2026-07-03 20:48:25,481 - Reading Coords - INFO - syri:134 - Reading input from BAM file
2026-07-03 20:48:48,133 - Reading BAM/SAM file - WARNING - syri:134 - NC_036392.1 do not align with any reference chromosome and cannot be analysed
2026-07-03 20:48:48,287 - Reading Coords - INFO - syri:134 - Filtering low-quality alignments (alignment quality < 90, alignment length < 100)
2026-07-03 20:48:58,070 - syri - INFO - syri:215 - starting
2026-07-03 20:48:58,083 - 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 20:48:58,269 - syri.NC_052307.1 - INFO - mapstar:48 - NC_052307.1 (680, 11)
2026-07-03 20:48:58,269 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052307.1
2026-07-03 20:48:58,295 - syri.NC_052308.1 - INFO - mapstar:48 - NC_052308.1 (696, 11)
2026-07-03 20:48:58,295 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052308.1
2026-07-03 20:48:58,318 - syri.NC_052309.1 - INFO - mapstar:48 - NC_052309.1 (769, 11)
2026-07-03 20:48:58,319 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052309.1
2026-07-03 20:48:58,347 - syri.NC_052310.1 - INFO - mapstar:48 - NC_052310.1 (506, 11)
2026-07-03 20:48:58,347 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052310.1
2026-07-03 20:48:58,374 - syri.NC_052311.1 - INFO - mapstar:48 - NC_052311.1 (856, 11)
2026-07-03 20:48:58,375 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052311.1
2026-07-03 20:48:58,378 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052307.1
2026-07-03 20:48:58,398 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052308.1
2026-07-03 20:48:58,401 - syri.NC_052312.1 - INFO - mapstar:48 - NC_052312.1 (461, 11)
2026-07-03 20:48:58,402 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052312.1
2026-07-03 20:48:58,426 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052310.1
2026-07-03 20:48:58,431 - syri.NC_052313.1 - INFO - mapstar:48 - NC_052313.1 (474, 11)
2026-07-03 20:48:58,431 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052313.1
2026-07-03 20:48:58,440 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052309.1
2026-07-03 20:48:58,456 - syri.NC_052314.1 - INFO - mapstar:48 - NC_052314.1 (579, 11)
2026-07-03 20:48:58,457 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052314.1
2026-07-03 20:48:58,480 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052312.1
2026-07-03 20:48:58,483 - syri.NC_052315.1 - INFO - mapstar:48 - NC_052315.1 (187, 11)
2026-07-03 20:48:58,483 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052315.1
2026-07-03 20:48:58,512 - syri.NC_052316.1 - INFO - mapstar:48 - NC_052316.1 (310, 11)
2026-07-03 20:48:58,512 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052316.1
2026-07-03 20:48:58,514 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052313.1
2026-07-03 20:48:58,524 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052311.1
2026-07-03 20:48:58,528 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052315.1
2026-07-03 20:48:58,540 - syri.NC_052317.1 - INFO - mapstar:48 - NC_052317.1 (362, 11)
2026-07-03 20:48:58,540 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052317.1
2026-07-03 20:48:58,558 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052314.1
2026-07-03 20:48:58,569 - syri.NC_052318.1 - INFO - mapstar:48 - NC_052318.1 (284, 11)
2026-07-03 20:48:58,570 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052318.1
2026-07-03 20:48:58,573 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052316.1
2026-07-03 20:48:58,595 - syri.NC_052319.1 - INFO - mapstar:48 - NC_052319.1 (250, 11)
2026-07-03 20:48:58,595 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052319.1
2026-07-03 20:48:58,610 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052317.1
2026-07-03 20:48:58,624 - syri.NC_052320.1 - INFO - mapstar:48 - NC_052320.1 (284, 11)
2026-07-03 20:48:58,625 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052320.1
2026-07-03 20:48:58,629 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052318.1
2026-07-03 20:48:58,650 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052319.1
2026-07-03 20:48:58,655 - syri.NC_052321.1 - INFO - mapstar:48 - NC_052321.1 (279, 11)
2026-07-03 20:48:58,655 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052321.1
2026-07-03 20:48:58,685 - syri.NC_052322.1 - INFO - mapstar:48 - NC_052322.1 (329, 11)
2026-07-03 20:48:58,685 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052322.1
2026-07-03 20:48:58,685 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052320.1
2026-07-03 20:48:58,714 - syri.NC_052323.1 - INFO - mapstar:48 - NC_052323.1 (363, 11)
2026-07-03 20:48:58,715 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052323.1
2026-07-03 20:48:58,717 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052321.1
2026-07-03 20:48:58,746 - syri.NC_052324.1 - INFO - mapstar:48 - NC_052324.1 (386, 11)
2026-07-03 20:48:58,746 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052324.1
2026-07-03 20:48:58,751 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052322.1
2026-07-03 20:48:58,781 - syri.NC_052325.1 - INFO - mapstar:48 - NC_052325.1 (320, 11)
