Typing of 81 S. epidermidis samples (Luise)

gene_x 0 like s 458 view s

Tags: processing, pipeline

ggtree_and_gheatmap_Luise_81samples

  1. prepare the bacto environment

    1. cd ~/DATA/Data_Luise_Sepi_STKN
    2. cp /home/jhuang/Tools/bacto/bacto-0.1.json .
    3. cp /home/jhuang/Tools/bacto/cluster.json .
    4. cp /home/jhuang/Tools/bacto/Snakefile .
    5. ln -s /home/jhuang/Tools/bacto/local .
    6. ln -s /home/jhuang/Tools/bacto/db .
    7. ln -s /home/jhuang/Tools/bacto/envs .

  2. prepare raw_data

    1. mkdir raw_data; cd raw_data
    3. ln -s ../raw_data_batch2/mibi2312/Luise_1_S33_R1_001.fastq.gz mibi2312_R1.fastq.gz
    4. ln -s ../raw_data_batch2/mibi2312/Luise_1_S33_R2_001.fastq.gz mibi2312_R2.fastq.gz
    5. ln -s ../raw_data_batch2/mibi2379/Luise_2_S3_R1_001.fastq.gz  mibi2379_R1.fastq.gz
    6. ln -s ../raw_data_batch2/mibi2379/Luise_2_S3_R2_001.fastq.gz  mibi2379_R2.fastq.gz
    7. ln -s ../raw_data_batch2/mibi2313/Luise_3_S34_R1_001.fastq.gz mibi2313_R1.fastq.gz
    8. ln -s ../raw_data_batch2/mibi2313/Luise_3_S34_R2_001.fastq.gz mibi2313_R2.fastq.gz
    9. ln -s ../raw_data_batch2/mibi2380/Luise_4_S4_R1_001.fastq.gz  mibi2380_R1.fastq.gz
    10. ln -s ../raw_data_batch2/mibi2380/Luise_4_S4_R2_001.fastq.gz  mibi2380_R2.fastq.gz
    11. ln -s ../raw_data_batch2/mibi2314/Luise_5_S35_R1_001.fastq.gz mibi2314_R1.fastq.gz
    12. ln -s ../raw_data_batch2/mibi2314/Luise_5_S35_R2_001.fastq.gz mibi2314_R2.fastq.gz
    13. ln -s ../raw_data_batch2/mibi2315/Luise_6_S36_R1_001.fastq.gz mibi2315_R1.fastq.gz
    14. ln -s ../raw_data_batch2/mibi2315/Luise_6_S36_R2_001.fastq.gz mibi2315_R2.fastq.gz
    15. ln -s ../raw_data_batch2/mibi2381/Luise_7_S5_R1_001.fastq.gz  mibi2381_R1.fastq.gz
    16. ln -s ../raw_data_batch2/mibi2381/Luise_7_S5_R2_001.fastq.gz  mibi2381_R2.fastq.gz
    17. ln -s ../raw_data_batch2/mibi2316/Luise_8_S37_R1_001.fastq.gz mibi2316_R1.fastq.gz
    18. ln -s ../raw_data_batch2/mibi2316/Luise_8_S37_R2_001.fastq.gz mibi2316_R2.fastq.gz
    19. ln -s ../raw_data_batch2/mibi2317/Luise_9_S38_R1_001.fastq.gz mibi2317_R1.fastq.gz
    20. ln -s ../raw_data_batch2/mibi2317/Luise_9_S38_R2_001.fastq.gz mibi2317_R2.fastq.gz
    21. ln -s ../raw_data_batch2/mibi2318/Luise_10_S39_R1_001.fastq.gz mibi2318_R1.fastq.gz
    22. ln -s ../raw_data_batch2/mibi2318/Luise_10_S39_R2_001.fastq.gz mibi2318_R2.fastq.gz
    23. ln -s ../raw_data_batch2/mibi2319/Luise_11_S40_R1_001.fastq.gz mibi2319_R1.fastq.gz
    24. ln -s ../raw_data_batch2/mibi2319/Luise_11_S40_R2_001.fastq.gz mibi2319_R2.fastq.gz
    25. ln -s ../raw_data_batch2/mibi2320/Luise_12_S41_R1_001.fastq.gz mibi2320_R1.fastq.gz
    26. ln -s ../raw_data_batch2/mibi2320/Luise_12_S41_R2_001.fastq.gz mibi2320_R2.fastq.gz
    27. ln -s ../raw_data_batch2/mibi2321/Luise_13_S42_R1_001.fastq.gz mibi2321_R1.fastq.gz
    28. ln -s ../raw_data_batch2/mibi2321/Luise_13_S42_R2_001.fastq.gz mibi2321_R2.fastq.gz
    30. # raw_data_batch1: mibi1435 - mibi1506
    31. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1435/S_epi_K_38_S1_R1_001.fastq.gz mibi1435_R1.fastq.gz
    32. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1435/S_epi_K_38_S1_R2_001.fastq.gz mibi1435_R2.fastq.gz
    33. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1436/S_epi_K_68_S2_R1_001.fastq.gz mibi1436_R1.fastq.gz
    34. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1436/S_epi_K_68_S2_R2_001.fastq.gz mibi1436_R2.fastq.gz
    35. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1437/S_epi_K_70_S3_R1_001.fastq.gz mibi1437_R1.fastq.gz
    36. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1437/S_epi_K_70_S3_R2_001.fastq.gz mibi1437_R2.fastq.gz
    37. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1438/S_epi_K_71_S4_R1_001.fastq.gz mibi1438_R1.fastq.gz
    38. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1438/S_epi_K_71_S4_R2_001.fastq.gz mibi1438_R2.fastq.gz
    39. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1439/S_epi_K_48_S5_R1_001.fastq.gz mibi1439_R1.fastq.gz
    40. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1439/S_epi_K_48_S5_R2_001.fastq.gz mibi1439_R2.fastq.gz
    41. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1440/S_epi_K_51_S6_R1_001.fastq.gz mibi1440_R1.fastq.gz
    42. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1440/S_epi_K_51_S6_R2_001.fastq.gz mibi1440_R2.fastq.gz
    43. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1441/S_epi_K_53_S7_R1_001.fastq.gz mibi1441_R1.fastq.gz
    44. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1441/S_epi_K_53_S7_R2_001.fastq.gz mibi1441_R2.fastq.gz
    45. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1442/S_epi_K_54_S8_R1_001.fastq.gz mibi1442_R1.fastq.gz
    46. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1442/S_epi_K_54_S8_R2_001.fastq.gz mibi1442_R2.fastq.gz
    47. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1443/S_epi_K_56_S9_R1_001.fastq.gz mibi1443_R1.fastq.gz
    48. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1443/S_epi_K_56_S9_R2_001.fastq.gz mibi1443_R2.fastq.gz
    49. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1444/S_epi_K_63_S10_R1_001.fastq.gz mibi1444_R1.fastq.gz
    50. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1444/S_epi_K_63_S10_R2_001.fastq.gz mibi1444_R2.fastq.gz
    51. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1445/S_epi_K_64_S11_R1_001.fastq.gz mibi1445_R1.fastq.gz
    52. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1445/S_epi_K_64_S11_R2_001.fastq.gz mibi1445_R2.fastq.gz
    53. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1446/S_epi_K_65_S12_R1_001.fastq.gz mibi1446_R1.fastq.gz
    54. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1446/S_epi_K_65_S12_R2_001.fastq.gz mibi1446_R2.fastq.gz
    55. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1447/S_epi_K_75_S13_R1_001.fastq.gz mibi1447_R1.fastq.gz
    56. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1447/S_epi_K_75_S13_R2_001.fastq.gz mibi1447_R2.fastq.gz
    57. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1448/S_epi_K_11_S14_R1_001.fastq.gz mibi1448_R1.fastq.gz
    58. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1448/S_epi_K_11_S14_R2_001.fastq.gz mibi1448_R2.fastq.gz
    59. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1449/S_epi_K_12_S15_R1_001.fastq.gz mibi1449_R1.fastq.gz
    60. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1449/S_epi_K_12_S15_R2_001.fastq.gz mibi1449_R2.fastq.gz
    61. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1450/S_epi_K_13_S16_R1_001.fastq.gz mibi1450_R1.fastq.gz
    62. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1450/S_epi_K_13_S16_R2_001.fastq.gz mibi1450_R2.fastq.gz
    63. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1451/S_epi_K_77_S17_R1_001.fastq.gz mibi1451_R1.fastq.gz
    64. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1451/S_epi_K_77_S17_R2_001.fastq.gz mibi1451_R2.fastq.gz
    65. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1452/S_epi_K_79_S18_R1_001.fastq.gz mibi1452_R1.fastq.gz
    66. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1452/S_epi_K_79_S18_R2_001.fastq.gz mibi1452_R2.fastq.gz
    67. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1453/S_epi_K_80_S19_R1_001.fastq.gz mibi1453_R1.fastq.gz
    68. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1453/S_epi_K_80_S19_R2_001.fastq.gz mibi1453_R2.fastq.gz
    69. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1454/S_epi_K_1_gross_S20_R1_001.fastq.gz mibi1454_R1.fastq.gz
    70. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1454/S_epi_K_1_gross_S20_R2_001.fastq.gz mibi1454_R2.fastq.gz
    71. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1455/S_epi_K_2_S21_R1_001.fastq.gz mibi1455_R1.fastq.gz
    72. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1455/S_epi_K_2_S21_R2_001.fastq.gz mibi1455_R2.fastq.gz
    73. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1456/S_epi_K_3_S22_R1_001.fastq.gz mibi1456_R1.fastq.gz
    74. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1456/S_epi_K_3_S22_R2_001.fastq.gz mibi1456_R2.fastq.gz
    75. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1457/S_epi_K_6_S23_R1_001.fastq.gz mibi1457_R1.fastq.gz
    76. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1457/S_epi_K_6_S23_R2_001.fastq.gz mibi1457_R2.fastq.gz
    77. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1458/S_epi_K_8_S24_R1_001.fastq.gz mibi1458_R1.fastq.gz
    78. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1458/S_epi_K_8_S24_R2_001.fastq.gz mibi1458_R2.fastq.gz
    79. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1459/S_epi_K_17_S25_R1_001.fastq.gz mibi1459_R1.fastq.gz
    80. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1459/S_epi_K_17_S25_R2_001.fastq.gz mibi1459_R2.fastq.gz
    81. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1460/S_epi_K_26_S26_R1_001.fastq.gz mibi1460_R1.fastq.gz
    82. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1460/S_epi_K_26_S26_R2_001.fastq.gz mibi1460_R2.fastq.gz
    83. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1461/S_epi_K_34_S27_R1_001.fastq.gz mibi1461_R1.fastq.gz
    84. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1461/S_epi_K_34_S27_R2_001.fastq.gz mibi1461_R2.fastq.gz
    85. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1462/S_epi_K_35_S28_R1_001.fastq.gz mibi1462_R1.fastq.gz
    86. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1462/S_epi_K_35_S28_R2_001.fastq.gz mibi1462_R2.fastq.gz
    87. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1463/S_epi_K_19_S29_R1_001.fastq.gz mibi1463_R1.fastq.gz
    88. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1463/S_epi_K_19_S29_R2_001.fastq.gz mibi1463_R2.fastq.gz
    89. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1464/S_epi_K_22_S30_R1_001.fastq.gz mibi1464_R1.fastq.gz
    90. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1464/S_epi_K_22_S30_R2_001.fastq.gz mibi1464_R2.fastq.gz
    91. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1465/S_epi_K_23_S31_R1_001.fastq.gz mibi1465_R1.fastq.gz
    92. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1465/S_epi_K_23_S31_R2_001.fastq.gz mibi1465_R2.fastq.gz
    93. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1466/S_epi_K_24_S32_R1_001.fastq.gz mibi1466_R1.fastq.gz
    94. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1466/S_epi_K_24_S32_R2_001.fastq.gz mibi1466_R2.fastq.gz
    95. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1467/S_epi_K_30_S33_R1_001.fastq.gz mibi1467_R1.fastq.gz
    96. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1467/S_epi_K_30_S33_R2_001.fastq.gz mibi1467_R2.fastq.gz
    97. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1468/S_epi_K_31_S34_R1_001.fastq.gz mibi1468_R1.fastq.gz
    98. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1468/S_epi_K_31_S34_R2_001.fastq.gz mibi1468_R2.fastq.gz
    99. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1469/S_epi_K_32_S35_R1_001.fastq.gz mibi1469_R1.fastq.gz
    100. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1469/S_epi_K_32_S35_R2_001.fastq.gz mibi1469_R2.fastq.gz
    101. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1470/S_epi_K_1_klein_S36_R1_001.fastq.gz mibi1470_R1.fastq.gz
    102. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1470/S_epi_K_1_klein_S36_R2_001.fastq.gz mibi1470_R2.fastq.gz
    103. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1471/S_epi_K_37_S37_R1_001.fastq.gz mibi1471_R1.fastq.gz
    104. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1471/S_epi_K_37_S37_R2_001.fastq.gz mibi1471_R2.fastq.gz
    105. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1472/S_epi_K_46_S38_R1_001.fastq.gz mibi1472_R1.fastq.gz
    106. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1472/S_epi_K_46_S38_R2_001.fastq.gz mibi1472_R2.fastq.gz
    107. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1473/S_epi_K_57_S39_R1_001.fastq.gz mibi1473_R1.fastq.gz
    108. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1473/S_epi_K_57_S39_R2_001.fastq.gz mibi1473_R2.fastq.gz
    109. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1474/S_epi_K_59_S40_R1_001.fastq.gz mibi1474_R1.fastq.gz
    110. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1474/S_epi_K_59_S40_R2_001.fastq.gz mibi1474_R2.fastq.gz
    111. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1475/S_epi_K_58_S41_R1_001.fastq.gz mibi1475_R1.fastq.gz
    112. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1475/S_epi_K_58_S41_R2_001.fastq.gz mibi1475_R2.fastq.gz
    113. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1476/S_epi_K_60_S42_R1_001.fastq.gz mibi1476_R1.fastq.gz
    114. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1476/S_epi_K_60_S42_R2_001.fastq.gz mibi1476_R2.fastq.gz
    115. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1477/S_epi_K_61_S43_R1_001.fastq.gz mibi1477_R1.fastq.gz
    116. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1477/S_epi_K_61_S43_R2_001.fastq.gz mibi1477_R2.fastq.gz
    117. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1478/S_epi_K_28_S44_R1_001.fastq.gz mibi1478_R1.fastq.gz
    118. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1478/S_epi_K_28_S44_R2_001.fastq.gz mibi1478_R2.fastq.gz
    119. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1479/S_epi_K_33_S45_R1_001.fastq.gz mibi1479_R1.fastq.gz
    120. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1479/S_epi_K_33_S45_R2_001.fastq.gz mibi1479_R2.fastq.gz
    121. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1480/S_epi_K_39_S46_R1_001.fastq.gz mibi1480_R1.fastq.gz
    122. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1480/S_epi_K_39_S46_R2_001.fastq.gz mibi1480_R2.fastq.gz
    123. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1481/S_epi_K_40_S47_R1_001.fastq.gz mibi1481_R1.fastq.gz
    124. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1481/S_epi_K_40_S47_R2_001.fastq.gz mibi1481_R2.fastq.gz
    125. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1482/S_epi_K_43_S48_R1_001.fastq.gz mibi1482_R1.fastq.gz
    126. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1482/S_epi_K_43_S48_R2_001.fastq.gz mibi1482_R2.fastq.gz
    127. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1483/S_epi_K_97_S49_R1_001.fastq.gz mibi1483_R1.fastq.gz
    128. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1483/S_epi_K_97_S49_R2_001.fastq.gz mibi1483_R2.fastq.gz
    129. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1484/S_epi_K_84_S50_R1_001.fastq.gz mibi1484_R1.fastq.gz
    130. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1484/S_epi_K_84_S50_R2_001.fastq.gz mibi1484_R2.fastq.gz
    131. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1485/S_epi_K_85_S51_R1_001.fastq.gz mibi1485_R1.fastq.gz
    132. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1485/S_epi_K_85_S51_R2_001.fastq.gz mibi1485_R2.fastq.gz
    133. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1486/S_epi_K_86_S52_R1_001.fastq.gz mibi1486_R1.fastq.gz
    134. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1486/S_epi_K_86_S52_R2_001.fastq.gz mibi1486_R2.fastq.gz
    135. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1487/S_epi_K_116_S53_R1_001.fastq.gz mibi1487_R1.fastq.gz
    136. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1487/S_epi_K_116_S53_R2_001.fastq.gz mibi1487_R2.fastq.gz
    137. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1488/S_epi_K_118_S54_R1_001.fastq.gz mibi1488_R1.fastq.gz
    138. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1488/S_epi_K_118_S54_R2_001.fastq.gz mibi1488_R2.fastq.gz
    139. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1489/S_epi_K_120_S55_R1_001.fastq.gz mibi1489_R1.fastq.gz
    140. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1489/S_epi_K_120_S55_R2_001.fastq.gz mibi1489_R2.fastq.gz
    141. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1490/S_epi_K_123_S56_R1_001.fastq.gz mibi1490_R1.fastq.gz
    142. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1490/S_epi_K_123_S56_R2_001.fastq.gz mibi1490_R2.fastq.gz
    143. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1491/S_epi_K_124_S57_R1_001.fastq.gz mibi1491_R1.fastq.gz
    144. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1491/S_epi_K_124_S57_R2_001.fastq.gz mibi1491_R2.fastq.gz
    145. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1492/S_epi_K_127_S58_R1_001.fastq.gz mibi1492_R1.fastq.gz
    146. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1492/S_epi_K_127_S58_R2_001.fastq.gz mibi1492_R2.fastq.gz
    147. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1493/S_epi_K_29_S59_R1_001.fastq.gz mibi1493_R1.fastq.gz
    148. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1493/S_epi_K_29_S59_R2_001.fastq.gz mibi1493_R2.fastq.gz
    149. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1494/S_epi_K_72_S60_R1_001.fastq.gz mibi1494_R1.fastq.gz
    150. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1494/S_epi_K_72_S60_R2_001.fastq.gz mibi1494_R2.fastq.gz
    151. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1495/S_epi_K_89_S61_R1_001.fastq.gz mibi1495_R1.fastq.gz
    152. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1495/S_epi_K_89_S61_R2_001.fastq.gz mibi1495_R2.fastq.gz
    153. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1496/S_epi_K_110_S62_R1_001.fastq.gz mibi1496_R1.fastq.gz
    154. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1496/S_epi_K_110_S62_R2_001.fastq.gz mibi1496_R2.fastq.gz
    155. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1497/S_epi_K_112_S63_R1_001.fastq.gz mibi1497_R1.fastq.gz
    156. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1497/S_epi_K_112_S63_R2_001.fastq.gz mibi1497_R2.fastq.gz
    157. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1498/S_epi_K_114_S64_R1_001.fastq.gz mibi1498_R1.fastq.gz
    158. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1498/S_epi_K_114_S64_R2_001.fastq.gz mibi1498_R2.fastq.gz
    159. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1499/S_epi_K_91_S65_R1_001.fastq.gz mibi1499_R1.fastq.gz
    160. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1499/S_epi_K_91_S65_R2_001.fastq.gz mibi1499_R2.fastq.gz
    161. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1500/S_epi_K_92_S66_R1_001.fastq.gz mibi1500_R1.fastq.gz
    162. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1500/S_epi_K_92_S66_R2_001.fastq.gz mibi1500_R2.fastq.gz
    163. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1501/S_epi_K_95_S67_R1_001.fastq.gz mibi1501_R1.fastq.gz
    164. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1501/S_epi_K_95_S67_R2_001.fastq.gz mibi1501_R2.fastq.gz
    165. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1502/S_epi_K_96_S68_R1_001.fastq.gz mibi1502_R1.fastq.gz
    166. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1502/S_epi_K_96_S68_R2_001.fastq.gz mibi1502_R2.fastq.gz
    167. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1503/S_epi_K_98_S69_R1_001.fastq.gz mibi1503_R1.fastq.gz
    168. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1503/S_epi_K_98_S69_R2_001.fastq.gz mibi1503_R2.fastq.gz
    169. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1504/S_epi_K_100_S70_R1_001.fastq.gz mibi1504_R1.fastq.gz
    170. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1504/S_epi_K_100_S70_R2_001.fastq.gz mibi1504_R2.fastq.gz
    171. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1505/S_epi_K_106_S71_R1_001.fastq.gz mibi1505_R1.fastq.gz
    172. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1505/S_epi_K_106_S71_R2_001.fastq.gz mibi1505_R2.fastq.gz
    173. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1506/S_epi_K_108_S72_R1_001.fastq.gz mibi1506_R1.fastq.gz
    174. ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1506/S_epi_K_108_S72_R2_001.fastq.gz mibi1506_R2.fastq.gz

  3. start bacto pipeline until step shovill (set true for the first 2 steps: assembly + typing_mlst)

    1. (bengal3_ac3) jhuang@WS-2290C:~/DATA/Data_Luise_Sepi_STKN$ /home/jhuang/miniconda3/envs/snakemake_4_3_1/bin/snakemake --printshellcmds

