20:39:53,774 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052343.1
2026-07-03 20:39:53,775 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052342.1
2026-07-03 20:39:53,780 - syri.NC_052346.1 - INFO - mapstar:48 - NC_052346.1 (193, 11)
2026-07-03 20:39:53,780 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052346.1
2026-07-03 20:39:53,816 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052344.1
2026-07-03 20:39:53,833 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052346.1
2026-07-03 20:39:53,843 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052345.1
2026-07-03 20:39:55,537 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052315.1
2026-07-03 20:39:55,547 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052316.1
2026-07-03 20:39:55,547 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052331.1
2026-07-03 20:39:55,547 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052343.1
2026-07-03 20:39:55,547 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052317.1
2026-07-03 20:39:55,547 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052342.1
2026-07-03 20:39:55,548 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052335.1
2026-07-03 20:39:55,548 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052332.1
2026-07-03 20:39:55,548 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052320.1
2026-07-03 20:39:55,548 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052325.1
2026-07-03 20:39:55,549 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052330.1
2026-07-03 20:39:55,549 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052311.1
2026-07-03 20:39:55,549 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052310.1
2026-07-03 20:39:55,550 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052326.1
2026-07-03 20:39:55,550 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052329.1
2026-07-03 20:39:55,551 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052346.1
2026-07-03 20:39:55,552 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052312.1
2026-07-03 20:39:55,556 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052307.1
2026-07-03 20:39:55,557 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052322.1
2026-07-03 20:39:55,557 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052337.1
2026-07-03 20:39:55,557 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052339.1
2026-07-03 20:39:55,557 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052338.1
2026-07-03 20:39:55,557 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052323.1
2026-07-03 20:39:55,557 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052334.1
2026-07-03 20:39:55,557 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052321.1
2026-07-03 20:39:55,557 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052345.1
2026-07-03 20:39:55,557 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052318.1
2026-07-03 20:39:55,558 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052313.1
2026-07-03 20:39:55,558 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052340.1
2026-07-03 20:39:55,558 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052333.1
2026-07-03 20:39:55,558 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052341.1
2026-07-03 20:39:55,559 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052336.1
2026-07-03 20:39:55,559 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052344.1
2026-07-03 20:39:55,559 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052324.1
2026-07-03 20:39:55,560 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052309.1
2026-07-03 20:39:55,560 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052319.1
2026-07-03 20:39:55,562 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052314.1
2026-07-03 20:39:55,565 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052327.1
2026-07-03 20:39:55,568 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052308.1
2026-07-03 20:39:55,574 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052328.1
2026-07-03 20:39:55,762 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.698204040527344e-05. iterations remaining 36
2026-07-03 20:39:55,839 - syri.NC_052347.1 - INFO - mapstar:48 - NC_052347.1 (94, 11)
2026-07-03 20:39:55,839 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052347.1
2026-07-03 20:39:55,845 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0054399967193603516. iterations remaining 23
2026-07-03 20:39:55,852 - syri.NC_052348.1 - INFO - mapstar:48 - NC_052348.1 (249, 11)
2026-07-03 20:39:55,852 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052348.1
2026-07-03 20:39:55,874 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.00010013580322265625. iterations remaining 36
2026-07-03 20:39:55,879 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052347.1
2026-07-03 20:39:55,883 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 7.3909759521484375e-06. iterations remaining 44
2026-07-03 20:39:55,920 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052348.1
2026-07-03 20:39:55,928 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052347.1
2026-07-03 20:39:55,986 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052348.1
2026-07-03 20:39:56,023 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 3.5762786865234375e-05. iterations remaining 36
2026-07-03 20:39:56,106 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0006296634674072266. iterations remaining 29
2026-07-03 20:39:56,214 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.4557113647460938e-05. iterations remaining 46
2026-07-03 20:39:56,219 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 9.5367431640625e-07. iterations remaining 47
2026-07-03 20:39:56,279 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0002143383026123047. iterations remaining 40
2026-07-03 20:39:56,313 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0001285076141357422. iterations remaining 49
2026-07-03 20:39:56,698 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 6.389617919921875e-05. iterations remaining 38
2026-07-03 20:40:33,438 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.000102996826171875. iterations remaining 34
2026-07-03 20:40:35,424 - getCTX - INFO - syri:215 - Identifying cross-chromosomal translocation and duplication for chromosome2026-07-03 20:40:35.424022
2026-07-03 20:40:39,870 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0008935928344726562. iterations remaining 28
2026-07-03 20:40:40,201 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 7.081031799316406e-05. iterations remaining 38
2026-07-03 20:40:40,326 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 1.3113021850585938e-05. iterations remaining 45
2026-07-03 20:40:40,373 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0007240772247314453. iterations remaining 37
2026-07-03 20:40:41,575 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 9.036064147949219e-05. iterations remaining 39
2026-07-03 20:40:43,321 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.00012683868408203125. iterations remaining 43
2026-07-03 20:40:44,921 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.76837158203125e-07. iterations remaining 47
2026-07-03 20:40:45,436 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.0042362213134765625. iterations remaining 24
2026-07-03 20:40:46,381 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 1.1920928955078125e-06. iterations remaining 45
2026-07-03 20:40:47,720 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 3.075599670410156e-05. iterations remaining 45
2026-07-03 20:41:07,359 - local_variation - INFO - syri:226 - Finding SVs in synOut.txt, invOut.txt, TLOut.txt, invTLOut.txt, ctxOut.txt
2026-07-03 20:41:44,240 - local_variation - INFO - syri:246 - Finding SNPs and small indels
2026-07-03 20:44:14,057 - local_variation - INFO - syri:258 - Combining outputs
2026-07-03 20:44:14,069 - local_variation - INFO - syri:263 - Generating table output
2026-07-03 20:47:45,341 - local_variation - INFO - syri:268 - Generating VCF
2026-07-03 20:47:59,671 - local_variation - INFO - syri:276 - Finished syri