2026-07-03 20:48:58,782 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052325.1
2026-07-03 20:48:58,785 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052323.1
2026-07-03 20:48:58,807 - syri.NC_052326.1 - INFO - mapstar:48 - NC_052326.1 (240, 11)
2026-07-03 20:48:58,808 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052326.1
2026-07-03 20:48:58,821 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052324.1
2026-07-03 20:48:58,846 - syri.NC_052327.1 - INFO - mapstar:48 - NC_052327.1 (302, 11)
2026-07-03 20:48:58,846 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052327.1
2026-07-03 20:48:58,862 - syri.NC_052307.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052307.1
2026-07-03 20:48:58,864 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052326.1
2026-07-03 20:48:58,878 - syri.NC_052328.1 - INFO - mapstar:48 - NC_052328.1 (312, 11)
2026-07-03 20:48:58,878 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052328.1
2026-07-03 20:48:58,886 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052325.1
2026-07-03 20:48:58,887 - syri.NC_052308.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052308.1
2026-07-03 20:48:58,899 - syri.NC_052310.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052310.1
2026-07-03 20:48:58,901 - syri.NC_052329.1 - INFO - mapstar:48 - NC_052329.1 (269, 11)
2026-07-03 20:48:58,902 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052329.1
2026-07-03 20:48:58,939 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052327.1
2026-07-03 20:48:58,941 - syri.NC_052330.1 - INFO - mapstar:48 - NC_052330.1 (223, 11)
2026-07-03 20:48:58,941 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052330.1
2026-07-03 20:48:58,948 - syri.NC_052309.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052309.1
2026-07-03 20:48:58,953 - syri.NC_052312.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052312.1
2026-07-03 20:48:58,963 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052329.1
2026-07-03 20:48:58,971 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052328.1
2026-07-03 20:48:58,971 - syri.NC_052331.1 - INFO - mapstar:48 - NC_052331.1 (195, 11)
2026-07-03 20:48:58,972 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052331.1
2026-07-03 20:48:58,991 - syri.NC_052313.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052313.1
2026-07-03 20:48:58,997 - syri.NC_052315.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052315.1
2026-07-03 20:48:59,001 - syri.NC_052311.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052311.1
2026-07-03 20:48:59,002 - syri.NC_052332.1 - INFO - mapstar:48 - NC_052332.1 (250, 11)
2026-07-03 20:48:59,003 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052332.1
2026-07-03 20:48:59,021 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052330.1
2026-07-03 20:48:59,034 - syri.NC_052333.1 - INFO - mapstar:48 - NC_052333.1 (431, 11)
2026-07-03 20:48:59,034 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052333.1
2026-07-03 20:48:59,051 - syri.NC_052316.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052316.1
2026-07-03 20:48:59,054 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052331.1
2026-07-03 20:48:59,064 - syri.NC_052314.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052314.1
2026-07-03 20:48:59,064 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052332.1
2026-07-03 20:48:59,064 - syri.NC_052334.1 - INFO - mapstar:48 - NC_052334.1 (336, 11)
2026-07-03 20:48:59,064 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052334.1
2026-07-03 20:48:59,092 - syri.NC_052317.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052317.1
2026-07-03 20:48:59,092 - syri.NC_052335.1 - INFO - mapstar:48 - NC_052335.1 (163, 11)
2026-07-03 20:48:59,092 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052335.1
2026-07-03 20:48:59,101 - syri.NC_052318.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052318.1
2026-07-03 20:48:59,128 - syri.NC_052336.1 - INFO - mapstar:48 - NC_052336.1 (408, 11)
2026-07-03 20:48:59,128 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052336.1
2026-07-03 20:48:59,150 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052335.1
2026-07-03 20:48:59,157 - syri.NC_052320.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052320.1
2026-07-03 20:48:59,158 - syri.NC_052337.1 - INFO - mapstar:48 - NC_052337.1 (258, 11)
2026-07-03 20:48:59,158 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052337.1
2026-07-03 20:48:59,178 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052333.1
2026-07-03 20:48:59,182 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052334.1
2026-07-03 20:48:59,191 - syri.NC_052338.1 - INFO - mapstar:48 - NC_052338.1 (298, 11)
2026-07-03 20:48:59,192 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052338.1
2026-07-03 20:48:59,225 - syri.NC_052339.1 - INFO - mapstar:48 - NC_052339.1 (238, 11)
2026-07-03 20:48:59,225 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052339.1
2026-07-03 20:48:59,236 - syri.NC_052322.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052322.1