  4. concate the first assembly

    1. find . -name "contigs.fa" -exec sh -c 'echo -n "{}: "; wc -c < "{}"; echo " contigs: $(grep -c ">" "{}")"' \;
    2. find . -name "contigs.fa" -exec sh -c 'wc -c < "{}" | tr -d "\n" | awk "{print \"{}: \" \$0 \" contigs: \" \$(grep -c \">\" \"{}\")} " ' \; | sort -k2,2n -k4,4n
    3. find . -name "contigs.fa" -exec sh -c 'size=$(wc -c < "{}"); contig_count=$(grep -c ">" "{}"); printf "%s: %d bytes, contigs: %d\n" "{}" "$size" "$contig_count"' \; | sort -t: -k4,4n
    5. grep -v '^>' contigs.fa | awk '{ total += length($0) } END { print total }'
    6. #2399339
    8. find . -name "contigs.fa" -exec sh -c 'total_length=$(grep -v "^>" "{}" | awk "{ total += length(\$0) } END { print total }"); printf "%s: %d\n" "{}" "$total_length"' \; | sort -t: -k2,2n
    9.         ./mibi2381/contigs.fa: 1077606
    10.         ./mibi1472/contigs.fa: 1145583
    11.         ./mibi2380/contigs.fa: 1478149
    12.         ./mibi1458/contigs.fa: 2345604
    13.         ./mibi1466/contigs.fa: 2349339
    14.         ./mibi1451/contigs.fa: 2375432
    15.         ./mibi1441/contigs.fa: 2390897
    16.         ./mibi1471/contigs.fa: 2399056
    17.         ./mibi1435/contigs.fa: 2399339
    18.         ./mibi1473/contigs.fa: 2416173
    19.         ./mibi1474/contigs.fa: 2419849
    20.         ./mibi1495/contigs.fa: 2423463
    21.         ./mibi1497/contigs.fa: 2427317
    22.         ./mibi1476/contigs.fa: 2428189
    23.         ./mibi1463/contigs.fa: 2430568
    24.         ./mibi2313/contigs.fa: 2434775
    25.         ./mibi2321/contigs.fa: 2435584
    26.         ./mibi1494/contigs.fa: 2436708
    27.         ./mibi1481/contigs.fa: 2437976
    28.         ./mibi1464/contigs.fa: 2438603
    29.         ./mibi1450/contigs.fa: 2439465
    30.         ./mibi1483/contigs.fa: 2440401
    31.         ./mibi1506/contigs.fa: 2440413
    32.         ./mibi1462/contigs.fa: 2441903
    33.         ./mibi1443/contigs.fa: 2445186
    34.         ./mibi1448/contigs.fa: 2447751
    35.         ./mibi1439/contigs.fa: 2453223
    36.         ./mibi1501/contigs.fa: 2454766
    37.         ./mibi1505/contigs.fa: 2455113
    38.         ./mibi1436/contigs.fa: 2457498
    39.         ./mibi1499/contigs.fa: 2459216
    40.         ./mibi1452/contigs.fa: 2467292
    41.         ./mibi1500/contigs.fa: 2467976
    42.         ./mibi1455/contigs.fa: 2468334
    43.         ./mibi1445/contigs.fa: 2469433
    44.         ./mibi1479/contigs.fa: 2471443
    45.         ./mibi1482/contigs.fa: 2473012
    46.         ./mibi1469/contigs.fa: 2475757
    47.         ./mibi1468/contigs.fa: 2478455
    48.         ./mibi1438/contigs.fa: 2482554
    49.         ./mibi2379/contigs.fa: 2483292
    50.         ./mibi1493/contigs.fa: 2483445
    51.         ./mibi1488/contigs.fa: 2484950
    52.         ./mibi1486/contigs.fa: 2485023
    53.         ./mibi1442/contigs.fa: 2488933
    54.         ./mibi1437/contigs.fa: 2489787
    55.         ./mibi1460/contigs.fa: 2491014
    56.         ./mibi2312/contigs.fa: 2494588
    57.         ./mibi1489/contigs.fa: 2495771
    58.         ./mibi1504/contigs.fa: 2501045
    59.         ./mibi2317/contigs.fa: 2504746
    60.         ./mibi1444/contigs.fa: 2504874
    61.         ./mibi1446/contigs.fa: 2508952
    62.         ./mibi1465/contigs.fa: 2509542
    63.         ./mibi1467/contigs.fa: 2509571
    64.         ./mibi2314/contigs.fa: 2510798
    65.         ./mibi2315/contigs.fa: 2511464
    66.         ./mibi1457/contigs.fa: 2513005
    67.         ./mibi1490/contigs.fa: 2514271
    68.         ./mibi1491/contigs.fa: 2519558
    69.         ./mibi1449/contigs.fa: 2520352
    70.         ./mibi1503/contigs.fa: 2521179
    71.         ./mibi1475/contigs.fa: 2526469
    72.         ./mibi1484/contigs.fa: 2530724
    73.         ./mibi1447/contigs.fa: 2538610
    74.         ./mibi1453/contigs.fa: 2543893
    75.         ./mibi1477/contigs.fa: 2550922
    76.         ./mibi1454/contigs.fa: 2553326
    77.         ./mibi1498/contigs.fa: 2556315
    78.         ./mibi2316/contigs.fa: 2556628
    79.         ./mibi1492/contigs.fa: 2558492
    80.         ./mibi1470/contigs.fa: 2563169
    81.         ./mibi2320/contigs.fa: 2571421
    82.         ./mibi1461/contigs.fa: 2582715
    83.         ./mibi1478/contigs.fa: 2584524
    84.         ./mibi2318/contigs.fa: 2594120
    85.         ./mibi1459/contigs.fa: 2595990
    86.         ./mibi1440/contigs.fa: 2604213
    87.         ./mibi1456/contigs.fa: 2605647
    88.         ./mibi1487/contigs.fa: 2614950
    89.         ./mibi1496/contigs.fa: 2616533
    90.         ./mibi2319/contigs.fa: 2621258
    91.         ./mibi1480/contigs.fa: 2621312
    92.         ./mibi1485/contigs.fa: 2665904
    93.         ./mibi1502/contigs.fa: 2668891
    95. cd mibi1502
    96. awk '/^>/ {if(seen_header++) print "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"; next} {printf "%s", $0} END {print ""}' contigs.fa > concatenated_contigs.fasta
    97. awk '/^>/ {if(seen_header++) print ""; print $0; next} {printf "%s", $0} END {print ""}' concatenated_contigs.fasta > concatenated_contigs.fa
    98. sed -i '1s/^/>mibi1502\n/' concatenated_contigs.fa
    99. seqkit seq -i concatenated_contigs.fa -m 100 > ../mibi1502.fasta
    101. bakta --db /mnt/nvme0n1p1/bakta_db mibi1502.fasta
    103. ATCC 14990
    104. Genes (total)                     :: 2,368
    105.         CDSs (total)                      :: 2,284
    106.         Genes (coding)                    :: 2,231
    107.         CDSs (with protein)               :: 2,231
    108.         Genes (RNA)                       :: 84
    109.         rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
    110.         complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
    111.         tRNAs                             :: 61
    112.         ncRNAs                            :: 4
    113.         Pseudo Genes (total)              :: 53
    114.         CDSs (without protein)            :: 53
    115.         Pseudo Genes (ambiguous residues) :: 0 of 53
    116.         Pseudo Genes (frameshifted)       :: 34 of 53
    117.         Pseudo Genes (incomplete)         :: 31 of 53
    118.         Pseudo Genes (internal stop)      :: 24 of 53
    120. Detected IPSs: 2369 This likely refers to insertion sequences or insertional plasmids (depending on the specific context). In this case, 2,369 insertion sequences were detected in the analysis, which could indicate mobile genetic elements that might affect the genome's stability or function.
    122. predict tRNAs...
    123.         found: 61
    124. predict tmRNAs...
    125.         found: 1
    126. predict rRNAs...
    127.         found: 12
    128. predict ncRNAs...
    129.         found: 55
    130. predict ncRNA regions...
    131.         found: 26
    132. predict CRISPR arrays...
    133.         found: 0
    134. predict & annotate CDSs...
    135.         predicted: 2529
    136.         discarded spurious: 0
    137.         revised translational exceptions: 0
    138.         detected IPSs: 2369
    139.         found PSCs: 117
    140.         found PSCCs: 26
    141.         lookup annotations...
    142.         conduct expert systems...
    143.                 amrfinder: 20
    144.                 protein sequences: 54
    145.         combine annotations and mark hypotheticals...
    146.         detect pseudogenes...
    147.                 pseudogene candidates: 15
    148.                 found pseudogenes: 7
    149. analyze hypothetical proteins: 96
    150.         detected Pfam hits: 1
    151.         calculated proteins statistics
    152.         revise special cases...
    153. extract sORF...
    154.         potential: 46973
    155.         discarded due to overlaps: 37990
    156.         discarded spurious: 0
    157.         detected IPSs: 9
    158.         found PSCs: 2
    159.         lookup annotations...
    160.         filter and combine annotations...
    161.         filtered sORFs: 9
    162. detect gaps...
    163.         found: 113
    164. detect oriCs/oriVs...
    165.         found: 1
    166. detect oriTs...
    167.         found: 0
    168. apply feature overlap filters...
    169. select features and create locus tags...
    170. selected: 2801
    171. improve annotations...
    172.         revised gene symbols: 9

  5. generate genebank in snpEff and run spandx

    1. #mkdir ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/NZ_CP035288
    2. #cp NZ_CP035288.gb ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/NZ_CP035288/genes.gbk
    3. #vim ~/miniconda3/envs/spandx/share/snpeff-5.1-2/snpEff.config
    4. #/home/jhuang/miniconda3/envs/spandx/bin/snpEff build -genbank NZ_CP035288      #-d
    6. cp mibi1502.gbff ../db/mibi1502.gb
    7. #Then replace contig_1 to mibi1502 in the gb-file
    8. cp mibi1502.fasta ../db/mibi1502.fasta
    10. mkdir ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/mibi1502
    11. cp mibi1502.gb ~/miniconda3/envs/spandx/share/snpeff-5.1-2/data/mibi1502/genes.gbk
    12. vim ~/miniconda3/envs/spandx/share/snpeff-5.1-2/snpEff.config
    13. #Protein check:  mibi1502        OK: 2525        Not found: 7    Errors: 0       Error percentage: 0.0%
    14. /home/jhuang/miniconda3/envs/spandx/bin/snpEff build -genbank mibi1502      #-d
    16. # run the first 5 steps in bacto-pipeline ("pangenome"+"variants_calling"+"phylogeny_fasttree"+"phylogeny_raxml"+"recombination")
    17. /home/jhuang/miniconda3/envs/snakemake_4_3_1/bin/snakemake --printshellcmds
    19. ln -s /home/jhuang/Tools/spandx/ spandx
    20. # cp trimmed trimmed_gzipped; cd trimmed_gzipped; gzip *.fastq; cd ..
    21. (spandx) nextflow run spandx/main.nf --fastq "trimmed_gzipped/*_P_{1,2}.fastq.gz" --ref db/mibi1502.fasta --annotation --database mibi1502 -resume
    22. mv work work_mibi1502
    23. mv Outputs Outputs_mibi1502

  6. filter out 4 samples for downstream analyses

    1. #The coverages of shovill/mibi1470/contigs.fa and shovill/mibi1472/contigs.fa, and shovill/mibi2381/contigs.fa are low.
    2. #mibi1470 could not be identified as S. epidermidis based on its MLST type.
    3. #remove: mibi1470 2.5M
    4. #remove: ./mibi1472/contigs.fa: 1145583
    5. #remove: ./mibi2380/contigs.fa: 1478149
    6. #remove: ./mibi2381/contigs.fa: 1077606
    7. #Then we have 81 samples for downstream analysis: mibi1435 -- mibi1506 (72); mibi2312 -- mibi2321 (10); mibi2379 -- mibi2381 (3)

  7. SCCmec typing and drawing with clinker

    1. #https://www.genomicepidemiology.org/
    2. #https://cge.food.dtu.dk/services/SCCmecFinder/
    3. mkdir contigs; cd contigs
    4. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    5. cp ../${sample}/contigs.fa ${sample}_contigs.fa
    6. done
    8. #Predicted SCCmec element
    9. grep "Predicted SCCmec element" *.txt
    10. grep "2 SCCmec" *.txt
    11. grep "ccr class" *.txt
    12. grep "mec class" *.txt
    14. mibi1435_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVb(2B)
    15. mibi1436_SCCmec_out.txt:Predicted SCCmec element: none
    16. mibi1437_SCCmec_out.txt:Predicted SCCmec element: none
    17. mibi1438_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
    18. mibi1439_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
    20. mibi1440_SCCmec_out.txt:Predicted SCCmec element: none
    21. mibi1441_SCCmec_out.txt:Predicted SCCmec element: none
    22. mibi1442_SCCmec_out.txt:Predicted SCCmec element: none
    23. mibi1443_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
    24. mibi1444_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
    25. mibi1445_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
    26. mibi1446_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    27. mibi1447_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    28. mibi1448_SCCmec_out.txt:Predicted SCCmec element: none
    29. mibi1449_SCCmec_out.txt:Predicted SCCmec element: none
    31. mibi1450_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
    32. mibi1451_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
    33. mibi1452_SCCmec_out.txt:Predicted SCCmec element: none
    34. mibi1453_SCCmec_out.txt:Predicted SCCmec element: none
    35. mibi1454_SCCmec_out.txt:Predicted SCCmec element: none
    36. mibi1455_SCCmec_out.txt:Predicted SCCmec element: none
    37. mibi1456_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
    38. mibi1457_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    39. mibi1458_SCCmec_out.txt:Predicted SCCmec element: none
    40. mibi1459_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
    42. mibi1460_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
    43. mibi1461_SCCmec_out.txt:Predicted SCCmec element: none
    44. mibi1462_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
    45. mibi1463_SCCmec_out.txt:Predicted SCCmec element: none
    46. mibi1464_SCCmec_out.txt:Predicted SCCmec element: none
    47. mibi1465_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
    48. mibi1466_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    49. mibi1467_SCCmec_out.txt:Predicted SCCmec element: none
    50. mibi1468_SCCmec_out.txt:Predicted SCCmec element: none
    51. mibi1469_SCCmec_out.txt:Predicted SCCmec element: none
    53. mibi1471_SCCmec_out.txt:Predicted SCCmec element: none
    54. mibi1473_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
    55. mibi1474_SCCmec_out.txt:Predicted SCCmec element: none
    56. mibi1475_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    57. mibi1476_SCCmec_out.txt:Predicted SCCmec element: none
    58. mibi1477_SCCmec_out.txt:Predicted SCCmec element: none
    59. mibi1478_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
    60. mibi1479_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    62. mibi1480_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
    63. mibi1481_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_II(2A)
    64. mibi1482_SCCmec_out.txt:Predicted SCCmec element: none
    65. mibi1483_SCCmec_out.txt:Predicted SCCmec element: none
    66. mibi1484_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
    67. mibi1485_SCCmec_out.txt:Predicted SCCmec element: none
    68. mibi1486_SCCmec_out.txt:Predicted SCCmec element: none
    69. mibi1487_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
    70. mibi1488_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
    71. mibi1489_SCCmec_out.txt:Predicted SCCmec element: none
    73. mibi1490_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    74. mibi1491_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    75. mibi1492_SCCmec_out.txt:Predicted SCCmec element: none
    76. mibi1493_SCCmec_out.txt:Predicted SCCmec element: none
    77. mibi1494_SCCmec_out.txt:Predicted SCCmec element: none
    78. mibi1495_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
    79. mibi1496_SCCmec_out.txt:Predicted SCCmec element: none
    80. mibi1497_SCCmec_out.txt:Predicted SCCmec element: none
    81. mibi1498_SCCmec_out.txt:Predicted SCCmec element: none
    82. mibi1499_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
    84. mibi1500_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
    85. mibi1501_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
    86. mibi1502_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
    87. mibi1503_SCCmec_out.txt:Predicted SCCmec element: none
    88. mibi1504_SCCmec_out.txt:Predicted SCCmec element: none
    89. mibi1505_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
    90. mibi1506_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
    92. mibi2312_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
    93. mibi2313_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
    94. mibi2314_SCCmec_out.txt:Predicted SCCmec element: none
    95. mibi2315_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
    96. mibi2316_SCCmec_out.txt:Predicted SCCmec element: none
    97. mibi2317_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
    98. mibi2318_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
    99. mibi2319_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
    100. mibi2320_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
    101. mibi2321_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
    102. mibi2379_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
    104. mibi1441_SCCmec_out.txt:ccr class 2
    105. mibi1446_SCCmec_out.txt:ccr class 2
    106. mibi1446_SCCmec_out.txt:ccr class 4
    107. mibi1447_SCCmec_out.txt:ccr class 2
    108. mibi1447_SCCmec_out.txt:ccr class 4
    109. mibi1452_SCCmec_out.txt:ccr class 5
    110. mibi1455_SCCmec_out.txt:ccr class 2
    112. mibi1457_SCCmec_out.txt:ccr class 2
    113. mibi1457_SCCmec_out.txt:ccr class 4
    115. mibi1464_SCCmec_out.txt:ccr class 2
    116. mibi1466_SCCmec_out.txt:ccr class 2
    117. mibi1466_SCCmec_out.txt:ccr class 4
    118. mibi1467_SCCmec_out.txt:ccr class 5
    119. mibi1475_SCCmec_out.txt:ccr class 2
    120. mibi1475_SCCmec_out.txt:ccr class 4
    122. mibi1477_SCCmec_out.txt:ccr class 9
    123. mibi1478_SCCmec_out.txt:ccr class 3
    124. mibi1478_SCCmec_out.txt:ccr class 4
    126. mibi1479_SCCmec_out.txt:ccr class 2
    127. mibi1479_SCCmec_out.txt:ccr class 4
    129. mibi1480_SCCmec_out.txt:ccr class 3
    130. mibi1480_SCCmec_out.txt:ccr class 4
    132. mibi1482_SCCmec_out.txt:ccr class 5
    133. mibi1483_SCCmec_out.txt:ccr class 5
    134. mibi1486_SCCmec_out.txt:ccr class 2
    136. mibi1487_SCCmec_out.txt:ccr class 3
    137. mibi1487_SCCmec_out.txt:ccr class 4
    139. mibi1489_SCCmec_out.txt:ccr class 2
    141. mibi1490_SCCmec_out.txt:ccr class 2
    142. mibi1490_SCCmec_out.txt:ccr class 4
    144. mibi1491_SCCmec_out.txt:ccr class 2
    145. mibi1491_SCCmec_out.txt:ccr class 4
    147. mibi1492_SCCmec_out.txt:ccr class 2
    148. mibi1494_SCCmec_out.txt:ccr class 5
    150. mibi1501_SCCmec_out.txt:ccr class 2
    151. mibi1501_SCCmec_out.txt:ccr class 4
    153. mibi1504_SCCmec_out.txt:ccr class 2
    154. mibi1504_SCCmec_out.txt:ccr class 5&5
    156. mibi2316_SCCmec_out.txt:ccr class 2
    157. mibi2319_SCCmec_out.txt:ccr class 3
    158. mibi2319_SCCmec_out.txt:ccr class 4
    160. mibi1446_SCCmec_out.txt:mec class B
    161. mibi1447_SCCmec_out.txt:mec class B
    163. mibi1457_SCCmec_out.txt:mec class B
    164. mibi1463_SCCmec_out.txt:mec class B
    165. mibi1466_SCCmec_out.txt:mec class B
    166. mibi1475_SCCmec_out.txt:mec class B
    167. mibi1478_SCCmec_out.txt:mec class A
    168. mibi1479_SCCmec_out.txt:mec class B
    169. mibi1480_SCCmec_out.txt:mec class A
    171. mibi1483_SCCmec_out.txt:mec class A
    172. mibi1487_SCCmec_out.txt:mec class A
    173. mibi1490_SCCmec_out.txt:mec class B
    174. mibi1491_SCCmec_out.txt:mec class B
    175. mibi1501_SCCmec_out.txt:mec class B
    176. mibi2319_SCCmec_out.txt:mec class A

  8. agr typing

    1. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2. bakta --db /mnt/nvme0n1p1/bakta_db shovill/${sample}/contigs.fa --prefix ${sample}
    3. done
    5. grep "agrD" mibi1436.gbff
    6. mibi1435    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    7. mibi1436    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    8. mibi1437    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    9. mibi1438    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    10. mibi1439    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    11. mibi1440    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    12. mibi1441    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
    13. mibi1442    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    14. mibi1443    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    15. mibi1444    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    16. mibi1445    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    17. mibi1446    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    18. mibi1447    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    19. mibi1448    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    20. mibi1449    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
    21. mibi1450    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    22. mibi1451    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    23. mibi1452    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
    24. mibi1453    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    25. mibi1454    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    26. mibi1455    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    27. mibi1456    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    28. mibi1457    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    29. mibi1458    MENIFNLFIK I FTTILEF V GTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I* (with a 2-codon difference)
    30. mibi1459    MENIFNLFIK F FTTILEF I GTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    31. mibi1460    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    32. mibi1461    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    33. mibi1462    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    34. mibi1463    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    35. mibi1464    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
    36. mibi1465    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    37. mibi1466    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    38. mibi1467    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    39. mibi1468    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    40. mibi1469    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    41. mibi1471    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    42. mibi1473    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    43. mibi1474    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    44. mibi1475    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    45. mibi1476    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    46. mibi1477    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    47. mibi1478    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    48. mibi1479    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    49. mibi1480    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    50. mibi1481    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    51. mibi1482    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    52. mibi1483    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    53. mibi1484    none
    54. mibi1485    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    55. mibi1486    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    56. mibi1487    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    57. mibi1488    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    58. mibi1489    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    59. mibi1490    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    60. mibi1491    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    61. mibi1492    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    62. mibi1493    MNLLGGL F LK I FSNFMAVIGNA A KYNPC AS YLDEPQVPEELTKLDE  AgrD III* (with a 2-codon difference)
    63. mibi1494    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    64. mibi1495    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    65. mibi1496    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    66. mibi1497    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    67. mibi1498    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    68. mibi1499    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    69. mibi1500    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    70. mibi1501    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    71. mibi1502    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    72. mibi1503    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
    73. mibi1504    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
    74. mibi1505    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    75. mibi1506    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    76. mibi2312    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    77. mibi2313    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    78. mibi2314    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    79. mibi2315    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    80. mibi2316    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    81. mibi2317    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    82. mibi2318    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    83. mibi2319    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    84. mibi2320    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    85. mibi2321    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
    86. mibi2379    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
    88.     #MNLLGGL L LK L FSNFMAVIGNA A KYNPC AS YLDEPQVPEELTKLDE  AgrD III (2)
    89.     #MNLLGGL L LK I FSNFMAVIGNA S KYNPC SN YLDEPQVPEELTKLDE  AgrD II  (4)
    91. -- AgrD I --
    92. Query  1       MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE  46
    93.         M  +  L +K F+  +  IG  +  + C  Y DEP+VPEELTKL E
    94. Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688
    95. -- AgrD II --
    96. Query  1       MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE  46
    97.         MNLLGGLLLKIFSNFMAVIGNASKYNPC  YLDEPQVPEELTKLDE
    98. Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688
    99. -- AgrD III --
    100. Query  1       MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE  46
    101.         MNLLGGLLLK+FSNFMAVIGNA+KYNPC  YLDEPQVPEELTKLDE
    102. Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688

  9. Calulate the presence-absence-matrix by searching keyword gene=gene_name in gff3-files

    1. cut -d',' -f1 plotTreeHeatmap/typing.csv > all_isolate_names.txt
    2. grep "gene=gyrB" *.gff3 > temp
    3. cut -d'.' -f1 temp > temp1
    4. diff all_isolate_names.txt temp1
    6. grep "gene=fumC" *.gff3 > temp
    7. cut -d'.' -f1 temp > temp1
    8. diff all_isolate_names.txt temp1
    10. grep "gene=gltA" *.gff3 > temp
    11. cut -d'.' -f1 temp > temp1
    12. diff all_isolate_names.txt temp1
    14. grep "gene=icd" *.gff3 > temp
    15. cut -d'.' -f1 temp > temp1
    16. diff all_isolate_names.txt temp1
    18. grep "gene=apsS" *.gff3 > temp
    19. cut -d'.' -f1 temp > temp1
    20. diff all_isolate_names.txt temp1 | wc -l
    21. #TODO, using sequence comparisons for one record!
    23. grep "gene=sigB" *.gff3 > temp
    24. cut -d'.' -f1 temp > temp1
    25. diff all_isolate_names.txt temp1
    26. #27d26
    27. #< mibi1461
    29. grep "gene=sarA" *.gff3 > temp
    30. cut -d'.' -f1 temp > temp1
    31. diff all_isolate_names.txt temp1
    32. #17d16
    33. #< mibi1451
    34. #32d30
    35. #< mibi1466
    36. #45d42
    37. #< mibi1481
    39. grep "gene=agrC" *.gff3 > temp
    40. cut -d'.' -f1 temp > temp1
    41. diff all_isolate_names.txt temp1 | wc -l
    42. #TODO, using sequence comparisons for one record!
    44. grep "gene=yycG" *.gff3 > temp
    45. cut -d'.' -f1 temp > temp1
    46. diff all_isolate_names.txt temp1 | wc -l
    47. #TODO, using sequence comparisons for one record!
    49. grep "PSM-beta" *.gff3 > temp
    50. cut -d'.' -f1 temp > temp1
    51. diff all_isolate_names.txt temp1 | wc -l
    52. #TODO, using sequence comparisons for one record!
    54. grep "PSM-delta" *.gff3 > temp
    55. cut -d'.' -f1 temp > temp1
    56. diff all_isolate_names.txt temp1
    57. #9d8
    58. #< mibi1443
    60. grep "hlb" *.gff3 > temp
    61. cut -d'.' -f1 temp > temp1
    62. diff all_isolate_names.txt temp1 | wc -l
    63. #TODO, using sequence comparisons for one record!
    65. grep "atlE" *.gff3 > temp
    66. cut -d'.' -f1 temp > temp1
    67. diff all_isolate_names.txt temp1 | wc -l
    68. #TODO, using sequence comparisons for one record!
    70. grep "gene=atl" *.gff3 > temp
    71. cut -d'.' -f1 temp > temp1
    72. diff all_isolate_names.txt temp1
    73. #19d18
    74. #< mibi1453
    76. grep "gene=sdrG" *.gff3 > temp
    77. cut -d'.' -f1 temp > temp1
    78. diff all_isolate_names.txt temp1
    79. #2d1
    80. < mibi1436
    81. 5d3
    82. < mibi1439
    83. 8,9d5
    84. < mibi1442
    85. < mibi1443
    86. 11,12d6
    87. < mibi1445
    88. < mibi1446
    89. 14d7
    90. < mibi1448
    91. 18,19d10
    92. < mibi1452
    93. < mibi1453
    94. 30,32d20
    95. < mibi1464
    96. < mibi1465
    97. < mibi1466
    98. 34,35d21
    99. < mibi1468
    100. < mibi1469
    101. 37d22
    102. < mibi1473
    103. 39d23
    104. < mibi1475
    105. 41d24
    106. < mibi1477
    107. 43d25
    108. < mibi1479
    109. 47d28
    110. < mibi1483
    111. 50d30
    112. < mibi1486
    113. 52d31
    114. < mibi1488
    115. 55d33
    116. < mibi1491
    117. 63,64d40
    118. < mibi1499
    119. < mibi1500
    120. 67d42
    121. < mibi1503
    122. 76d50
    123. < mibi2317
    124. 79d52
    125. < mibi2320
    126. 81d53
    127. < mibi2379
    129. grep "gene=sdrH" *.gff3 > temp
    130. cut -d'.' -f1 temp > temp1
    131. diff all_isolate_names.txt temp1
    132. #24d23
    133. #< mibi1458
    134. #57d55
    135. #< mibi1493
    137. grep "gene=ebh" *.gff3 > temp
    138. cut -d'.' -f1 temp > temp1
    139. diff all_isolate_names.txt temp1
    140. #1d0
    141. #< mibi1435
    142. 6d4
    143. < mibi1440
    144. 11,13d8
    145. < mibi1445
    146. < mibi1446
    147. < mibi1447
    148. 16,18d10
    149. < mibi1450
    150. < mibi1451
    151. < mibi1452
    152. 20d11
    153. < mibi1454
    154. 22,23d12
    155. < mibi1456
    156. < mibi1457
    157. 25,27d13
    158. < mibi1459
    159. < mibi1460
    160. < mibi1461
    161. 29d14
    162. < mibi1463
    163. 31,32d15
    164. < mibi1465
    165. < mibi1466
    166. 37d19
    167. < mibi1473
    168. 39d20
    169. < mibi1475
    170. 41,44d21
    171. < mibi1477
    172. < mibi1478
    173. < mibi1479
    174. < mibi1480
    175. 47d23
    176. < mibi1483
    177. 49d24
    178. < mibi1485
    179. 51,52d25
    180. < mibi1487
    181. < mibi1488
    182. 54,55d26
    183. < mibi1490
    184. < mibi1491
    185. 59,60d29
    186. < mibi1495
    187. < mibi1496
    188. 62,63d30
    189. < mibi1498
    190. < mibi1499
    191. 66d32
    192. < mibi1502
    193. 71d36
    194. < mibi2312
    195. 74d38
    196. < mibi2315
    197. 76,79d39
    198. < mibi2317
    199. < mibi2318
    200. < mibi2319
    201. < mibi2320
    202. 81d40
    203. < mibi2379
    205. grep "gene=ebpS" *.gff3 > temp
    206. cut -d'.' -f1 temp > temp1
    207. diff all_isolate_names.txt temp1
    209. grep "gene=tagB" *.gff3 > temp
    210. cut -d'.' -f1 temp > temp1
    211. uniq temp1 > temp2    # 3 copies for each isolate
    212. diff all_isolate_names.txt temp2
    214. grep "gene=capC" *.gff3 > temp
    215. cut -d'.' -f1 temp > temp1
    216. diff all_isolate_names.txt temp1 | wc -l
    217. #TODO, using sequence comparisons for one record!
    219. grep "gene=sepA" *.gff3 > temp
    220. cut -d'.' -f1 temp > temp1
    221. uniq temp1 > temp2
    222. diff all_isolate_names.txt temp2
    224. grep "gene=dltA" *.gff3 > temp
    225. cut -d'.' -f1 temp > temp1
    226. diff all_isolate_names.txt temp1
    228. grep "gene=fmtC" *.gff3 > temp
    229. cut -d'.' -f1 temp > temp1
    230. diff all_isolate_names.txt temp1 | wc -l
    231. #TODO, using sequence comparisons for one record!
    233. grep "gene=lipA" *.gff3 > temp
    234. cut -d'.' -f1 temp > temp1
    235. diff all_isolate_names.txt temp1
    237. grep "gene=sceD" *.gff3 > temp
    238. cut -d'.' -f1 temp > temp1
    239. diff all_isolate_names.txt temp1
    241. #TODO: check the sdrG more detailed with sequence alignments, since SE0760 is not standard gene name.
    242. grep "gene=SE0760" *.gff3 > temp
    243. cut -d'.' -f1 temp > temp1
    244. diff all_isolate_names.txt temp1 | wc -l
    245. #TODO, using sequence comparisons for one record!
    247. grep "gene=esp" *.gff3 > temp
    248. cut -d'.' -f1 temp > temp1
    249. diff all_isolate_names.txt temp1 | wc -l
    250. #TODO, using sequence comparisons for one record!
    252. grep "gene=ecpA" *.gff3 > temp
    253. cut -d'.' -f1 temp > temp1
    254. diff all_isolate_names.txt temp1
    255. 17d16
    256. < mibi1451
    257. 37d35
    258. < mibi1473