2026-07-03 20:48:59,249 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052337.1
2026-07-03 20:48:59,251 - syri.NC_052321.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052321.1
2026-07-03 20:48:59,256 - syri.NC_052340.1 - INFO - mapstar:48 - NC_052340.1 (240, 11)
2026-07-03 20:48:59,257 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052340.1
2026-07-03 20:48:59,271 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052336.1
2026-07-03 20:48:59,285 - syri.NC_052341.1 - INFO - mapstar:48 - NC_052341.1 (204, 11)
2026-07-03 20:48:59,285 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052341.1
2026-07-03 20:48:59,303 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052338.1
2026-07-03 20:48:59,309 - syri.NC_052323.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052323.1
2026-07-03 20:48:59,318 - syri.NC_052342.1 - INFO - mapstar:48 - NC_052342.1 (331, 11)
2026-07-03 20:48:59,319 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052342.1
2026-07-03 20:48:59,322 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052339.1
2026-07-03 20:48:59,353 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 3.552436828613281e-05. iterations remaining 41
2026-07-03 20:48:59,353 - syri.NC_052343.1 - INFO - mapstar:48 - NC_052343.1 (157, 11)
2026-07-03 20:48:59,353 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052343.1
2026-07-03 20:48:59,354 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052340.1
2026-07-03 20:48:59,355 - syri.NC_052324.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052324.1
2026-07-03 20:48:59,371 - syri.NC_052326.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052326.1
2026-07-03 20:48:59,371 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052341.1
2026-07-03 20:48:59,373 - syri.NC_052319.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052319.1
2026-07-03 20:48:59,384 - syri.NC_052344.1 - INFO - mapstar:48 - NC_052344.1 (303, 11)
2026-07-03 20:48:59,385 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052344.1
2026-07-03 20:48:59,416 - syri.NC_052345.1 - INFO - mapstar:48 - NC_052345.1 (285, 11)
2026-07-03 20:48:59,416 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052345.1
2026-07-03 20:48:59,434 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.3882598876953125e-05. iterations remaining 36
2026-07-03 20:48:59,434 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052343.1
2026-07-03 20:48:59,438 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052342.1
2026-07-03 20:48:59,452 - syri.NC_052329.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052329.1
2026-07-03 20:48:59,452 - syri.NC_052346.1 - INFO - mapstar:48 - NC_052346.1 (206, 11)
2026-07-03 20:48:59,453 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052346.1
2026-07-03 20:48:59,460 - syri.NC_052347.1 - INFO - mapstar:48 - NC_052347.1 (81, 11)
2026-07-03 20:48:59,460 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052347.1
2026-07-03 20:48:59,487 - syri.NC_052348.1 - INFO - mapstar:48 - NC_052348.1 (326, 11)
2026-07-03 20:48:59,487 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying Synteny for chromosome NC_052348.1
2026-07-03 20:48:59,499 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052344.1
2026-07-03 20:48:59,523 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052345.1
2026-07-03 20:48:59,524 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052347.1
2026-07-03 20:48:59,526 - syri.NC_052327.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052327.1
2026-07-03 20:48:59,558 - 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 41
2026-07-03 20:48:59,565 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 6.9141387939453125e-06. iterations remaining 42
2026-07-03 20:48:59,590 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052346.1
2026-07-03 20:48:59,593 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying Inversions for chromosome NC_052348.1
2026-07-03 20:48:59,604 - syri.NC_052332.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052332.1
2026-07-03 20:48:59,633 - 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 34
2026-07-03 20:48:59,636 - syri.NC_052347.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052347.1
2026-07-03 20:48:59,680 - syri.NC_052325.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052325.1
2026-07-03 20:48:59,684 - syri.NC_052348.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052348.1
2026-07-03 20:48:59,737 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 1.3589859008789062e-05. iterations remaining 42
2026-07-03 20:48:59,741 - syri.NC_052330.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052330.1
2026-07-03 20:48:59,749 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 9.72747802734375e-05. iterations remaining 33
2026-07-03 20:48:59,752 - syri.NC_052328.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052328.1
2026-07-03 20:48:59,825 - syri.NC_052334.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052334.1
2026-07-03 20:48:59,840 - syri.NC_052331.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052331.1