  10. Calulate the presence-absence-matrix by local blastn searching

    1. (Optional online search) https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes
    2. #Title:Refseq prokaryote representative genomes (contains refseq assembly)
    3. #Molecule Type:mixed DNA
    4. #Update date:2024/10/16
    5. #Number of sequences:1038672
    7. #cat gyrB_revcomp.fasta fumC_revcomp.fasta gltA.fasta icd_revcomp.fasta apsS.fasta sigB_revcomp.fasta sarA_revcomp.fasta ...
    9. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/apsS.fasta .
    10. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/agrC.fasta .
    11. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/yycG.fasta .
    12. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/psm-beta.fasta .
    13. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/hlb_.fasta .
    14. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/atlE.fasta .
    15. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/capC.fasta .
    16. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/fmtC.fasta .
    17. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/SE0760.fasta .
    18. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/esp.fasta .
    19. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880870.fasta .
    20. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880871.fasta .
    21. cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880872.fasta .
    23. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    24. cd ../shovill/${sample}/
    25. makeblastdb -in contigs.fa -dbtype nucl
    26. cd ../../presence_absence_matrix_on_gene_list
    27. done
    29. # -length(apsS.fasta)=1041
    30. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    31. blastn -db ../shovill/${sample}/contigs.fa -query apsS.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > apsS_on_${sample}.blastn
    32. done
    33. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    34. python3 analyze_blastn_res.py apsS_on_${sample}.blastn
    35. done
    36. apsS_on_mibi1435.blastn: 1041
    37. apsS_on_mibi1436.blastn: 1041
    38. apsS_on_mibi1437.blastn: 1041
    39. apsS_on_mibi1438.blastn: 1041
    40. apsS_on_mibi1439.blastn: 1041
    41. apsS_on_mibi1440.blastn: 1041
    42. apsS_on_mibi1441.blastn: 1041
    43. apsS_on_mibi1442.blastn: 1041
    44. apsS_on_mibi1443.blastn: 1041
    45. apsS_on_mibi1444.blastn: 1041
    46. apsS_on_mibi1445.blastn: 1041
    47. apsS_on_mibi1446.blastn: 1041
    48. apsS_on_mibi1447.blastn: 1041
    49. apsS_on_mibi1448.blastn: 1041
    50. apsS_on_mibi1449.blastn: 1041
    51. apsS_on_mibi1450.blastn: 1041
    52. apsS_on_mibi1451.blastn: 1041
    53. apsS_on_mibi1452.blastn: 1041
    54. apsS_on_mibi1453.blastn: 1041
    55. apsS_on_mibi1454.blastn: 1041
    56. apsS_on_mibi1455.blastn: 1041
    57. apsS_on_mibi1456.blastn: 1041
    58. apsS_on_mibi1457.blastn: 1041
    59. apsS_on_mibi1458.blastn: 1041
    60. apsS_on_mibi1459.blastn: 1041
    61. apsS_on_mibi1460.blastn: 1041
    62. apsS_on_mibi1461.blastn: 1041
    63. apsS_on_mibi1462.blastn: 1041
    64. apsS_on_mibi1463.blastn: 1041
    65. apsS_on_mibi1464.blastn: 1041
    66. apsS_on_mibi1465.blastn: 1041
    67. apsS_on_mibi1466.blastn: 1041
    68. apsS_on_mibi1467.blastn: 1041
    69. apsS_on_mibi1468.blastn: 1041
    70. apsS_on_mibi1469.blastn: 1041
    71. apsS_on_mibi1471.blastn: 1041
    72. apsS_on_mibi1473.blastn: 1041
    73. apsS_on_mibi1474.blastn: 1041
    74. apsS_on_mibi1475.blastn: 1041
    75. apsS_on_mibi1476.blastn: 1041
    76. apsS_on_mibi1477.blastn: 1041
    77. apsS_on_mibi1478.blastn: 1041
    78. apsS_on_mibi1479.blastn: 1041
    79. apsS_on_mibi1480.blastn: 1041
    80. apsS_on_mibi1481.blastn: 1041
    81. apsS_on_mibi1482.blastn: 1041
    82. apsS_on_mibi1483.blastn: 1041
    83. apsS_on_mibi1484.blastn: 1041
    84. apsS_on_mibi1485.blastn: 1041
    85. apsS_on_mibi1486.blastn: 1041
    86. apsS_on_mibi1487.blastn: 1041
    87. apsS_on_mibi1488.blastn: 1041
    88. apsS_on_mibi1489.blastn: 1041
    89. apsS_on_mibi1490.blastn: 1041
    90. apsS_on_mibi1491.blastn: 1041
    91. apsS_on_mibi1492.blastn: 1041
    92. apsS_on_mibi1493.blastn: 1041
    93. apsS_on_mibi1494.blastn: 1041
    94. apsS_on_mibi1495.blastn: 1041
    95. apsS_on_mibi1496.blastn: 1041
    96. apsS_on_mibi1497.blastn: 1041
    97. apsS_on_mibi1498.blastn: 1041
    98. apsS_on_mibi1499.blastn: 1041
    99. apsS_on_mibi1500.blastn: 1041
    100. apsS_on_mibi1501.blastn: 1041
    101. apsS_on_mibi1502.blastn: 1041
    102. apsS_on_mibi1503.blastn: 1041
    103. apsS_on_mibi1504.blastn: 1041
    104. apsS_on_mibi1505.blastn: 1041
    105. apsS_on_mibi1506.blastn: 1041
    106. apsS_on_mibi2312.blastn: 1041
    107. apsS_on_mibi2313.blastn: 1041
    108. apsS_on_mibi2314.blastn: 1041
    109. apsS_on_mibi2315.blastn: 1041
    110. apsS_on_mibi2316.blastn: 1041
    111. apsS_on_mibi2317.blastn: 1041
    112. apsS_on_mibi2318.blastn: 1041
    113. apsS_on_mibi2319.blastn: 1041
    114. apsS_on_mibi2320.blastn: 1041
    115. apsS_on_mibi2321.blastn: 1041
    116. apsS_on_mibi2379.blastn: 1041
    118. # -length(sigB_revcomp.fasta)=771
    119. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    120. blastn -db ../shovill/${sample}/contigs.fa -query sigB_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sigB_on_${sample}.blastn
    121. done
    122. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    123. python3 analyze_blastn_res.py sigB_on_${sample}.blastn
    124. done
    125. sigB_on_mibi1435.blastn: 771
    126. sigB_on_mibi1436.blastn: 771
    127. sigB_on_mibi1437.blastn: 771
    128. sigB_on_mibi1438.blastn: 771
    129. sigB_on_mibi1439.blastn: 771
    130. sigB_on_mibi1440.blastn: 771
    131. sigB_on_mibi1441.blastn: 771
    132. sigB_on_mibi1442.blastn: 771
    133. sigB_on_mibi1443.blastn: 771
    134. sigB_on_mibi1444.blastn: 771
    135. sigB_on_mibi1445.blastn: 771
    136. sigB_on_mibi1446.blastn: 771
    137. sigB_on_mibi1447.blastn: 771
    138. sigB_on_mibi1448.blastn: 771
    139. sigB_on_mibi1449.blastn: 771
    140. sigB_on_mibi1450.blastn: 771
    141. sigB_on_mibi1451.blastn: 771
    142. sigB_on_mibi1452.blastn: 771
    143. sigB_on_mibi1453.blastn: 771
    144. sigB_on_mibi1454.blastn: 771
    145. sigB_on_mibi1455.blastn: 771
    146. sigB_on_mibi1456.blastn: 771
    147. sigB_on_mibi1457.blastn: 771
    148. sigB_on_mibi1458.blastn: 771
    149. sigB_on_mibi1459.blastn: 771
    150. sigB_on_mibi1460.blastn: 771
    151. sigB_on_mibi1461.blastn: 0 *
    152. sigB_on_mibi1462.blastn: 771
    153. sigB_on_mibi1463.blastn: 771
    154. sigB_on_mibi1464.blastn: 771
    155. sigB_on_mibi1465.blastn: 771
    156. sigB_on_mibi1466.blastn: 771
    157. sigB_on_mibi1467.blastn: 771
    158. sigB_on_mibi1468.blastn: 771
    159. sigB_on_mibi1469.blastn: 771
    160. sigB_on_mibi1471.blastn: 771
    161. sigB_on_mibi1473.blastn: 771
    162. sigB_on_mibi1474.blastn: 771
    163. sigB_on_mibi1475.blastn: 771
    164. sigB_on_mibi1476.blastn: 771
    165. sigB_on_mibi1477.blastn: 771
    166. sigB_on_mibi1478.blastn: 771
    167. sigB_on_mibi1479.blastn: 771
    168. sigB_on_mibi1480.blastn: 771
    169. sigB_on_mibi1481.blastn: 771
    170. sigB_on_mibi1482.blastn: 771
    171. sigB_on_mibi1483.blastn: 771
    172. sigB_on_mibi1484.blastn: 771
    173. sigB_on_mibi1485.blastn: 771
    174. sigB_on_mibi1486.blastn: 771
    175. sigB_on_mibi1487.blastn: 771
    176. sigB_on_mibi1488.blastn: 771
    177. sigB_on_mibi1489.blastn: 771
    178. sigB_on_mibi1490.blastn: 771
    179. sigB_on_mibi1491.blastn: 771
    180. sigB_on_mibi1492.blastn: 771
    181. sigB_on_mibi1493.blastn: 771
    182. sigB_on_mibi1494.blastn: 771
    183. sigB_on_mibi1495.blastn: 771
    184. sigB_on_mibi1496.blastn: 771
    185. sigB_on_mibi1497.blastn: 771
    186. sigB_on_mibi1498.blastn: 771
    187. sigB_on_mibi1499.blastn: 771
    188. sigB_on_mibi1500.blastn: 771
    189. sigB_on_mibi1501.blastn: 771
    190. sigB_on_mibi1502.blastn: 771
    191. sigB_on_mibi1503.blastn: 771
    192. sigB_on_mibi1504.blastn: 771
    193. sigB_on_mibi1505.blastn: 771
    194. sigB_on_mibi1506.blastn: 771
    195. sigB_on_mibi2312.blastn: 771
    196. sigB_on_mibi2313.blastn: 771
    197. sigB_on_mibi2314.blastn: 771
    198. sigB_on_mibi2315.blastn: 771
    199. sigB_on_mibi2316.blastn: 771
    200. sigB_on_mibi2317.blastn: 771
    201. sigB_on_mibi2318.blastn: 771
    202. sigB_on_mibi2319.blastn: 771
    203. sigB_on_mibi2320.blastn: 771
    204. sigB_on_mibi2321.blastn: 771
    205. sigB_on_mibi2379.blastn: 771
    207. # - length(sarA_revcomp.fasta)=375
    208. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    209. blastn -db ../shovill/${sample}/contigs.fa -query sarA_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sarA_on_${sample}.blastn
    210. done
    211. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    212. python3 analyze_blastn_res.py sarA_on_${sample}.blastn
    213. done
    214. sarA_on_mibi1435.blastn: 375
    215. sarA_on_mibi1436.blastn: 375
    216. sarA_on_mibi1437.blastn: 375
    217. sarA_on_mibi1438.blastn: 375
    218. sarA_on_mibi1439.blastn: 375
    219. sarA_on_mibi1440.blastn: 375
    220. sarA_on_mibi1441.blastn: 375
    221. sarA_on_mibi1442.blastn: 375
    222. sarA_on_mibi1443.blastn: 375
    223. sarA_on_mibi1444.blastn: 375
    224. sarA_on_mibi1445.blastn: 375
    225. sarA_on_mibi1446.blastn: 375
    226. sarA_on_mibi1447.blastn: 375
    227. sarA_on_mibi1448.blastn: 375
    228. sarA_on_mibi1449.blastn: 375
    229. sarA_on_mibi1450.blastn: 375
    230. sarA_on_mibi1451.blastn: 0 *
    231. sarA_on_mibi1452.blastn: 375
    232. sarA_on_mibi1453.blastn: 375
    233. sarA_on_mibi1454.blastn: 375
    234. sarA_on_mibi1455.blastn: 375
    235. sarA_on_mibi1456.blastn: 375
    236. sarA_on_mibi1457.blastn: 375
    237. sarA_on_mibi1458.blastn: 375
    238. sarA_on_mibi1459.blastn: 375
    239. sarA_on_mibi1460.blastn: 375
    240. sarA_on_mibi1461.blastn: 375
    241. sarA_on_mibi1462.blastn: 375
    242. sarA_on_mibi1463.blastn: 375
    243. sarA_on_mibi1464.blastn: 375
    244. sarA_on_mibi1465.blastn: 375
    245. sarA_on_mibi1466.blastn: 208 *
    246. sarA_on_mibi1467.blastn: 375
    247. sarA_on_mibi1468.blastn: 375
    248. sarA_on_mibi1469.blastn: 375
    249. sarA_on_mibi1471.blastn: 375
    250. sarA_on_mibi1473.blastn: 375
    251. sarA_on_mibi1474.blastn: 375
    252. sarA_on_mibi1475.blastn: 375
    253. sarA_on_mibi1476.blastn: 375
    254. sarA_on_mibi1477.blastn: 375
    255. sarA_on_mibi1478.blastn: 375
    256. sarA_on_mibi1479.blastn: 375
    257. sarA_on_mibi1480.blastn: 375
    258. sarA_on_mibi1481.blastn: 248 *
    259. sarA_on_mibi1482.blastn: 375
    260. sarA_on_mibi1483.blastn: 375
    261. sarA_on_mibi1484.blastn: 375
    262. sarA_on_mibi1485.blastn: 375
    263. sarA_on_mibi1486.blastn: 375
    264. sarA_on_mibi1487.blastn: 375
    265. sarA_on_mibi1488.blastn: 375
    266. sarA_on_mibi1489.blastn: 375
    267. sarA_on_mibi1490.blastn: 375
    268. sarA_on_mibi1491.blastn: 375
    269. sarA_on_mibi1492.blastn: 375
    270. sarA_on_mibi1493.blastn: 375
    271. sarA_on_mibi1494.blastn: 375
    272. sarA_on_mibi1495.blastn: 375
    273. sarA_on_mibi1496.blastn: 375
    274. sarA_on_mibi1497.blastn: 375
    275. sarA_on_mibi1498.blastn: 375
    276. sarA_on_mibi1499.blastn: 375
    277. sarA_on_mibi1500.blastn: 375
    278. sarA_on_mibi1501.blastn: 375
    279. sarA_on_mibi1502.blastn: 375
    280. sarA_on_mibi1503.blastn: 375
    281. sarA_on_mibi1504.blastn: 375
    282. sarA_on_mibi1505.blastn: 375
    283. sarA_on_mibi1506.blastn: 357
    284. sarA_on_mibi2312.blastn: 375
    285. sarA_on_mibi2313.blastn: 375
    286. sarA_on_mibi2314.blastn: 375
    287. sarA_on_mibi2315.blastn: 375
    288. sarA_on_mibi2316.blastn: 375
    289. sarA_on_mibi2317.blastn: 375
    290. sarA_on_mibi2318.blastn: 375
    291. sarA_on_mibi2319.blastn: 375
    292. sarA_on_mibi2320.blastn: 375
    293. sarA_on_mibi2321.blastn: 375
    294. sarA_on_mibi2379.blastn: 375
    296. # -length(agrC.fasta)=1290
    297. samtools faidx agrABCD_hld.fasta "gi|3320006|emb|Z49220.1|":1494-2783
    299. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    300. blastn -db ../shovill/${sample}/contigs.fa -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_${sample}.blastn
    301. done
    302. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    303. python3 analyze_blastn_res.py agrC_on_${sample}.blastn
    304. done
    305. agrC_on_mibi1435.blastn: 1002
    306. agrC_on_mibi1436.blastn: 1290
    307. agrC_on_mibi1437.blastn: 688
    308. agrC_on_mibi1438.blastn: 1290
    309. agrC_on_mibi1439.blastn: 688
    310. agrC_on_mibi1440.blastn: 1290
    311. agrC_on_mibi1441.blastn: 861
    312. agrC_on_mibi1442.blastn: 688
    313. agrC_on_mibi1443.blastn: 1290
    314. agrC_on_mibi1444.blastn: 1290
    315. agrC_on_mibi1445.blastn: 688
    316. agrC_on_mibi1446.blastn: 688
    317. agrC_on_mibi1447.blastn: 688
    318. agrC_on_mibi1448.blastn: 1290
    319. agrC_on_mibi1449.blastn: 861
    320. agrC_on_mibi1450.blastn: 1290
    321. agrC_on_mibi1451.blastn: 688
    322. agrC_on_mibi1452.blastn: 818
    323. agrC_on_mibi1453.blastn: 1290
    324. agrC_on_mibi1454.blastn: 1290
    325. agrC_on_mibi1455.blastn: 1290
    326. agrC_on_mibi1456.blastn: 1290
    327. agrC_on_mibi1457.blastn: 688
    328. agrC_on_mibi1458.blastn: 1290
    329. agrC_on_mibi1459.blastn: 1290
    330. agrC_on_mibi1460.blastn: 688
    331. agrC_on_mibi1461.blastn: 1290
    332. agrC_on_mibi1462.blastn: 1290
    333. agrC_on_mibi1463.blastn: 1290
    334. agrC_on_mibi1464.blastn: 861
    335. agrC_on_mibi1465.blastn: 688
    336. agrC_on_mibi1466.blastn: 541
    337. agrC_on_mibi1467.blastn: 688
    338. agrC_on_mibi1468.blastn: 1290
    339. agrC_on_mibi1469.blastn: 1290
    340. agrC_on_mibi1471.blastn: 1165
    341. agrC_on_mibi1473.blastn: 688
    342. agrC_on_mibi1474.blastn: 1290
    343. agrC_on_mibi1475.blastn: 688
    344. agrC_on_mibi1476.blastn: 1290
    345. agrC_on_mibi1477.blastn: 688
    346. agrC_on_mibi1478.blastn: 442
    347. agrC_on_mibi1479.blastn: 688
    348. agrC_on_mibi1480.blastn: 1290
    349. agrC_on_mibi1481.blastn: 862
    350. agrC_on_mibi1482.blastn: 1290
    351. agrC_on_mibi1483.blastn: 1290
    352. agrC_on_mibi1484.blastn: 491
    353. agrC_on_mibi1485.blastn: 1290
    354. agrC_on_mibi1486.blastn: 1290
    355. agrC_on_mibi1487.blastn: 1290
    356. agrC_on_mibi1488.blastn: 1290
    357. agrC_on_mibi1489.blastn: 688
    358. agrC_on_mibi1490.blastn: 688
    359. agrC_on_mibi1491.blastn: 688
    360. agrC_on_mibi1492.blastn: 688
    361. agrC_on_mibi1493.blastn: 818
    362. agrC_on_mibi1494.blastn: 1290
    363. agrC_on_mibi1495.blastn: 688
    364. agrC_on_mibi1496.blastn: 1290
    365. agrC_on_mibi1497.blastn: 911
    366. agrC_on_mibi1498.blastn: 1290
    367. agrC_on_mibi1499.blastn: 688
    368. agrC_on_mibi1500.blastn: 1290
    369. agrC_on_mibi1501.blastn: 1290
    370. agrC_on_mibi1502.blastn: 1094
    371. agrC_on_mibi1503.blastn: 818
    372. agrC_on_mibi1504.blastn: 861
    373. agrC_on_mibi1505.blastn: 1290
    374. agrC_on_mibi1506.blastn: 1290
    375. agrC_on_mibi2312.blastn: 688
    376. agrC_on_mibi2313.blastn: 1290
    377. agrC_on_mibi2314.blastn: 1290
    378. agrC_on_mibi2315.blastn: 1290
    379. agrC_on_mibi2316.blastn: 688
    380. agrC_on_mibi2317.blastn: 688
    381. agrC_on_mibi2318.blastn: 1290
    382. agrC_on_mibi2319.blastn: 1290
    383. agrC_on_mibi2320.blastn: 688
    384. agrC_on_mibi2321.blastn: 1290
    385. agrC_on_mibi2379.blastn: 688
    387. partial, 1002/1290 nt present
    388. +
    389. partial, 688/1290 nt present
    390. +
    391. partial, 688/1290 nt present
    392. +
    393. partial, 861/1290 nt present
    394. partial, 688/1290 nt present
    395. +
    396. +
    397. partial, 688/1290 nt present
    398. partial, 688/1290 nt present
    399. partial, 688/1290 nt present
    400. +
    401. partial, 861/1290 nt present
    402. +
    403. partial, 688/1290 nt present
    404. partial, 818/1290 nt present
    405. +
    406. +
    407. +
    408. +
    409. partial, 688/1290 nt present
    410. +
    411. +
    412. partial, 688/1290 nt present
    413. +
    414. +
    415. +
    416. partial, 861/1290 nt present
    417. partial, 688/1290 nt present
    418. partial, 541/1290 nt present
    419. partial, 688/1290 nt present
    420. +
    421. +
    422. partial, 1165/1290 nt present
    423. partial, 688/1290 nt present
    424. +
    425. partial, 688/1290 nt present
    426. +
    427. partial, 688/1290 nt present
    428. partial, 442/1290 nt present
    429. partial, 688/1290 nt present
    430. +
    431. partial, 862/1290 nt present
    432. +
    433. +
    434. partial, 491/1290 nt present
    435. +
    436. +
    437. +
    438. +
    439. partial, 688/1290 nt present
    440. partial, 688/1290 nt present
    441. partial, 688/1290 nt present
    442. partial, 688/1290 nt present
    443. partial, 818/1290 nt present
    444. +
    445. partial, 688/1290 nt present
    446. +
    447. partial, 911/1290 nt present
    448. +
    449. partial, 688/1290 nt present
    450. +
    451. +
    452. partial, 1094/1290 nt present
    453. partial, 818/1290 nt present
    454. partial, 861/1290 nt present
    455. +
    456. +
    457. partial, 688/1290 nt present
    458. +
    459. +
    460. +
    461. partial, 688/1290 nt present
    462. partial, 688/1290 nt present
    463. +
    464. +
    465. partial, 688/1290 nt present
    466. +
    467. partial, 688/1290 nt present
    469. # - length(yycG.fasta)=1827
    470. gene            complement(2589240..2591072)
    471.                 /gene="yycG"
    472. samtools faidx CP000029.fasta "gi|57636010|gb|CP000029.1|":2589240-2591072 > yycG.fasta
    473. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    474. blastn -db ../shovill/${sample}/contigs.fa -query yycG_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_${sample}.blastn
    475. done
    476. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    477. python3 analyze_blastn_res.py yycG_on_${sample}.blastn
    478. done
    479. #-->WARNING: Only 80% similarity, not the same gene!
    480. yycG_on_mibi1435.blastn: 1833
    481. yycG_on_mibi1436.blastn: 1833
    482. yycG_on_mibi1437.blastn: 1833
    483. yycG_on_mibi1438.blastn: 1833
    484. yycG_on_mibi1439.blastn: 1833
    485. yycG_on_mibi1440.blastn: 1833
    486. yycG_on_mibi1441.blastn: 1833
    487. yycG_on_mibi1442.blastn: 1833
    488. yycG_on_mibi1443.blastn: 1833
    489. yycG_on_mibi1444.blastn: 1833
    490. yycG_on_mibi1445.blastn: 1833
    491. yycG_on_mibi1446.blastn: 1833
    492. yycG_on_mibi1447.blastn: 1833
    493. yycG_on_mibi1448.blastn: 1833
    494. yycG_on_mibi1449.blastn: 1833
    495. yycG_on_mibi1450.blastn: 1833
    496. yycG_on_mibi1451.blastn: 1833
    497. yycG_on_mibi1452.blastn: 1833
    498. yycG_on_mibi1453.blastn: 1833
    499. yycG_on_mibi1454.blastn: 1833
    500. yycG_on_mibi1455.blastn: 1833
    501. yycG_on_mibi1456.blastn: 1833
    502. yycG_on_mibi1457.blastn: 1833
    503. yycG_on_mibi1458.blastn: 1833
    504. yycG_on_mibi1459.blastn: 1833
    505. yycG_on_mibi1460.blastn: 1833
    506. yycG_on_mibi1461.blastn: 1833
    507. yycG_on_mibi1462.blastn: 1833
    508. yycG_on_mibi1463.blastn: 1833
    509. yycG_on_mibi1464.blastn: 1833
    510. yycG_on_mibi1465.blastn: 1833
    511. yycG_on_mibi1466.blastn: 1833
    512. yycG_on_mibi1467.blastn: 1833
    513. yycG_on_mibi1468.blastn: 1833
    514. yycG_on_mibi1469.blastn: 1833
    515. yycG_on_mibi1471.blastn: 1833
    516. yycG_on_mibi1473.blastn: 1833
    517. yycG_on_mibi1474.blastn: 1833
    518. yycG_on_mibi1475.blastn: 1833
    519. yycG_on_mibi1476.blastn: 1833
    520. yycG_on_mibi1477.blastn: 1833
    521. yycG_on_mibi1478.blastn: 1833
    522. yycG_on_mibi1479.blastn: 1833
    523. yycG_on_mibi1480.blastn: 1833
    524. yycG_on_mibi1481.blastn: 1833
    525. yycG_on_mibi1482.blastn: 1833
    526. yycG_on_mibi1483.blastn: 1833
    527. yycG_on_mibi1484.blastn: 1833
    528. yycG_on_mibi1485.blastn: 1833
    529. yycG_on_mibi1486.blastn: 1833
    530. yycG_on_mibi1487.blastn: 1833
    531. yycG_on_mibi1488.blastn: 1833
    532. yycG_on_mibi1489.blastn: 1833
    533. yycG_on_mibi1490.blastn: 1833
    534. yycG_on_mibi1491.blastn: 1833
    535. yycG_on_mibi1492.blastn: 1833
    536. yycG_on_mibi1493.blastn: 1833
    537. yycG_on_mibi1494.blastn: 1833
    538. yycG_on_mibi1495.blastn: 1833
    539. yycG_on_mibi1496.blastn: 1833
    540. yycG_on_mibi1497.blastn: 1833
    541. yycG_on_mibi1498.blastn: 1833
    542. yycG_on_mibi1499.blastn: 1833
    543. yycG_on_mibi1500.blastn: 1833
    544. yycG_on_mibi1501.blastn: 1833
    545. yycG_on_mibi1502.blastn: 1833
    546. yycG_on_mibi1503.blastn: 1833
    547. yycG_on_mibi1504.blastn: 1833
    548. yycG_on_mibi1505.blastn: 1833
    549. yycG_on_mibi1506.blastn: 1833
    550. yycG_on_mibi2312.blastn: 1833
    551. yycG_on_mibi2313.blastn: 1833
    552. yycG_on_mibi2314.blastn: 1833
    553. yycG_on_mibi2315.blastn: 1833
    554. yycG_on_mibi2316.blastn: 1833
    555. yycG_on_mibi2317.blastn: 1833
    556. yycG_on_mibi2318.blastn: 1833
    557. yycG_on_mibi2319.blastn: 1833
    558. yycG_on_mibi2320.blastn: 1833
    559. yycG_on_mibi2321.blastn: 1833
    560. yycG_on_mibi2379.blastn: 1833
    562. #TODOs: exact the gene sequence for psm-delta and atl
    563. #https://www.ncbi.nlm.nih.gov/nuccore    (psm gene) AND "Staphylococcus aureus"[porgn:__txid1280]
    564. #grep "PSM-delta" mibi1435.gbff
    565. #                     /product="Phenol-soluble modulin PSM-delta"
    566. #grep "atl" mibi1435.gbff
    567. #                     /gene="atl"
    568. #                     /gene="atl"
    570. https://www.ncbi.nlm.nih.gov/nuccore/JQ066320.1
    571. # -length(psm-beta1.fasta)=135
    572. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    573. blastn -db ../shovill/${sample}/contigs.fa -query psm-beta1.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_${sample}.blastn
    574. done
    575. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    576. python3 analyze_blastn_res.py psm-beta1_on_${sample}.blastn
    577. done
    578. psm-beta1_on_mibi1435.blastn: 0
    579. psm-beta1_on_mibi1436.blastn: 0
    580. psm-beta1_on_mibi1437.blastn: 0
    581. psm-beta1_on_mibi1438.blastn: 0
    582. psm-beta1_on_mibi1439.blastn: 0
    583. psm-beta1_on_mibi1440.blastn: 0
    584. psm-beta1_on_mibi1441.blastn: 0
    585. psm-beta1_on_mibi1442.blastn: 0
    586. psm-beta1_on_mibi1443.blastn: 0
    587. psm-beta1_on_mibi1444.blastn: 0
    588. psm-beta1_on_mibi1445.blastn: 0
    589. psm-beta1_on_mibi1446.blastn: 0
    590. psm-beta1_on_mibi1447.blastn: 0
    591. psm-beta1_on_mibi1448.blastn: 0
    592. psm-beta1_on_mibi1449.blastn: 0
    593. psm-beta1_on_mibi1450.blastn: 0
    594. psm-beta1_on_mibi1451.blastn: 0
    595. psm-beta1_on_mibi1452.blastn: 0
    596. psm-beta1_on_mibi1453.blastn: 0
    597. psm-beta1_on_mibi1454.blastn: 0
    598. psm-beta1_on_mibi1455.blastn: 0
    599. psm-beta1_on_mibi1456.blastn: 0
    600. psm-beta1_on_mibi1457.blastn: 0
    601. psm-beta1_on_mibi1458.blastn: 0
    602. psm-beta1_on_mibi1459.blastn: 0
    603. psm-beta1_on_mibi1460.blastn: 0
    604. psm-beta1_on_mibi1461.blastn: 0
    605. psm-beta1_on_mibi1462.blastn: 0
    606. psm-beta1_on_mibi1463.blastn: 0
    607. psm-beta1_on_mibi1464.blastn: 0
    608. psm-beta1_on_mibi1465.blastn: 0
    609. psm-beta1_on_mibi1466.blastn: 0
    610. psm-beta1_on_mibi1467.blastn: 0
    611. psm-beta1_on_mibi1468.blastn: 0
    612. psm-beta1_on_mibi1469.blastn: 0
    613. psm-beta1_on_mibi1471.blastn: 0
    614. psm-beta1_on_mibi1473.blastn: 0
    615. psm-beta1_on_mibi1474.blastn: 0
    616. psm-beta1_on_mibi1475.blastn: 0
    617. psm-beta1_on_mibi1476.blastn: 0
    618. psm-beta1_on_mibi1477.blastn: 0
    619. psm-beta1_on_mibi1478.blastn: 0
    620. psm-beta1_on_mibi1479.blastn: 0
    621. psm-beta1_on_mibi1480.blastn: 0
    622. psm-beta1_on_mibi1481.blastn: 0
    623. psm-beta1_on_mibi1482.blastn: 0
    624. psm-beta1_on_mibi1483.blastn: 0
    625. psm-beta1_on_mibi1484.blastn: 0
    626. psm-beta1_on_mibi1485.blastn: 0
    627. psm-beta1_on_mibi1486.blastn: 0
    628. psm-beta1_on_mibi1487.blastn: 0
    629. psm-beta1_on_mibi1488.blastn: 0
    630. psm-beta1_on_mibi1489.blastn: 0
    631. psm-beta1_on_mibi1490.blastn: 0
    632. psm-beta1_on_mibi1491.blastn: 0
    633. psm-beta1_on_mibi1492.blastn: 0
    634. psm-beta1_on_mibi1493.blastn: 0
    635. psm-beta1_on_mibi1494.blastn: 0
    636. psm-beta1_on_mibi1495.blastn: 0
    637. psm-beta1_on_mibi1496.blastn: 0
    638. psm-beta1_on_mibi1497.blastn: 0
    639. psm-beta1_on_mibi1498.blastn: 0
    640. psm-beta1_on_mibi1499.blastn: 0
    641. psm-beta1_on_mibi1500.blastn: 0
    642. psm-beta1_on_mibi1501.blastn: 0
    643. psm-beta1_on_mibi1502.blastn: 0
    644. psm-beta1_on_mibi1503.blastn: 0
    645. psm-beta1_on_mibi1504.blastn: 0
    646. psm-beta1_on_mibi1505.blastn: 0
    647. psm-beta1_on_mibi1506.blastn: 0
    648. psm-beta1_on_mibi2312.blastn: 0
    649. psm-beta1_on_mibi2313.blastn: 0
    650. psm-beta1_on_mibi2314.blastn: 0
    651. psm-beta1_on_mibi2315.blastn: 0
    652. psm-beta1_on_mibi2316.blastn: 0
    653. psm-beta1_on_mibi2317.blastn: 0
    654. psm-beta1_on_mibi2318.blastn: 0
    655. psm-beta1_on_mibi2319.blastn: 0
    656. psm-beta1_on_mibi2320.blastn: 0
    657. psm-beta1_on_mibi2321.blastn: 0
    658. psm-beta1_on_mibi2379.blastn: 0
    660. # -length(hlb.fasta)=993
    661. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    662. blastn -db ../shovill/${sample}/contigs.fa -query psm-beta.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_${sample}.blastn
    663. done
    664. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    665. python3 analyze_blastn_res.py hlb_on_${sample}.blastn
    666. done
    667. hlb_on_mibi1435.blastn: 0
    668. hlb_on_mibi1436.blastn: 0
    669. hlb_on_mibi1437.blastn: 0
    670. hlb_on_mibi1438.blastn: 0
    671. hlb_on_mibi1439.blastn: 0
    672. hlb_on_mibi1440.blastn: 0
    673. hlb_on_mibi1441.blastn: 0
    674. hlb_on_mibi1442.blastn: 0
    675. hlb_on_mibi1443.blastn: 0
    676. hlb_on_mibi1444.blastn: 0
    677. hlb_on_mibi1445.blastn: 0
    678. hlb_on_mibi1446.blastn: 0
    679. hlb_on_mibi1447.blastn: 0
    680. hlb_on_mibi1448.blastn: 0
    681. hlb_on_mibi1449.blastn: 0
    682. hlb_on_mibi1450.blastn: 0
    683. hlb_on_mibi1451.blastn: 0
    684. hlb_on_mibi1452.blastn: 0
    685. hlb_on_mibi1453.blastn: 0
    686. hlb_on_mibi1454.blastn: 0
    687. hlb_on_mibi1455.blastn: 0
    688. hlb_on_mibi1456.blastn: 0
    689. hlb_on_mibi1457.blastn: 0
    690. hlb_on_mibi1458.blastn: 0
    691. hlb_on_mibi1459.blastn: 0
    692. hlb_on_mibi1460.blastn: 0
    693. hlb_on_mibi1461.blastn: 0
    694. hlb_on_mibi1462.blastn: 0
    695. hlb_on_mibi1463.blastn: 0
    696. hlb_on_mibi1464.blastn: 0
    697. hlb_on_mibi1465.blastn: 0
    698. hlb_on_mibi1466.blastn: 0
    699. hlb_on_mibi1467.blastn: 0
    700. hlb_on_mibi1468.blastn: 0
    701. hlb_on_mibi1469.blastn: 0
    702. hlb_on_mibi1471.blastn: 0
    703. hlb_on_mibi1473.blastn: 0
    704. hlb_on_mibi1474.blastn: 0
    705. hlb_on_mibi1475.blastn: 0
    706. hlb_on_mibi1476.blastn: 0
    707. hlb_on_mibi1477.blastn: 0
    708. hlb_on_mibi1478.blastn: 0
    709. hlb_on_mibi1479.blastn: 0
    710. hlb_on_mibi1480.blastn: 0
    711. hlb_on_mibi1481.blastn: 0
    712. hlb_on_mibi1482.blastn: 0
    713. hlb_on_mibi1483.blastn: 0
    714. hlb_on_mibi1484.blastn: 0
    715. hlb_on_mibi1485.blastn: 0
    716. hlb_on_mibi1486.blastn: 0
    717. hlb_on_mibi1487.blastn: 0
    718. hlb_on_mibi1488.blastn: 0
    719. hlb_on_mibi1489.blastn: 0
    720. hlb_on_mibi1490.blastn: 0
    721. hlb_on_mibi1491.blastn: 0
    722. hlb_on_mibi1492.blastn: 0
    723. hlb_on_mibi1493.blastn: 0
    724. hlb_on_mibi1494.blastn: 0
    725. hlb_on_mibi1495.blastn: 0
    726. hlb_on_mibi1496.blastn: 0
    727. hlb_on_mibi1497.blastn: 0
    728. hlb_on_mibi1498.blastn: 0
    729. hlb_on_mibi1499.blastn: 0
    730. hlb_on_mibi1500.blastn: 0
    731. hlb_on_mibi1501.blastn: 0
    732. hlb_on_mibi1502.blastn: 0
    733. hlb_on_mibi1503.blastn: 0
    734. hlb_on_mibi1504.blastn: 0
    735. hlb_on_mibi1505.blastn: 0
    736. hlb_on_mibi1506.blastn: 0
    737. hlb_on_mibi2312.blastn: 0
    738. hlb_on_mibi2313.blastn: 0
    739. hlb_on_mibi2314.blastn: 0
    740. hlb_on_mibi2315.blastn: 0
    741. hlb_on_mibi2316.blastn: 0
    742. hlb_on_mibi2317.blastn: 0
    743. hlb_on_mibi2318.blastn: 0
    744. hlb_on_mibi2319.blastn: 0
    745. hlb_on_mibi2320.blastn: 0
    746. hlb_on_mibi2321.blastn: 0
    747. hlb_on_mibi2379.blastn: 0
    749. ## -length(altE_revcomp.fasta)=4008
    750. #gene            complement(627656..631663)
    751. #                     /gene="atlE"
    752. #samtools faidx CP000029.fasta gi|57636010|gb|CP000029.1|
    753. samtools faidx CP000029.fasta "gi|57636010|gb|CP000029.1|":627656-631663 > atlE.fasta
    754. revcomp atlE.fasta > atlE_revcomp.fasta
    755. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    756. blastn -db ../shovill/${sample}/contigs.fa -query atlE_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_${sample}.blastn
    757. done
    758. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    759. python3 analyze_blastn_res.py atlE_on_${sample}.blastn
    760. done
    761. atlE_on_mibi1435.blastn: 4008
    762. atlE_on_mibi1436.blastn: 4008
    763. atlE_on_mibi1437.blastn: 4465
    764. atlE_on_mibi1438.blastn: 4008
    765. atlE_on_mibi1439.blastn: 4008
    766. atlE_on_mibi1440.blastn: 4008
    767. atlE_on_mibi1441.blastn: 4450
    768. atlE_on_mibi1442.blastn: 4450
    769. atlE_on_mibi1443.blastn: 4008
    770. atlE_on_mibi1444.blastn: 4008
    771. atlE_on_mibi1445.blastn: 4008
    772. atlE_on_mibi1446.blastn: 4008
    773. atlE_on_mibi1447.blastn: 4008
    774. atlE_on_mibi1448.blastn: 4008
    775. atlE_on_mibi1449.blastn: 4008
    776. atlE_on_mibi1450.blastn: 4008
    777. atlE_on_mibi1451.blastn: 4008
    778. atlE_on_mibi1452.blastn: 4450
    779. atlE_on_mibi1453.blastn: 4008
    780. atlE_on_mibi1454.blastn: 4008
    781. atlE_on_mibi1455.blastn: 4008
    782. atlE_on_mibi1456.blastn: 4008
    783. atlE_on_mibi1457.blastn: 4008
    784. atlE_on_mibi1458.blastn: 4450
    785. atlE_on_mibi1459.blastn: 4008
    786. atlE_on_mibi1460.blastn: 4008
    787. atlE_on_mibi1461.blastn: 4008
    788. atlE_on_mibi1462.blastn: 4008
    789. atlE_on_mibi1463.blastn: 4450
    790. atlE_on_mibi1464.blastn: 4450
    791. atlE_on_mibi1465.blastn: 4008
    792. atlE_on_mibi1466.blastn: 4008
    793. atlE_on_mibi1467.blastn: 4450
    794. atlE_on_mibi1468.blastn: 4465
    795. atlE_on_mibi1469.blastn: 4465
    796. atlE_on_mibi1471.blastn: 4008
    797. atlE_on_mibi1473.blastn: 4008
    798. atlE_on_mibi1474.blastn: 4008
    799. atlE_on_mibi1475.blastn: 4008
    800. atlE_on_mibi1476.blastn: 4008
    801. atlE_on_mibi1477.blastn: 4008
    802. atlE_on_mibi1478.blastn: 4008
    803. atlE_on_mibi1479.blastn: 4008
    804. atlE_on_mibi1480.blastn: 4008
    805. atlE_on_mibi1481.blastn: 4008
    806. atlE_on_mibi1482.blastn: 4008
    807. atlE_on_mibi1483.blastn: 4450
    808. atlE_on_mibi1484.blastn: 4008
    809. atlE_on_mibi1485.blastn: 4008
    810. atlE_on_mibi1486.blastn: 4450
    811. atlE_on_mibi1487.blastn: 4008
    812. atlE_on_mibi1488.blastn: 4008
    813. atlE_on_mibi1489.blastn: 4450
    814. atlE_on_mibi1490.blastn: 4008
    815. atlE_on_mibi1491.blastn: 4008
    816. atlE_on_mibi1492.blastn: 4008
    817. atlE_on_mibi1493.blastn: 4450
    818. atlE_on_mibi1494.blastn: 4008
    819. atlE_on_mibi1495.blastn: 4008
    820. atlE_on_mibi1496.blastn: 4008
    821. atlE_on_mibi1497.blastn: 4008
    822. atlE_on_mibi1498.blastn: 4008
    823. atlE_on_mibi1499.blastn: 4008
    824. atlE_on_mibi1500.blastn: 4008
    825. atlE_on_mibi1501.blastn: 4008
    826. atlE_on_mibi1502.blastn: 4008
    827. atlE_on_mibi1503.blastn: 4008
    828. atlE_on_mibi1504.blastn: 4450
    829. atlE_on_mibi1505.blastn: 4008
    830. atlE_on_mibi1506.blastn: 4008
    831. atlE_on_mibi2312.blastn: 4008
    832. atlE_on_mibi2313.blastn: 4008
    833. atlE_on_mibi2314.blastn: 4008
    834. atlE_on_mibi2315.blastn: 4008
    835. atlE_on_mibi2316.blastn: 4008
    836. atlE_on_mibi2317.blastn: 4008
    837. atlE_on_mibi2318.blastn: 4008
    838. atlE_on_mibi2319.blastn: 4008
    839. atlE_on_mibi2320.blastn: 4008
    840. atlE_on_mibi2321.blastn: 4008
    841. atlE_on_mibi2379.blastn: 4008
    843. # -length(sdrG)=2796
    844. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    845. blastn -db ../shovill/${sample}/contigs.fa -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_${sample}.blastn
    846. done
    847. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    848. python3 analyze_blastn_res.py sdrG_on_${sample}.blastn
    849. done
    850. sdrG_on_mibi1435.blastn: 2973
    851. sdrG_on_mibi1436.blastn: 2967
    852. sdrG_on_mibi1437.blastn: 2821
    853. sdrG_on_mibi1438.blastn: 2796
    854. sdrG_on_mibi1439.blastn: 3155
    855. sdrG_on_mibi1440.blastn: 2967
    856. sdrG_on_mibi1441.blastn: 2797
    857. sdrG_on_mibi1442.blastn: 2801
    858. sdrG_on_mibi1443.blastn: 2966
    859. sdrG_on_mibi1444.blastn: 2796
    860. sdrG_on_mibi1445.blastn: 3158
    861. sdrG_on_mibi1446.blastn: 3155
    862. sdrG_on_mibi1447.blastn: 2966
    863. sdrG_on_mibi1448.blastn: 2797
    864. sdrG_on_mibi1449.blastn: 2712
    865. sdrG_on_mibi1450.blastn: 2794
    866. sdrG_on_mibi1451.blastn: 2946
    867. sdrG_on_mibi1452.blastn: 3166
    868. sdrG_on_mibi1453.blastn: 2970