2026-07-03 20:48:59,890 - syri.NC_052335.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052335.1
2026-07-03 20:48:59,938 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.0503997802734375e-05. iterations remaining 37
2026-07-03 20:48:59,950 - syri.NC_052342.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052342.1
2026-07-03 20:48:59,994 - syri.NC_052338.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052338.1
2026-07-03 20:49:00,018 - syri.NC_052333.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052333.1
2026-07-03 20:49:00,019 - syri.NC_052339.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052339.1
2026-07-03 20:49:00,023 - syri.NC_052337.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052337.1
2026-07-03 20:49:00,036 - syri.NC_052340.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052340.1
2026-07-03 20:49:00,088 - syri.NC_052336.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052336.1
2026-07-03 20:49:00,117 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.435943603515625e-05. iterations remaining 44
2026-07-03 20:49:00,144 - syri.NC_052345.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052345.1
2026-07-03 20:49:00,164 - syri.NC_052343.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052343.1
2026-07-03 20:49:00,173 - syri.NC_052341.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052341.1
2026-07-03 20:49:00,253 - syri.NC_052344.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052344.1
2026-07-03 20:49:00,276 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 3.528594970703125e-05. iterations remaining 37
2026-07-03 20:49:00,293 - syri.NC_052346.1 - INFO - mapstar:48 - Identifying translocation and duplication for chromosome NC_052346.1
2026-07-03 20:49:00,409 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 3.0517578125e-05. iterations remaining 36
2026-07-03 20:49:00,932 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.3473644256591797. iterations remaining 13
2026-07-03 20:49:02,918 - getCTX - INFO - syri:215 - Identifying cross-chromosomal translocation and duplication for chromosome2026-07-03 20:49:02.918729
2026-07-03 20:49:17,256 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.054473876953125e-05. iterations remaining 35
2026-07-03 20:49:19,112 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.1021575927734375e-05. iterations remaining 41
2026-07-03 20:49:22,057 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 9.369850158691406e-05. iterations remaining 35
2026-07-03 20:49:22,945 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.6226043701171875e-06. iterations remaining 49
2026-07-03 20:49:24,215 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 0.00013184547424316406. iterations remaining 35
2026-07-03 20:49:24,486 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.553794860839844e-05. iterations remaining 44
2026-07-03 20:49:33,316 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 7.390975952148438e-05. iterations remaining 36
2026-07-03 20:49:37,572 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.863739013671875e-05. iterations remaining 36
2026-07-03 20:49:39,437 - 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 41
2026-07-03 20:49:43,727 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 3.814697265625e-06. iterations remaining 43
2026-07-03 20:49:44,894 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.602836608886719e-05. iterations remaining 41
2026-07-03 20:49:45,144 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.86102294921875e-06. iterations remaining 49
2026-07-03 20:49:48,064 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 1.239776611328125e-05. iterations remaining 40
2026-07-03 20:49:49,530 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.57763671875e-05. iterations remaining 43
2026-07-03 20:49:54,950 - 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
2026-07-03 20:49:55,342 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 4.649162292480469e-05. iterations remaining 46
2026-07-03 20:49:55,395 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 5.7220458984375e-06. iterations remaining 44
2026-07-03 20:49:56,066 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 6.67572021484375e-06. iterations remaining 45
2026-07-03 20:49:56,181 - Brute-force TD identification - INFO - mapstar:48 - Cluster is too big for Brute Force, using randomized-greedy approach
Time taken for last iteration 2.3603439331054688e-05. iterations remaining 44
2026-07-03 20:49:56,434 - 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
2026-07-03 20:50:08,365 - local_variation - INFO - syri:226 - Finding SVs in synOut.txt, invOut.txt, TLOut.txt, invTLOut.txt, ctxOut.txt
2026-07-03 20:50:44,110 - local_variation - INFO - syri:246 - Finding SNPs and small indels
2026-07-03 20:53:54,747 - local_variation - INFO - syri:258 - Combining outputs
2026-07-03 20:53:54,748 - local_variation - INFO - syri:263 - Generating table output
2026-07-03 20:59:27,568 - local_variation - INFO - syri:268 - Generating VCF
2026-07-03 20:59:43,282 - local_variation - INFO - syri:276 - Finished syri