    869. sdrG_on_mibi1454.blastn: 2976
    870. sdrG_on_mibi1455.blastn: 2797
    871. sdrG_on_mibi1456.blastn: 2967
    872. sdrG_on_mibi1457.blastn: 2963
    873. sdrG_on_mibi1458.blastn: 2794
    874. sdrG_on_mibi1459.blastn: 3153
    875. sdrG_on_mibi1460.blastn: 2566
    876. sdrG_on_mibi1461.blastn: 2500
    877. sdrG_on_mibi1462.blastn: 2966
    878. sdrG_on_mibi1463.blastn: 2971
    879. sdrG_on_mibi1464.blastn: 2530
    880. sdrG_on_mibi1465.blastn: 2981
    881. sdrG_on_mibi1466.blastn: 1547 *
    882. sdrG_on_mibi1467.blastn: 2794
    883. sdrG_on_mibi1468.blastn: 2967
    884. sdrG_on_mibi1469.blastn: 2967
    885. sdrG_on_mibi1471.blastn: 2796
    886. sdrG_on_mibi1473.blastn: 2976
    887. sdrG_on_mibi1474.blastn: 2797
    888. sdrG_on_mibi1475.blastn: 2981
    889. sdrG_on_mibi1476.blastn: 2794
    890. sdrG_on_mibi1477.blastn: 2967
    891. sdrG_on_mibi1478.blastn: 1511 *
    892. sdrG_on_mibi1479.blastn: 2966
    893. sdrG_on_mibi1480.blastn: 2976
    894. sdrG_on_mibi1481.blastn: 2797
    895. sdrG_on_mibi1482.blastn: 2797
    896. sdrG_on_mibi1483.blastn: 2797
    897. sdrG_on_mibi1484.blastn: 2976
    898. sdrG_on_mibi1485.blastn: 3001
    899. sdrG_on_mibi1486.blastn: 2797
    900. sdrG_on_mibi1487.blastn: 2976
    901. sdrG_on_mibi1488.blastn: 2963
    902. sdrG_on_mibi1489.blastn: 2797
    903. sdrG_on_mibi1490.blastn: 2981
    904. sdrG_on_mibi1491.blastn: 3155
    905. sdrG_on_mibi1492.blastn: 2982
    906. sdrG_on_mibi1493.blastn: 2904
    907. sdrG_on_mibi1494.blastn: 2980
    908. sdrG_on_mibi1495.blastn: 2976
    909. sdrG_on_mibi1496.blastn: 2994
    910. sdrG_on_mibi1497.blastn: 2797
    911. sdrG_on_mibi1498.blastn: 2967
    912. sdrG_on_mibi1499.blastn: 2976
    913. sdrG_on_mibi1500.blastn: 2797
    914. sdrG_on_mibi1501.blastn: 2797
    915. sdrG_on_mibi1502.blastn: 2976
    916. sdrG_on_mibi1503.blastn: 2976
    917. sdrG_on_mibi1504.blastn: 2634
    918. sdrG_on_mibi1505.blastn: 2970
    919. sdrG_on_mibi1506.blastn: 2985
    920. sdrG_on_mibi2312.blastn: 2866
    921. sdrG_on_mibi2313.blastn: 2794
    922. sdrG_on_mibi2314.blastn: 3171
    923. sdrG_on_mibi2315.blastn: 2797
    924. sdrG_on_mibi2316.blastn: 3158
    925. sdrG_on_mibi2317.blastn: 2975
    926. sdrG_on_mibi2318.blastn: 2976
    927. sdrG_on_mibi2319.blastn: 2613
    928. sdrG_on_mibi2320.blastn: 2972
    929. sdrG_on_mibi2321.blastn: 2794
    930. sdrG_on_mibi2379.blastn: 2975
    932. ##length(sdrH)=1446
    933. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    934. blastn -db ../shovill/${sample}/contigs.fa -query sdrH_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrH_on_${sample}.blastn
    935. done
    936. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    937. python3 analyze_blastn_res.py sdrH_on_${sample}.blastn
    938. done
    939. sdrH_on_mibi1435.blastn: 1647
    940. sdrH_on_mibi1436.blastn: 1683
    941. sdrH_on_mibi1437.blastn: 1482
    942. sdrH_on_mibi1438.blastn: 1608
    943. sdrH_on_mibi1439.blastn: 1739
    944. sdrH_on_mibi1440.blastn: 1644
    945. sdrH_on_mibi1441.blastn: 1446
    946. sdrH_on_mibi1442.blastn: 1482
    947. sdrH_on_mibi1443.blastn: 1683
    948. sdrH_on_mibi1444.blastn: 1683
    949. sdrH_on_mibi1445.blastn: 1482
    950. sdrH_on_mibi1446.blastn: 1482
    951. sdrH_on_mibi1447.blastn: 1482
    952. sdrH_on_mibi1448.blastn: 1446
    953. sdrH_on_mibi1449.blastn: 1450
    954. sdrH_on_mibi1450.blastn: 1446
    955. sdrH_on_mibi1451.blastn: 1487
    956. sdrH_on_mibi1452.blastn: 1446
    957. sdrH_on_mibi1453.blastn: 1464
    958. sdrH_on_mibi1454.blastn: 1647
    959. sdrH_on_mibi1455.blastn: 1644
    960. sdrH_on_mibi1456.blastn: 1647
    961. sdrH_on_mibi1457.blastn: 1572
    962. sdrH_on_mibi1458.blastn: 1632
    963. sdrH_on_mibi1459.blastn: 1647
    964. sdrH_on_mibi1460.blastn: 1482
    965. sdrH_on_mibi1461.blastn: 1647
    966. sdrH_on_mibi1462.blastn: 1683
    967. sdrH_on_mibi1463.blastn: 1647
    968. sdrH_on_mibi1464.blastn: 1739
    969. sdrH_on_mibi1465.blastn: 1464
    970. sdrH_on_mibi1466.blastn: 1305
    971. sdrH_on_mibi1467.blastn: 1482
    972. sdrH_on_mibi1468.blastn: 1559
    973. sdrH_on_mibi1469.blastn: 1556
    974. sdrH_on_mibi1471.blastn: 1572
    975. sdrH_on_mibi1473.blastn: 1482
    976. sdrH_on_mibi1474.blastn: 1446
    977. sdrH_on_mibi1475.blastn: 1482
    978. sdrH_on_mibi1476.blastn: 1458
    979. sdrH_on_mibi1477.blastn: 1647
    980. sdrH_on_mibi1478.blastn: 710 *
    981. sdrH_on_mibi1479.blastn: 1482
    982. sdrH_on_mibi1480.blastn: 1647
    983. sdrH_on_mibi1481.blastn: 1412
    984. sdrH_on_mibi1482.blastn: 1647
    985. sdrH_on_mibi1483.blastn: 1647
    986. sdrH_on_mibi1484.blastn: 1448
    987. sdrH_on_mibi1485.blastn: 1647
    988. sdrH_on_mibi1486.blastn: 1827
    989. sdrH_on_mibi1487.blastn: 1647
    990. sdrH_on_mibi1488.blastn: 1683
    991. sdrH_on_mibi1489.blastn: 1739
    992. sdrH_on_mibi1490.blastn: 1482
    993. sdrH_on_mibi1491.blastn: 1482
    994. sdrH_on_mibi1492.blastn: 1482
    995. sdrH_on_mibi1493.blastn: 1440
    996. sdrH_on_mibi1494.blastn: 1458
    997. sdrH_on_mibi1495.blastn: 1482
    998. sdrH_on_mibi1496.blastn: 1644
    999. sdrH_on_mibi1497.blastn: 1736
    1000. sdrH_on_mibi1498.blastn: 1647
    1001. sdrH_on_mibi1499.blastn: 1482
    1002. sdrH_on_mibi1500.blastn: 1683
    1003. sdrH_on_mibi1501.blastn: 1647
    1004. sdrH_on_mibi1502.blastn: 1647
    1005. sdrH_on_mibi1503.blastn: 1745
    1006. sdrH_on_mibi1504.blastn: 1683
    1007. sdrH_on_mibi1505.blastn: 1736
    1008. sdrH_on_mibi1506.blastn: 1683
    1009. sdrH_on_mibi2312.blastn: 1556
    1010. sdrH_on_mibi2313.blastn: 1464
    1011. sdrH_on_mibi2314.blastn: 1464
    1012. sdrH_on_mibi2315.blastn: 1683
    1013. sdrH_on_mibi2316.blastn: 1482
    1014. sdrH_on_mibi2317.blastn: 1464
    1015. sdrH_on_mibi2318.blastn: 1647
    1016. sdrH_on_mibi2319.blastn: 1644
    1017. sdrH_on_mibi2320.blastn: 1464
    1018. sdrH_on_mibi2321.blastn: 1464
    1019. sdrH_on_mibi2379.blastn: 1647
    1021. # -length(ebh_revcomp.fasta)=30450
    1022. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1023. blastn -db ../shovill/${sample}/contigs.fa -query ebh_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ebh_on_${sample}.blastn
    1024. done
    1025. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1026. python3 analyze_blastn_res.py ebh_on_${sample}.blastn
    1027. done
    1029. ebh_on_mibi1435.blastn: 30450
    1030. ebh_on_mibi1436.blastn: 30450
    1031. ebh_on_mibi1437.blastn: 29490
    1032. ebh_on_mibi1438.blastn: 25428
    1033. ebh_on_mibi1439.blastn: 30452
    1034. ebh_on_mibi1440.blastn: 11933
    1035. ebh_on_mibi1441.blastn: 30450
    1036. ebh_on_mibi1442.blastn: 30463
    1037. ebh_on_mibi1443.blastn: 30450
    1038. ebh_on_mibi1444.blastn: 30450
    1039. ebh_on_mibi1445.blastn: 30450
    1040. ebh_on_mibi1446.blastn: 30450
    1041. ebh_on_mibi1447.blastn: 30450
    1042. ebh_on_mibi1448.blastn: 30450
    1043. ebh_on_mibi1449.blastn: 30450
    1044. ebh_on_mibi1450.blastn: 30450
    1045. ebh_on_mibi1451.blastn: 30450
    1046. ebh_on_mibi1452.blastn: 21401
    1047. ebh_on_mibi1453.blastn: 30450
    1048. ebh_on_mibi1454.blastn: 11933
    1049. ebh_on_mibi1455.blastn: 30450
    1050. ebh_on_mibi1456.blastn: 11933
    1051. ebh_on_mibi1457.blastn: 30450
    1052. ebh_on_mibi1458.blastn: 29955
    1053. ebh_on_mibi1459.blastn: 11933
    1054. ebh_on_mibi1460.blastn: 30450
    1055. ebh_on_mibi1461.blastn: 11933
    1056. ebh_on_mibi1462.blastn: 30450
    1057. ebh_on_mibi1463.blastn: 20602
    1058. ebh_on_mibi1464.blastn: 30450
    1059. ebh_on_mibi1465.blastn: 30450
    1060. ebh_on_mibi1466.blastn: 14964
    1061. ebh_on_mibi1467.blastn: 30463
    1062. ebh_on_mibi1468.blastn: 30450
    1063. ebh_on_mibi1469.blastn: 30450
    1064. ebh_on_mibi1471.blastn: 25428
    1065. ebh_on_mibi1473.blastn: 30450
    1066. ebh_on_mibi1474.blastn: 30450
    1067. ebh_on_mibi1475.blastn: 30450
    1068. ebh_on_mibi1476.blastn: 30450
    1069. ebh_on_mibi1477.blastn: 30384
    1070. ebh_on_mibi1478.blastn: 11933
    1071. ebh_on_mibi1479.blastn: 30450
    1072. ebh_on_mibi1480.blastn: 11933
    1073. ebh_on_mibi1481.blastn: 25694
    1074. ebh_on_mibi1482.blastn: 30450
    1075. ebh_on_mibi1483.blastn: 30450
    1076. ebh_on_mibi1484.blastn: 30450
    1077. ebh_on_mibi1485.blastn: 11933
    1078. ebh_on_mibi1486.blastn: 30450
    1079. ebh_on_mibi1487.blastn: 11933
    1080. ebh_on_mibi1488.blastn: 30450
    1081. ebh_on_mibi1489.blastn: 30450
    1082. ebh_on_mibi1490.blastn: 30450
    1083. ebh_on_mibi1491.blastn: 30450
    1084. ebh_on_mibi1492.blastn: 30450
    1085. ebh_on_mibi1493.blastn: 30465
    1086. ebh_on_mibi1494.blastn: 30450
    1087. ebh_on_mibi1495.blastn: 30450
    1088. ebh_on_mibi1496.blastn: 11933
    1089. ebh_on_mibi1497.blastn: 30450
    1090. ebh_on_mibi1498.blastn: 11933
    1091. ebh_on_mibi1499.blastn: 30450
    1092. ebh_on_mibi1500.blastn: 30450
    1093. ebh_on_mibi1501.blastn: 30450
    1094. ebh_on_mibi1502.blastn: 11933
    1095. ebh_on_mibi1503.blastn: 30450
    1096. ebh_on_mibi1504.blastn: 30450
    1097. ebh_on_mibi1505.blastn: 30450
    1098. ebh_on_mibi1506.blastn: 30450
    1099. ebh_on_mibi2312.blastn: 30450
    1100. ebh_on_mibi2313.blastn: 30450
    1101. ebh_on_mibi2314.blastn: 30450
    1102. ebh_on_mibi2315.blastn: 30461
    1103. ebh_on_mibi2316.blastn: 30450
    1104. ebh_on_mibi2317.blastn: 30450
    1105. ebh_on_mibi2318.blastn: 11933
    1106. ebh_on_mibi2319.blastn: 11933
    1107. ebh_on_mibi2320.blastn: 30110
    1108. ebh_on_mibi2321.blastn: 30450
    1109. ebh_on_mibi2379.blastn: 30450
    1111. #For gene: ebpS, tagB, capC, sepA, dltA, fmtC
    1112. # -length(SE0760)=1383
    1113. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1114. blastn -db ../shovill/${sample}/contigs.fa -query ebpS_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ebpS_on_${sample}.blastn
    1115. done
    1116. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1117. python3 analyze_blastn_res.py ebpS_on_${sample}.blastn
    1118. done
    1119. ebpS_on_mibi1435.blastn: 1383
    1120. ebpS_on_mibi1436.blastn: 1383
    1121. ebpS_on_mibi1437.blastn: 1383
    1122. ebpS_on_mibi1438.blastn: 1383
    1123. ebpS_on_mibi1439.blastn: 1383
    1124. ebpS_on_mibi1440.blastn: 1383
    1125. ebpS_on_mibi1441.blastn: 1383
    1126. ebpS_on_mibi1442.blastn: 1408
    1127. ebpS_on_mibi1443.blastn: 1383
    1128. ebpS_on_mibi1444.blastn: 1383
    1129. ebpS_on_mibi1445.blastn: 1383
    1130. ebpS_on_mibi1446.blastn: 1383
    1131. ebpS_on_mibi1447.blastn: 1383
    1132. ebpS_on_mibi1448.blastn: 1383
    1133. ebpS_on_mibi1449.blastn: 1383
    1134. ebpS_on_mibi1450.blastn: 1383
    1135. ebpS_on_mibi1451.blastn: 1383
    1136. ebpS_on_mibi1452.blastn: 1408
    1137. ebpS_on_mibi1453.blastn: 1383
    1138. ebpS_on_mibi1454.blastn: 1383
    1139. ebpS_on_mibi1455.blastn: 1383
    1140. ebpS_on_mibi1456.blastn: 1383
    1141. ebpS_on_mibi1457.blastn: 1383
    1142. ebpS_on_mibi1458.blastn: 1408
    1143. ebpS_on_mibi1459.blastn: 1383
    1144. ebpS_on_mibi1460.blastn: 1383
    1145. ebpS_on_mibi1461.blastn: 1383
    1146. ebpS_on_mibi1462.blastn: 1383
    1147. ebpS_on_mibi1463.blastn: 1383
    1148. ebpS_on_mibi1464.blastn: 1392
    1149. ebpS_on_mibi1465.blastn: 1383
    1150. ebpS_on_mibi1466.blastn: 1383
    1151. ebpS_on_mibi1467.blastn: 1420
    1152. ebpS_on_mibi1468.blastn: 1383
    1153. ebpS_on_mibi1469.blastn: 1383
    1154. ebpS_on_mibi1471.blastn: 1383
    1155. ebpS_on_mibi1473.blastn: 1383
    1156. ebpS_on_mibi1474.blastn: 1383
    1157. ebpS_on_mibi1475.blastn: 1383
    1158. ebpS_on_mibi1476.blastn: 1383
    1159. ebpS_on_mibi1477.blastn: 1275
    1160. ebpS_on_mibi1478.blastn: 1383
    1161. ebpS_on_mibi1479.blastn: 1383
    1162. ebpS_on_mibi1480.blastn: 1383
    1163. ebpS_on_mibi1481.blastn: 1383
    1164. ebpS_on_mibi1482.blastn: 1383
    1165. ebpS_on_mibi1483.blastn: 1383
    1166. ebpS_on_mibi1484.blastn: 1383
    1167. ebpS_on_mibi1485.blastn: 1383
    1168. ebpS_on_mibi1486.blastn: 1383
    1169. ebpS_on_mibi1487.blastn: 1383
    1170. ebpS_on_mibi1488.blastn: 1383
    1171. ebpS_on_mibi1489.blastn: 1383
    1172. ebpS_on_mibi1490.blastn: 1383
    1173. ebpS_on_mibi1491.blastn: 1383
    1174. ebpS_on_mibi1492.blastn: 1383
    1175. ebpS_on_mibi1493.blastn: 1420
    1176. ebpS_on_mibi1494.blastn: 1383
    1177. ebpS_on_mibi1495.blastn: 1383
    1178. ebpS_on_mibi1496.blastn: 1383
    1179. ebpS_on_mibi1497.blastn: 1383
    1180. ebpS_on_mibi1498.blastn: 1383
    1181. ebpS_on_mibi1499.blastn: 1383
    1182. ebpS_on_mibi1500.blastn: 1383
    1183. ebpS_on_mibi1501.blastn: 1383
    1184. ebpS_on_mibi1502.blastn: 1383
    1185. ebpS_on_mibi1503.blastn: 1383
    1186. ebpS_on_mibi1504.blastn: 1408
    1187. ebpS_on_mibi1505.blastn: 1383
    1188. ebpS_on_mibi1506.blastn: 1383
    1189. ebpS_on_mibi2312.blastn: 1383
    1190. ebpS_on_mibi2313.blastn: 1383
    1191. ebpS_on_mibi2314.blastn: 1383
    1192. ebpS_on_mibi2315.blastn: 1383
    1193. ebpS_on_mibi2316.blastn: 1383
    1194. ebpS_on_mibi2317.blastn: 1383
    1195. ebpS_on_mibi2318.blastn: 1383
    1196. ebpS_on_mibi2319.blastn: 1383
    1197. ebpS_on_mibi2320.blastn: 1383
    1198. ebpS_on_mibi2321.blastn: 1383
    1199. ebpS_on_mibi2379.blastn: 1383
    1201. # -length(tagB)=1680
    1202. #mibi1435.gff3:contig_2  Prodigal        CDS     146190  147869  .       -       0       ID=MMJCKL_03035;Name=CDP-glycerol glycerophosphotransferase%2C TagB/SpsB family;locus_tag=MMJCKL_03035;product=CDP-glycerol glycerophosphotransferase%2C TagB/SpsB family;Dbxref=COG:COG1887,COG:MI,RefSeq:WP_001831509.1,SO:0001217,UniParc:UPI00004BA7A8,UniRef:UniRef100_A0A4Q9W688,UniRef:UniRef50_A0A0H2VI21,UniRef:UniRef90_A0A0H2VI21;gene=tagB
    1203. samtools faidx mibi1435.fna contig_2:146190-147869 > tagB_mibi1435.fasta
    1204. revcomp tagB_mibi1435.fasta > tagB_mibi1435_revcomp.fasta
    1205. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1206. blastn -db ../shovill/${sample}/contigs.fa -query tagB_mibi1435_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_${sample}.blastn
    1207. done
    1208. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1209. python3 analyze_blastn_res.py tagB_on_${sample}.blastn
    1210. done
    1211. tagB_on_mibi1435.blastn: 1680
    1212. tagB_on_mibi1436.blastn: 1680
    1213. tagB_on_mibi1437.blastn: 1680
    1214. tagB_on_mibi1438.blastn: 1680
    1215. tagB_on_mibi1439.blastn: 1680
    1216. tagB_on_mibi1440.blastn: 1680
    1217. tagB_on_mibi1441.blastn: 1680
    1218. tagB_on_mibi1442.blastn: 1680
    1219. tagB_on_mibi1443.blastn: 1680
    1220. tagB_on_mibi1444.blastn: 1680
    1221. tagB_on_mibi1445.blastn: 1680
    1222. tagB_on_mibi1446.blastn: 1680
    1223. tagB_on_mibi1447.blastn: 1680
    1224. tagB_on_mibi1448.blastn: 1680
    1225. tagB_on_mibi1449.blastn: 1680
    1226. tagB_on_mibi1450.blastn: 1680
    1227. tagB_on_mibi1451.blastn: 1680
    1228. tagB_on_mibi1452.blastn: 1680
    1229. tagB_on_mibi1453.blastn: 1680
    1230. tagB_on_mibi1454.blastn: 1680
    1231. tagB_on_mibi1455.blastn: 1680
    1232. tagB_on_mibi1456.blastn: 1680
    1233. tagB_on_mibi1457.blastn: 1680
    1234. tagB_on_mibi1458.blastn: 1680
    1235. tagB_on_mibi1459.blastn: 1680
    1236. tagB_on_mibi1460.blastn: 1680
    1237. tagB_on_mibi1461.blastn: 1680
    1238. tagB_on_mibi1462.blastn: 1680
    1239. tagB_on_mibi1463.blastn: 1680
    1240. tagB_on_mibi1464.blastn: 1680
    1241. tagB_on_mibi1465.blastn: 1680
    1242. tagB_on_mibi1466.blastn: 1680
    1243. tagB_on_mibi1467.blastn: 1680
    1244. tagB_on_mibi1468.blastn: 1680
    1245. tagB_on_mibi1469.blastn: 1680
    1246. tagB_on_mibi1471.blastn: 1680
    1247. tagB_on_mibi1473.blastn: 1680
    1248. tagB_on_mibi1474.blastn: 1680
    1249. tagB_on_mibi1475.blastn: 1680
    1250. tagB_on_mibi1476.blastn: 1680
    1251. tagB_on_mibi1477.blastn: 1680
    1252. tagB_on_mibi1478.blastn: 1680
    1253. tagB_on_mibi1479.blastn: 1680
    1254. tagB_on_mibi1480.blastn: 1680
    1255. tagB_on_mibi1481.blastn: 1680
    1256. tagB_on_mibi1482.blastn: 1680
    1257. tagB_on_mibi1483.blastn: 1680
    1258. tagB_on_mibi1484.blastn: 1680
    1259. tagB_on_mibi1485.blastn: 1680
    1260. tagB_on_mibi1486.blastn: 1680
    1261. tagB_on_mibi1487.blastn: 1680
    1262. tagB_on_mibi1488.blastn: 1680
    1263. tagB_on_mibi1489.blastn: 1680
    1264. tagB_on_mibi1490.blastn: 1680
    1265. tagB_on_mibi1491.blastn: 1680
    1266. tagB_on_mibi1492.blastn: 1680
    1267. tagB_on_mibi1493.blastn: 1680
    1268. tagB_on_mibi1494.blastn: 1680
    1269. tagB_on_mibi1495.blastn: 1680
    1270. tagB_on_mibi1496.blastn: 1680
    1271. tagB_on_mibi1497.blastn: 1680
    1272. tagB_on_mibi1498.blastn: 1680
    1273. tagB_on_mibi1499.blastn: 1680
    1274. tagB_on_mibi1500.blastn: 1680
    1275. tagB_on_mibi1501.blastn: 1680
    1276. tagB_on_mibi1502.blastn: 1680
    1277. tagB_on_mibi1503.blastn: 1680
    1278. tagB_on_mibi1504.blastn: 1680
    1279. tagB_on_mibi1505.blastn: 1680
    1280. tagB_on_mibi1506.blastn: 1680
    1281. tagB_on_mibi2312.blastn: 1680
    1282. tagB_on_mibi2313.blastn: 1680
    1283. tagB_on_mibi2314.blastn: 1680
    1284. tagB_on_mibi2315.blastn: 1680
    1285. tagB_on_mibi2316.blastn: 1680
    1286. tagB_on_mibi2317.blastn: 1680
    1287. tagB_on_mibi2318.blastn: 1680
    1288. tagB_on_mibi2319.blastn: 1680
    1289. tagB_on_mibi2320.blastn: 1680
    1290. tagB_on_mibi2321.blastn: 1680
    1291. tagB_on_mibi2379.blastn: 1680
    1293. # -length(capC)=450
    1294. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1295. blastn -db ../shovill/${sample}/contigs.fa -query capC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_${sample}.blastn
    1296. done
    1297. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1298. python3 analyze_blastn_res.py capC_on_${sample}.blastn
    1299. done
    1300. capC_on_mibi1435.blastn: 0
    1301. capC_on_mibi1436.blastn: 0
    1302. capC_on_mibi1437.blastn: 0
    1303. capC_on_mibi1438.blastn: 0
    1304. capC_on_mibi1439.blastn: 0
    1305. capC_on_mibi1440.blastn: 0
    1306. capC_on_mibi1441.blastn: 0
    1307. capC_on_mibi1442.blastn: 0
    1308. capC_on_mibi1443.blastn: 0
    1309. capC_on_mibi1444.blastn: 0
    1310. capC_on_mibi1445.blastn: 0
    1311. capC_on_mibi1446.blastn: 0
    1312. capC_on_mibi1447.blastn: 0
    1313. capC_on_mibi1448.blastn: 0
    1314. capC_on_mibi1449.blastn: 0
    1315. capC_on_mibi1450.blastn: 0
    1316. capC_on_mibi1451.blastn: 0
    1317. capC_on_mibi1452.blastn: 0
    1318. capC_on_mibi1453.blastn: 0
    1319. capC_on_mibi1454.blastn: 0
    1320. capC_on_mibi1455.blastn: 0
    1321. capC_on_mibi1456.blastn: 0
    1322. capC_on_mibi1457.blastn: 0
    1323. capC_on_mibi1458.blastn: 0
    1324. capC_on_mibi1459.blastn: 0
    1325. capC_on_mibi1460.blastn: 0
    1326. capC_on_mibi1461.blastn: 0
    1327. capC_on_mibi1462.blastn: 0
    1328. capC_on_mibi1463.blastn: 0
    1329. capC_on_mibi1464.blastn: 0
    1330. capC_on_mibi1465.blastn: 0
    1331. capC_on_mibi1466.blastn: 0
    1332. capC_on_mibi1467.blastn: 0
    1333. capC_on_mibi1468.blastn: 0
    1334. capC_on_mibi1469.blastn: 0
    1335. capC_on_mibi1471.blastn: 0
    1336. capC_on_mibi1473.blastn: 0
    1337. capC_on_mibi1474.blastn: 0
    1338. capC_on_mibi1475.blastn: 0
    1339. capC_on_mibi1476.blastn: 0
    1340. capC_on_mibi1477.blastn: 0
    1341. capC_on_mibi1478.blastn: 0
    1342. capC_on_mibi1479.blastn: 0
    1343. capC_on_mibi1480.blastn: 0
    1344. capC_on_mibi1481.blastn: 0
    1345. capC_on_mibi1482.blastn: 0
    1346. capC_on_mibi1483.blastn: 0
    1347. capC_on_mibi1484.blastn: 0
    1348. capC_on_mibi1485.blastn: 0
    1349. capC_on_mibi1486.blastn: 0
    1350. capC_on_mibi1487.blastn: 0
    1351. capC_on_mibi1488.blastn: 0
    1352. capC_on_mibi1489.blastn: 0
    1353. capC_on_mibi1490.blastn: 0
    1354. capC_on_mibi1491.blastn: 0
    1355. capC_on_mibi1492.blastn: 0
    1356. capC_on_mibi1493.blastn: 0
    1357. capC_on_mibi1494.blastn: 0
    1358. capC_on_mibi1495.blastn: 0
    1359. capC_on_mibi1496.blastn: 0
    1360. capC_on_mibi1497.blastn: 0
    1361. capC_on_mibi1498.blastn: 0
    1362. capC_on_mibi1499.blastn: 0
    1363. capC_on_mibi1500.blastn: 0
    1364. capC_on_mibi1501.blastn: 0
    1365. capC_on_mibi1502.blastn: 0
    1366. capC_on_mibi1503.blastn: 0
    1367. capC_on_mibi1504.blastn: 0
    1368. capC_on_mibi1505.blastn: 0
    1369. capC_on_mibi1506.blastn: 0
    1370. capC_on_mibi2312.blastn: 0
    1371. capC_on_mibi2313.blastn: 0
    1372. capC_on_mibi2314.blastn: 0
    1373. capC_on_mibi2315.blastn: 0
    1374. capC_on_mibi2316.blastn: 0
    1375. capC_on_mibi2317.blastn: 0
    1376. capC_on_mibi2318.blastn: 0
    1377. capC_on_mibi2319.blastn: 0
    1378. capC_on_mibi2320.blastn: 0
    1379. capC_on_mibi2321.blastn: 0
    1380. capC_on_mibi2379.blastn: 0
    1382. # -length(sepA_mibi1435.fasta)=1524
    1383. #contig_7        Prodigal        CDS     52151   53674   .       +       0       ID=MMJCKL_06215;Name=Extracellular elastase;locus_tag=MMJCKL_06215;product=Extracellular elastase;Dbxref=COG:COG3227,COG:O,EC:3.4.24.-,GO:0004222,GO:0005576,GO:0006508,GO:0046872,KEGG:K01401,RefSeq:WP_002486087.1,SO:0001217,UniParc:UPI00024E17FE,UniRef:UniRef100_UPI00066C9785,UniRef:UniRef50_P0C0Q3,UniRef:UniRef90_P0C0Q3;gene=sepA
    1384. samtools faidx mibi1435.fna contig_7:52151-53674 > sepA_mibi1435.fasta
    1385. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1386. blastn -db ../shovill/${sample}/contigs.fa -query sepA_mibi1435.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_${sample}.blastn
    1387. done
    1388. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1389. python3 analyze_blastn_res.py sepA_on_${sample}.blastn
    1390. done
    1391. sepA_on_mibi1435.blastn: 1524
    1392. sepA_on_mibi1436.blastn: 1524
    1393. sepA_on_mibi1437.blastn: 1523
    1394. sepA_on_mibi1438.blastn: 1524
    1395. sepA_on_mibi1439.blastn: 1523
    1396. sepA_on_mibi1440.blastn: 1523
    1397. sepA_on_mibi1441.blastn: 1523
    1398. sepA_on_mibi1442.blastn: 1523
    1399. sepA_on_mibi1443.blastn: 1523
    1400. sepA_on_mibi1444.blastn: 1523
    1401. sepA_on_mibi1445.blastn: 1523
    1402. sepA_on_mibi1446.blastn: 1523
    1403. sepA_on_mibi1447.blastn: 1523
    1404. sepA_on_mibi1448.blastn: 1524
    1405. sepA_on_mibi1449.blastn: 1523
    1406. sepA_on_mibi1450.blastn: 1523
    1407. sepA_on_mibi1451.blastn: 1523
    1408. sepA_on_mibi1452.blastn: 1523
    1409. sepA_on_mibi1453.blastn: 1523
    1410. sepA_on_mibi1454.blastn: 1523
    1411. sepA_on_mibi1455.blastn: 1524
    1412. sepA_on_mibi1456.blastn: 1523
    1413. sepA_on_mibi1457.blastn: 1523
    1414. sepA_on_mibi1458.blastn: 1523
    1415. sepA_on_mibi1459.blastn: 1523
    1416. sepA_on_mibi1460.blastn: 1523
    1417. sepA_on_mibi1461.blastn: 1523
    1418. sepA_on_mibi1462.blastn: 1523
    1419. sepA_on_mibi1463.blastn: 1523
    1420. sepA_on_mibi1464.blastn: 1523
    1421. sepA_on_mibi1465.blastn: 1523
    1422. sepA_on_mibi1466.blastn: 1523
    1423. sepA_on_mibi1467.blastn: 1524
    1424. sepA_on_mibi1468.blastn: 1523
    1425. sepA_on_mibi1469.blastn: 1523
    1426. sepA_on_mibi1471.blastn: 1524
    1427. sepA_on_mibi1473.blastn: 1523
    1428. sepA_on_mibi1474.blastn: 1524
    1429. sepA_on_mibi1475.blastn: 1523
    1430. sepA_on_mibi1476.blastn: 1523
    1431. sepA_on_mibi1477.blastn: 1524
    1432. sepA_on_mibi1478.blastn: 1523
    1433. sepA_on_mibi1479.blastn: 1523
    1434. sepA_on_mibi1480.blastn: 1523
    1435. sepA_on_mibi1481.blastn: 1524
    1436. sepA_on_mibi1482.blastn: 1524
    1437. sepA_on_mibi1483.blastn: 1523
    1438. sepA_on_mibi1484.blastn: 1523
    1439. sepA_on_mibi1485.blastn: 1523
    1440. sepA_on_mibi1486.blastn: 1523
    1441. sepA_on_mibi1487.blastn: 1523
    1442. sepA_on_mibi1488.blastn: 1523
    1443. sepA_on_mibi1489.blastn: 1523
    1444. sepA_on_mibi1490.blastn: 1523
    1445. sepA_on_mibi1491.blastn: 1523
    1446. sepA_on_mibi1492.blastn: 1523
    1447. sepA_on_mibi1493.blastn: 1523
    1448. sepA_on_mibi1494.blastn: 1523
    1449. sepA_on_mibi1495.blastn: 1523
    1450. sepA_on_mibi1496.blastn: 1523
    1451. sepA_on_mibi1497.blastn: 1523
    1452. sepA_on_mibi1498.blastn: 1523
    1453. sepA_on_mibi1499.blastn: 1523
    1454. sepA_on_mibi1500.blastn: 1523
    1455. sepA_on_mibi1501.blastn: 1523
    1456. sepA_on_mibi1502.blastn: 1523
    1457. sepA_on_mibi1503.blastn: 1523
    1458. sepA_on_mibi1504.blastn: 1523
    1459. sepA_on_mibi1505.blastn: 1523
    1460. sepA_on_mibi1506.blastn: 1523
    1461. sepA_on_mibi2312.blastn: 1523
    1462. sepA_on_mibi2313.blastn: 1523
    1463. sepA_on_mibi2314.blastn: 1523
    1464. sepA_on_mibi2315.blastn: 1523
    1465. sepA_on_mibi2316.blastn: 1523
    1466. sepA_on_mibi2317.blastn: 1523
    1467. sepA_on_mibi2318.blastn: 1523
    1468. sepA_on_mibi2319.blastn: 1523
    1469. sepA_on_mibi2320.blastn: 1523
    1470. sepA_on_mibi2321.blastn: 1523
    1471. sepA_on_mibi2379.blastn: 1523
    1473. # -length(dltA.fasta)=1458
    1474. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1475. blastn -db ../shovill/${sample}/contigs.fa -query dltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > dltA_on_${sample}.blastn
    1476. done
    1477. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1478. python3 analyze_blastn_res.py dltA_on_${sample}.blastn
    1479. done
    1480. dltA_on_mibi1435.blastn: 1458
    1481. dltA_on_mibi1436.blastn: 1458
    1482. dltA_on_mibi1437.blastn: 1458
    1483. dltA_on_mibi1438.blastn: 1458
    1484. dltA_on_mibi1439.blastn: 1458
    1485. dltA_on_mibi1440.blastn: 1458
    1486. dltA_on_mibi1441.blastn: 1458
    1487. dltA_on_mibi1442.blastn: 1458
    1488. dltA_on_mibi1443.blastn: 1458
    1489. dltA_on_mibi1444.blastn: 1458
    1490. dltA_on_mibi1445.blastn: 1458
    1491. dltA_on_mibi1446.blastn: 1458
    1492. dltA_on_mibi1447.blastn: 1458
    1493. dltA_on_mibi1448.blastn: 1464
    1494. dltA_on_mibi1449.blastn: 1458
    1495. dltA_on_mibi1450.blastn: 1458
    1496. dltA_on_mibi1451.blastn: 1458
    1497. dltA_on_mibi1452.blastn: 1458
    1498. dltA_on_mibi1453.blastn: 1458
    1499. dltA_on_mibi1454.blastn: 1458
    1500. dltA_on_mibi1455.blastn: 1458
    1501. dltA_on_mibi1456.blastn: 1458
    1502. dltA_on_mibi1457.blastn: 1458
    1503. dltA_on_mibi1458.blastn: 1458
    1504. dltA_on_mibi1459.blastn: 1458
    1505. dltA_on_mibi1460.blastn: 1458
    1506. dltA_on_mibi1461.blastn: 1458
    1507. dltA_on_mibi1462.blastn: 1458
    1508. dltA_on_mibi1463.blastn: 1458
    1509. dltA_on_mibi1464.blastn: 1458
    1510. dltA_on_mibi1465.blastn: 1458
    1511. dltA_on_mibi1466.blastn: 1458
    1512. dltA_on_mibi1467.blastn: 1458
    1513. dltA_on_mibi1468.blastn: 1458
    1514. dltA_on_mibi1469.blastn: 1458
    1515. dltA_on_mibi1471.blastn: 1458
    1516. dltA_on_mibi1473.blastn: 1458
    1517. dltA_on_mibi1474.blastn: 1458
    1518. dltA_on_mibi1475.blastn: 1458
    1519. dltA_on_mibi1476.blastn: 1458
    1520. dltA_on_mibi1477.blastn: 1458
    1521. dltA_on_mibi1478.blastn: 1458
    1522. dltA_on_mibi1479.blastn: 1458
    1523. dltA_on_mibi1480.blastn: 1458
    1524. dltA_on_mibi1481.blastn: 1458
    1525. dltA_on_mibi1482.blastn: 1458
    1526. dltA_on_mibi1483.blastn: 1458
    1527. dltA_on_mibi1484.blastn: 1458
    1528. dltA_on_mibi1485.blastn: 1458
    1529. dltA_on_mibi1486.blastn: 1458
    1530. dltA_on_mibi1487.blastn: 1458
    1531. dltA_on_mibi1488.blastn: 1458
    1532. dltA_on_mibi1489.blastn: 1458
    1533. dltA_on_mibi1490.blastn: 1458
    1534. dltA_on_mibi1491.blastn: 1458
    1535. dltA_on_mibi1492.blastn: 1458
    1536. dltA_on_mibi1493.blastn: 1458
    1537. dltA_on_mibi1494.blastn: 1458
    1538. dltA_on_mibi1495.blastn: 1458
    1539. dltA_on_mibi1496.blastn: 1458
    1540. dltA_on_mibi1497.blastn: 1458
    1541. dltA_on_mibi1498.blastn: 1458
    1542. dltA_on_mibi1499.blastn: 1458
    1543. dltA_on_mibi1500.blastn: 1458
    1544. dltA_on_mibi1501.blastn: 1458
    1545. dltA_on_mibi1502.blastn: 1458
    1546. dltA_on_mibi1503.blastn: 1458
    1547. dltA_on_mibi1504.blastn: 1458
    1548. dltA_on_mibi1505.blastn: 1458
    1549. dltA_on_mibi1506.blastn: 1458
    1550. dltA_on_mibi2312.blastn: 1458
    1551. dltA_on_mibi2313.blastn: 1458
    1552. dltA_on_mibi2314.blastn: 1458
    1553. dltA_on_mibi2315.blastn: 1458
    1554. dltA_on_mibi2316.blastn: 1458
    1555. dltA_on_mibi2317.blastn: 1458
    1556. dltA_on_mibi2318.blastn: 1458
    1557. dltA_on_mibi2319.blastn: 1458
    1558. dltA_on_mibi2320.blastn: 1458
    1559. dltA_on_mibi2321.blastn: 1458
    1560. dltA_on_mibi2379.blastn: 1458
    1562. # -length(fmtC.fasta)=2523
    1563. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1564. blastn -db ../shovill/${sample}/contigs.fa -query fmtC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_${sample}.blastn
    1565. done
    1566. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1567. python3 analyze_blastn_res.py fmtC_on_${sample}.blastn
    1568. done
    1569. fmtC_on_mibi1435.blastn: 0
    1570. fmtC_on_mibi1436.blastn: 0
    1571. fmtC_on_mibi1437.blastn: 0
    1572. fmtC_on_mibi1438.blastn: 0
    1573. fmtC_on_mibi1439.blastn: 0
    1574. fmtC_on_mibi1440.blastn: 0
    1575. fmtC_on_mibi1441.blastn: 0
    1576. fmtC_on_mibi1442.blastn: 0
    1577. fmtC_on_mibi1443.blastn: 0
    1578. fmtC_on_mibi1444.blastn: 0
    1579. fmtC_on_mibi1445.blastn: 0
    1580. fmtC_on_mibi1446.blastn: 0
    1581. fmtC_on_mibi1447.blastn: 0
    1582. fmtC_on_mibi1448.blastn: 0
    1583. fmtC_on_mibi1449.blastn: 0
    1584. fmtC_on_mibi1450.blastn: 0
    1585. fmtC_on_mibi1451.blastn: 0
    1586. fmtC_on_mibi1452.blastn: 0
    1587. fmtC_on_mibi1453.blastn: 0
    1588. fmtC_on_mibi1454.blastn: 0
    1589. fmtC_on_mibi1455.blastn: 0
    1590. fmtC_on_mibi1456.blastn: 0
    1591. fmtC_on_mibi1457.blastn: 0
    1592. fmtC_on_mibi1458.blastn: 0
    1593. fmtC_on_mibi1459.blastn: 0
    1594. fmtC_on_mibi1460.blastn: 0
    1595. fmtC_on_mibi1461.blastn: 0
    1596. fmtC_on_mibi1462.blastn: 0
    1597. fmtC_on_mibi1463.blastn: 0
    1598. fmtC_on_mibi1464.blastn: 0
    1599. fmtC_on_mibi1465.blastn: 0
    1600. fmtC_on_mibi1466.blastn: 0
    1601. fmtC_on_mibi1467.blastn: 0
    1602. fmtC_on_mibi1468.blastn: 0
    1603. fmtC_on_mibi1469.blastn: 0
    1604. fmtC_on_mibi1471.blastn: 0
    1605. fmtC_on_mibi1473.blastn: 0
    1606. fmtC_on_mibi1474.blastn: 0
    1607. fmtC_on_mibi1475.blastn: 0
    1608. fmtC_on_mibi1476.blastn: 0
    1609. fmtC_on_mibi1477.blastn: 0
    1610. fmtC_on_mibi1478.blastn: 0
    1611. fmtC_on_mibi1479.blastn: 0
    1612. fmtC_on_mibi1480.blastn: 0
    1613. fmtC_on_mibi1481.blastn: 0
    1614. fmtC_on_mibi1482.blastn: 0
    1615. fmtC_on_mibi1483.blastn: 0
    1616. fmtC_on_mibi1484.blastn: 0
    1617. fmtC_on_mibi1485.blastn: 0
    1618. fmtC_on_mibi1486.blastn: 0
    1619. fmtC_on_mibi1487.blastn: 0
    1620. fmtC_on_mibi1488.blastn: 0
    1621. fmtC_on_mibi1489.blastn: 0
    1622. fmtC_on_mibi1490.blastn: 0
    1623. fmtC_on_mibi1491.blastn: 0
    1624. fmtC_on_mibi1492.blastn: 0
    1625. fmtC_on_mibi1493.blastn: 0
    1626. fmtC_on_mibi1494.blastn: 0
    1627. fmtC_on_mibi1495.blastn: 0
    1628. fmtC_on_mibi1496.blastn: 0
    1629. fmtC_on_mibi1497.blastn: 0
    1630. fmtC_on_mibi1498.blastn: 0
    1631. fmtC_on_mibi1499.blastn: 0
    1632. fmtC_on_mibi1500.blastn: 0
    1633. fmtC_on_mibi1501.blastn: 0
    1634. fmtC_on_mibi1502.blastn: 0
    1635. fmtC_on_mibi1503.blastn: 0
    1636. fmtC_on_mibi1504.blastn: 0
    1637. fmtC_on_mibi1505.blastn: 0
    1638. fmtC_on_mibi1506.blastn: 0
    1639. fmtC_on_mibi2312.blastn: 0
    1640. fmtC_on_mibi2313.blastn: 0
    1641. fmtC_on_mibi2314.blastn: 0
    1642. fmtC_on_mibi2315.blastn: 0
    1643. fmtC_on_mibi2316.blastn: 0
    1644. fmtC_on_mibi2317.blastn: 0
    1645. fmtC_on_mibi2318.blastn: 0
    1646. fmtC_on_mibi2319.blastn: 0
    1647. fmtC_on_mibi2320.blastn: 0
    1648. fmtC_on_mibi2321.blastn: 0
    1649. fmtC_on_mibi2379.blastn: 0
    1651. #-- For genes: lipA (915), sceD (699), esp (660), ecpA (1188)
    1652. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1653. blastn -db ../shovill/${sample}/contigs.fa -query lipA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./lipA_on_${sample}.blastn
    1654. done
    1655. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1656. python3 analyze_blastn_res.py lipA_on_${sample}.blastn
    1657. done
    1658. lipA_on_mibi1435.blastn: 915
    1659. lipA_on_mibi1436.blastn: 915
    1660. lipA_on_mibi1437.blastn: 915
    1661. lipA_on_mibi1438.blastn: 915
    1662. lipA_on_mibi1439.blastn: 915
    1663. lipA_on_mibi1440.blastn: 915
    1664. lipA_on_mibi1441.blastn: 915
    1665. lipA_on_mibi1442.blastn: 915
    1666. lipA_on_mibi1443.blastn: 915
    1667. lipA_on_mibi1444.blastn: 915
    1668. lipA_on_mibi1445.blastn: 915
    1669. lipA_on_mibi1446.blastn: 915
    1670. lipA_on_mibi1447.blastn: 915
    1671. lipA_on_mibi1448.blastn: 915
    1672. lipA_on_mibi1449.blastn: 915
    1673. lipA_on_mibi1450.blastn: 915
    1674. lipA_on_mibi1451.blastn: 915
    1675. lipA_on_mibi1452.blastn: 915
    1676. lipA_on_mibi1453.blastn: 915
    1677. lipA_on_mibi1454.blastn: 915
    1678. lipA_on_mibi1455.blastn: 915
    1679. lipA_on_mibi1456.blastn: 915
    1680. lipA_on_mibi1457.blastn: 915
    1681. lipA_on_mibi1458.blastn: 915
    1682. lipA_on_mibi1459.blastn: 915
    1683. lipA_on_mibi1460.blastn: 915
    1684. lipA_on_mibi1461.blastn: 915
    1685. lipA_on_mibi1462.blastn: 915
    1686. lipA_on_mibi1463.blastn: 915
    1687. lipA_on_mibi1464.blastn: 915
    1688. lipA_on_mibi1465.blastn: 915
    1689. lipA_on_mibi1466.blastn: 915
    1690. lipA_on_mibi1467.blastn: 915
    1691. lipA_on_mibi1468.blastn: 915
    1692. lipA_on_mibi1469.blastn: 915
    1693. lipA_on_mibi1471.blastn: 915
    1694. lipA_on_mibi1473.blastn: 915
    1695. lipA_on_mibi1474.blastn: 915
    1696. lipA_on_mibi1475.blastn: 915
    1697. lipA_on_mibi1476.blastn: 915
    1698. lipA_on_mibi1477.blastn: 915
    1699. lipA_on_mibi1478.blastn: 915
    1700. lipA_on_mibi1479.blastn: 915
    1701. lipA_on_mibi1480.blastn: 915
    1702. lipA_on_mibi1481.blastn: 915
    1703. lipA_on_mibi1482.blastn: 915
    1704. lipA_on_mibi1483.blastn: 915
    1705. lipA_on_mibi1484.blastn: 915
    1706. lipA_on_mibi1485.blastn: 915
    1707. lipA_on_mibi1486.blastn: 915
    1708. lipA_on_mibi1487.blastn: 915
    1709. lipA_on_mibi1488.blastn: 915
    1710. lipA_on_mibi1489.blastn: 915
    1711. lipA_on_mibi1490.blastn: 915
    1712. lipA_on_mibi1491.blastn: 915
    1713. lipA_on_mibi1492.blastn: 915
    1714. lipA_on_mibi1493.blastn: 915
    1715. lipA_on_mibi1494.blastn: 915
    1716. lipA_on_mibi1495.blastn: 915
    1717. lipA_on_mibi1496.blastn: 915
    1718. lipA_on_mibi1497.blastn: 915
    1719. lipA_on_mibi1498.blastn: 915
    1720. lipA_on_mibi1499.blastn: 915
    1721. lipA_on_mibi1500.blastn: 915
    1722. lipA_on_mibi1501.blastn: 915
    1723. lipA_on_mibi1502.blastn: 915
    1724. lipA_on_mibi1503.blastn: 915
    1725. lipA_on_mibi1504.blastn: 915
    1726. lipA_on_mibi1505.blastn: 915
    1727. lipA_on_mibi1506.blastn: 915
    1728. lipA_on_mibi2312.blastn: 915
    1729. lipA_on_mibi2313.blastn: 915
    1730. lipA_on_mibi2314.blastn: 915
    1731. lipA_on_mibi2315.blastn: 915
    1732. lipA_on_mibi2316.blastn: 915
    1733. lipA_on_mibi2317.blastn: 915
    1734. lipA_on_mibi2318.blastn: 915
    1735. lipA_on_mibi2319.blastn: 915
    1736. lipA_on_mibi2320.blastn: 915
    1737. lipA_on_mibi2321.blastn: 915
    1738. lipA_on_mibi2379.blastn: 915
    1740. #grep "gene=sceD" mibi1435.gff3
    1741. #contig_11       Prodigal        CDS     25537   26196   .       -       0       ID=MMJCKL_08095;Name=putative transglycosylase SceD;locus_tag=MMJCKL_08095;product=putative transglycosylase SceD;Dbxref=EC:3.2.-.-,GO:0005576,GO:0008152,GO:0016798,RefSeq:WP_001829904.1,SO:0001217,UniParc:UPI000003B952,UniRef:UniRef100_Q5HMC6,UniRef:UniRef50_Q5HEA4,UniRef:UniRef90_Q5HMC6;gene=sceD
    1742. samtools faidx mibi1435.fna contig_11:25537-26196 > sceD_mibi1435.fasta
    1743. revcomp sceD_mibi1435.fasta > sceD_mibi1435_revcomp.fasta
    1744. cp sceD_mibi1435_revcomp.fasta ../presence_absence_matrix_on_gene_list/
    1745. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1746. blastn -db ../shovill/${sample}/contigs.fa -query sceD_mibi1435_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./sceD_on_${sample}.blastn
    1747. done
    1748. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1749. python3 analyze_blastn_res.py sceD_on_${sample}.blastn
    1750. done
    1751. sceD_on_mibi1435.blastn: 660
    1752. sceD_on_mibi1436.blastn: 660
    1753. sceD_on_mibi1437.blastn: 660
    1754. sceD_on_mibi1438.blastn: 660
    1755. sceD_on_mibi1439.blastn: 660
    1756. sceD_on_mibi1440.blastn: 660
    1757. sceD_on_mibi1441.blastn: 660
    1758. sceD_on_mibi1442.blastn: 660
    1759. sceD_on_mibi1443.blastn: 660
    1760. sceD_on_mibi1444.blastn: 660
    1761. sceD_on_mibi1445.blastn: 660
    1762. sceD_on_mibi1446.blastn: 660
    1763. sceD_on_mibi1447.blastn: 660
    1764. sceD_on_mibi1448.blastn: 660
    1765. sceD_on_mibi1449.blastn: 660
    1766. sceD_on_mibi1450.blastn: 660
    1767. sceD_on_mibi1451.blastn: 660
    1768. sceD_on_mibi1452.blastn: 660
    1769. sceD_on_mibi1453.blastn: 660
    1770. sceD_on_mibi1454.blastn: 660
    1771. sceD_on_mibi1455.blastn: 660
    1772. sceD_on_mibi1456.blastn: 660
    1773. sceD_on_mibi1457.blastn: 660
    1774. sceD_on_mibi1458.blastn: 660
    1775. sceD_on_mibi1459.blastn: 660
    1776. sceD_on_mibi1460.blastn: 660
    1777. sceD_on_mibi1461.blastn: 660
    1778. sceD_on_mibi1462.blastn: 660
    1779. sceD_on_mibi1463.blastn: 660
    1780. sceD_on_mibi1464.blastn: 660
    1781. sceD_on_mibi1465.blastn: 660
    1782. sceD_on_mibi1466.blastn: 660
    1783. sceD_on_mibi1467.blastn: 660
    1784. sceD_on_mibi1468.blastn: 660
    1785. sceD_on_mibi1469.blastn: 660
    1786. sceD_on_mibi1471.blastn: 660
    1787. sceD_on_mibi1473.blastn: 660
    1788. sceD_on_mibi1474.blastn: 660
    1789. sceD_on_mibi1475.blastn: 660
    1790. sceD_on_mibi1476.blastn: 660
    1791. sceD_on_mibi1477.blastn: 660
    1792. sceD_on_mibi1478.blastn: 660
    1793. sceD_on_mibi1479.blastn: 660
    1794. sceD_on_mibi1480.blastn: 660
    1795. sceD_on_mibi1481.blastn: 660
    1796. sceD_on_mibi1482.blastn: 660
    1797. sceD_on_mibi1483.blastn: 660
    1798. sceD_on_mibi1484.blastn: 660
    1799. sceD_on_mibi1485.blastn: 660
    1800. sceD_on_mibi1486.blastn: 660
    1801. sceD_on_mibi1487.blastn: 660
    1802. sceD_on_mibi1488.blastn: 660
    1803. sceD_on_mibi1489.blastn: 660
    1804. sceD_on_mibi1490.blastn: 660
    1805. sceD_on_mibi1491.blastn: 660
    1806. sceD_on_mibi1492.blastn: 660
    1807. sceD_on_mibi1493.blastn: 660
    1808. sceD_on_mibi1494.blastn: 660
    1809. sceD_on_mibi1495.blastn: 660
    1810. sceD_on_mibi1496.blastn: 660
    1811. sceD_on_mibi1497.blastn: 660
    1812. sceD_on_mibi1498.blastn: 660
    1813. sceD_on_mibi1499.blastn: 660
    1814. sceD_on_mibi1500.blastn: 660
    1815. sceD_on_mibi1501.blastn: 660
    1816. sceD_on_mibi1502.blastn: 660
    1817. sceD_on_mibi1503.blastn: 660
    1818. sceD_on_mibi1504.blastn: 660
    1819. sceD_on_mibi1505.blastn: 660
    1820. sceD_on_mibi1506.blastn: 660
    1821. sceD_on_mibi2312.blastn: 660
    1822. sceD_on_mibi2313.blastn: 660
    1823. sceD_on_mibi2314.blastn: 660
    1824. sceD_on_mibi2315.blastn: 660
    1825. sceD_on_mibi2316.blastn: 660
    1826. sceD_on_mibi2317.blastn: 660
    1827. sceD_on_mibi2318.blastn: 660
    1828. sceD_on_mibi2319.blastn: 660
    1829. sceD_on_mibi2320.blastn: 660
    1830. sceD_on_mibi2321.blastn: 660
    1831. sceD_on_mibi2379.blastn: 660
    1833. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1834. blastn -db ../shovill/${sample}/contigs.fa -query esp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./esp_on_${sample}.blastn
    1835. done
    1836. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1837. python3 analyze_blastn_res.py esp_on_${sample}.blastn
    1838. done
    1839. esp_on_mibi1435.blastn: 0
    1840. esp_on_mibi1436.blastn: 0
    1841. esp_on_mibi1437.blastn: 0
    1842. esp_on_mibi1438.blastn: 0
    1843. esp_on_mibi1439.blastn: 0
    1844. esp_on_mibi1440.blastn: 0
    1845. esp_on_mibi1441.blastn: 0
    1846. esp_on_mibi1442.blastn: 0
    1847. esp_on_mibi1443.blastn: 0
    1848. esp_on_mibi1444.blastn: 0
    1849. esp_on_mibi1445.blastn: 0
    1850. esp_on_mibi1446.blastn: 0
    1851. esp_on_mibi1447.blastn: 0
    1852. esp_on_mibi1448.blastn: 0
    1853. esp_on_mibi1449.blastn: 0
    1854. esp_on_mibi1450.blastn: 0
    1855. esp_on_mibi1451.blastn: 0
    1856. esp_on_mibi1452.blastn: 0
    1857. esp_on_mibi1453.blastn: 0
    1858. esp_on_mibi1454.blastn: 0
    1859. esp_on_mibi1455.blastn: 0
    1860. esp_on_mibi1456.blastn: 0
    1861. esp_on_mibi1457.blastn: 0
    1862. esp_on_mibi1458.blastn: 0
    1863. esp_on_mibi1459.blastn: 0
    1864. esp_on_mibi1460.blastn: 0
    1865. esp_on_mibi1461.blastn: 0
    1866. esp_on_mibi1462.blastn: 0
    1867. esp_on_mibi1463.blastn: 0
    1868. esp_on_mibi1464.blastn: 0
    1869. esp_on_mibi1465.blastn: 0
    1870. esp_on_mibi1466.blastn: 0
    1871. esp_on_mibi1467.blastn: 0
    1872. esp_on_mibi1468.blastn: 0
    1873. esp_on_mibi1469.blastn: 0
    1874. esp_on_mibi1471.blastn: 0
    1875. esp_on_mibi1473.blastn: 0
    1876. esp_on_mibi1474.blastn: 0
    1877. esp_on_mibi1475.blastn: 0
    1878. esp_on_mibi1476.blastn: 0
    1879. esp_on_mibi1477.blastn: 0
    1880. esp_on_mibi1478.blastn: 0
    1881. esp_on_mibi1479.blastn: 0
    1882. esp_on_mibi1480.blastn: 0
    1883. esp_on_mibi1481.blastn: 0
    1884. esp_on_mibi1482.blastn: 0
    1885. esp_on_mibi1483.blastn: 0
    1886. esp_on_mibi1484.blastn: 0
    1887. esp_on_mibi1485.blastn: 0
    1888. esp_on_mibi1486.blastn: 0
    1889. esp_on_mibi1487.blastn: 0
    1890. esp_on_mibi1488.blastn: 0
    1891. esp_on_mibi1489.blastn: 0
    1892. esp_on_mibi1490.blastn: 0
    1893. esp_on_mibi1491.blastn: 0
    1894. esp_on_mibi1492.blastn: 0
    1895. esp_on_mibi1493.blastn: 0
    1896. esp_on_mibi1494.blastn: 0
    1897. esp_on_mibi1495.blastn: 0
    1898. esp_on_mibi1496.blastn: 0
    1899. esp_on_mibi1497.blastn: 0
    1900. esp_on_mibi1498.blastn: 0
    1901. esp_on_mibi1499.blastn: 0
    1902. esp_on_mibi1500.blastn: 0
    1903. esp_on_mibi1501.blastn: 0
    1904. esp_on_mibi1502.blastn: 0
    1905. esp_on_mibi1503.blastn: 0
    1906. esp_on_mibi1504.blastn: 0
    1907. esp_on_mibi1505.blastn: 0
    1908. esp_on_mibi1506.blastn: 0
    1909. esp_on_mibi2312.blastn: 0
    1910. esp_on_mibi2313.blastn: 0
    1911. esp_on_mibi2314.blastn: 0
    1912. esp_on_mibi2315.blastn: 0
    1913. esp_on_mibi2316.blastn: 0
    1914. esp_on_mibi2317.blastn: 0
    1915. esp_on_mibi2318.blastn: 0
    1916. esp_on_mibi2319.blastn: 0
    1917. esp_on_mibi2320.blastn: 0
    1918. esp_on_mibi2321.blastn: 0
    1919. esp_on_mibi2379.blastn: 0
    1921. #grep "gene=ecpA" mibi1435.gff3
    1922. #contig_9        Prodigal        CDS     6382    7569    .       -       0       ID=MMJCKL_07070;Name=Extracellular cysteine protease;locus_tag=MMJCKL_07070;product=Extracellular cysteine protease;Dbxref=EC:3.4.22.-,GO:0005576,GO:0006508,GO:0008234,KEGG:K08258,RefSeq:WP_002497714.1,SO:0001217,UniParc:UPI00026C1A6F,UniRef:UniRef100_UPI00026C1A6F,UniRef:UniRef50_P81297,UniRef:UniRef90_Q5HKF6;gene=ecpA
    1923. samtools faidx mibi1435.fna contig_9:6382-7569 > ecpA_mibi1435.fasta
    1924. revcomp ecpA_mibi1435.fasta > ecpA_mibi1435_revcomp.fasta
    1925. cp ecpA_mibi1435_revcomp.fasta ../presence_absence_matrix_on_gene_list/
    1926. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1927. blastn -db ../shovill/${sample}/contigs.fa -query ecpA_mibi1435_revcomp.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./ecpA_on_${sample}.blastn
    1928. done
    1929. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    1930. python3 analyze_blastn_res.py ecpA_on_${sample}.blastn
    1931. done
    1932. ecpA_on_mibi1435.blastn: 1188
    1933. ecpA_on_mibi1436.blastn: 1188
    1934. ecpA_on_mibi1437.blastn: 1188
    1935. ecpA_on_mibi1438.blastn: 1188
    1936. ecpA_on_mibi1439.blastn: 1188
    1937. ecpA_on_mibi1440.blastn: 1188
    1938. ecpA_on_mibi1441.blastn: 1188
    1939. ecpA_on_mibi1442.blastn: 1188
    1940. ecpA_on_mibi1443.blastn: 1188
    1941. ecpA_on_mibi1444.blastn: 1188
    1942. ecpA_on_mibi1445.blastn: 1188
    1943. ecpA_on_mibi1446.blastn: 1188
    1944. ecpA_on_mibi1447.blastn: 1188
    1945. ecpA_on_mibi1448.blastn: 1188
    1946. ecpA_on_mibi1449.blastn: 1188
    1947. ecpA_on_mibi1450.blastn: 1188
    1948. ecpA_on_mibi1451.blastn: 1188
    1949. ecpA_on_mibi1452.blastn: 1188
    1950. ecpA_on_mibi1453.blastn: 1188
    1951. ecpA_on_mibi1454.blastn: 1188
    1952. ecpA_on_mibi1455.blastn: 1188
    1953. ecpA_on_mibi1456.blastn: 1188
    1954. ecpA_on_mibi1457.blastn: 1188
    1955. ecpA_on_mibi1458.blastn: 1188
    1956. ecpA_on_mibi1459.blastn: 1188
    1957. ecpA_on_mibi1460.blastn: 1188
    1958. ecpA_on_mibi1461.blastn: 1188
    1959. ecpA_on_mibi1462.blastn: 1188
    1960. ecpA_on_mibi1463.blastn: 1188
    1961. ecpA_on_mibi1464.blastn: 1188
    1962. ecpA_on_mibi1465.blastn: 1188
    1963. ecpA_on_mibi1466.blastn: 1188
    1964. ecpA_on_mibi1467.blastn: 1188
    1965. ecpA_on_mibi1468.blastn: 1188
    1966. ecpA_on_mibi1469.blastn: 1188
    1967. ecpA_on_mibi1471.blastn: 1188
    1968. ecpA_on_mibi1473.blastn: 1188
    1969. ecpA_on_mibi1474.blastn: 1188
    1970. ecpA_on_mibi1475.blastn: 1188
    1971. ecpA_on_mibi1476.blastn: 1188
    1972. ecpA_on_mibi1477.blastn: 1188
    1973. ecpA_on_mibi1478.blastn: 1188
    1974. ecpA_on_mibi1479.blastn: 1188
    1975. ecpA_on_mibi1480.blastn: 1188
    1976. ecpA_on_mibi1481.blastn: 1188
    1977. ecpA_on_mibi1482.blastn: 1188
    1978. ecpA_on_mibi1483.blastn: 1188
    1979. ecpA_on_mibi1484.blastn: 1188
    1980. ecpA_on_mibi1485.blastn: 1188
    1981. ecpA_on_mibi1486.blastn: 1188
    1982. ecpA_on_mibi1487.blastn: 1188
    1983. ecpA_on_mibi1488.blastn: 1188
    1984. ecpA_on_mibi1489.blastn: 1188
    1985. ecpA_on_mibi1490.blastn: 1188
    1986. ecpA_on_mibi1491.blastn: 1188
    1987. ecpA_on_mibi1492.blastn: 1188
    1988. ecpA_on_mibi1493.blastn: 1188
    1989. ecpA_on_mibi1494.blastn: 1188
    1990. ecpA_on_mibi1495.blastn: 1188
    1991. ecpA_on_mibi1496.blastn: 1188
    1992. ecpA_on_mibi1497.blastn: 1188
    1993. ecpA_on_mibi1498.blastn: 1188
    1994. ecpA_on_mibi1499.blastn: 1188
    1995. ecpA_on_mibi1500.blastn: 1188
    1996. ecpA_on_mibi1501.blastn: 1188
    1997. ecpA_on_mibi1502.blastn: 1188
    1998. ecpA_on_mibi1503.blastn: 1188
    1999. ecpA_on_mibi1504.blastn: 1188
    2000. ecpA_on_mibi1505.blastn: 1188
    2001. ecpA_on_mibi1506.blastn: 1188
    2002. ecpA_on_mibi2312.blastn: 1188
    2003. ecpA_on_mibi2313.blastn: 1188
    2004. ecpA_on_mibi2314.blastn: 1188
    2005. ecpA_on_mibi2315.blastn: 1188
    2006. ecpA_on_mibi2316.blastn: 1188
    2007. ecpA_on_mibi2317.blastn: 1188
    2008. ecpA_on_mibi2318.blastn: 1188
    2009. ecpA_on_mibi2319.blastn: 1188
    2010. ecpA_on_mibi2320.blastn: 1188
    2011. ecpA_on_mibi2321.blastn: 1188
    2012. ecpA_on_mibi2379.blastn: 1188
    2014. # -length(SE0760)=798
    2015. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2016. blastn -db ../shovill/${sample}/contigs.fa -query SE0760.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_${sample}.blastn
    2017. done
    2018. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2019. python3 analyze_blastn_res.py SE0760_on_${sample}.blastn
    2020. done
    2021. SE0760_on_mibi1435.blastn: 798
    2022. SE0760_on_mibi1436.blastn: 798
    2023. SE0760_on_mibi1437.blastn: 798
    2024. SE0760_on_mibi1438.blastn: 798
    2025. SE0760_on_mibi1439.blastn: 798
    2026. SE0760_on_mibi1440.blastn: 798
    2027. SE0760_on_mibi1441.blastn: 798
    2028. SE0760_on_mibi1442.blastn: 798
    2029. SE0760_on_mibi1443.blastn: 798
    2030. SE0760_on_mibi1444.blastn: 798
    2031. SE0760_on_mibi1445.blastn: 798
    2032. SE0760_on_mibi1446.blastn: 798
    2033. SE0760_on_mibi1447.blastn: 798
    2034. SE0760_on_mibi1448.blastn: 798
    2035. SE0760_on_mibi1449.blastn: 798
    2036. SE0760_on_mibi1450.blastn: 798
    2037. SE0760_on_mibi1451.blastn: 798
    2038. SE0760_on_mibi1452.blastn: 798
    2039. SE0760_on_mibi1453.blastn: 798
    2040. SE0760_on_mibi1454.blastn: 798
    2041. SE0760_on_mibi1455.blastn: 798
    2042. SE0760_on_mibi1456.blastn: 798
    2043. SE0760_on_mibi1457.blastn: 798
    2044. SE0760_on_mibi1458.blastn: 798
    2045. SE0760_on_mibi1459.blastn: 798
    2046. SE0760_on_mibi1460.blastn: 798
    2047. SE0760_on_mibi1461.blastn: 798
    2048. SE0760_on_mibi1462.blastn: 798
    2049. SE0760_on_mibi1463.blastn: 798
    2050. SE0760_on_mibi1464.blastn: 798
    2051. SE0760_on_mibi1465.blastn: 798
    2052. SE0760_on_mibi1466.blastn: 798
    2053. SE0760_on_mibi1467.blastn: 799
    2054. SE0760_on_mibi1468.blastn: 798
    2055. SE0760_on_mibi1469.blastn: 798
    2056. SE0760_on_mibi1471.blastn: 798
    2057. SE0760_on_mibi1473.blastn: 798
    2058. SE0760_on_mibi1474.blastn: 798
    2059. SE0760_on_mibi1475.blastn: 798
    2060. SE0760_on_mibi1476.blastn: 798
    2061. SE0760_on_mibi1477.blastn: 798
    2062. SE0760_on_mibi1478.blastn: 798
    2063. SE0760_on_mibi1479.blastn: 798
    2064. SE0760_on_mibi1480.blastn: 798
    2065. SE0760_on_mibi1481.blastn: 798
    2066. SE0760_on_mibi1482.blastn: 798
    2067. SE0760_on_mibi1483.blastn: 798
    2068. SE0760_on_mibi1484.blastn: 798
    2069. SE0760_on_mibi1485.blastn: 798
    2070. SE0760_on_mibi1486.blastn: 798
    2071. SE0760_on_mibi1487.blastn: 798
    2072. SE0760_on_mibi1488.blastn: 798
    2073. SE0760_on_mibi1489.blastn: 798
    2074. SE0760_on_mibi1490.blastn: 798
    2075. SE0760_on_mibi1491.blastn: 798
    2076. SE0760_on_mibi1492.blastn: 798
    2077. SE0760_on_mibi1493.blastn: 798
    2078. SE0760_on_mibi1494.blastn: 798
    2079. SE0760_on_mibi1495.blastn: 798
    2080. SE0760_on_mibi1496.blastn: 798
    2081. SE0760_on_mibi1497.blastn: 798
    2082. SE0760_on_mibi1498.blastn: 798
    2083. SE0760_on_mibi1499.blastn: 798
    2084. SE0760_on_mibi1500.blastn: 798
    2085. SE0760_on_mibi1501.blastn: 798
    2086. SE0760_on_mibi1502.blastn: 798
    2087. SE0760_on_mibi1503.blastn: 798
    2088. SE0760_on_mibi1504.blastn: 798
    2089. SE0760_on_mibi1505.blastn: 798
    2090. SE0760_on_mibi1506.blastn: 798
    2091. SE0760_on_mibi2312.blastn: 798
    2092. SE0760_on_mibi2313.blastn: 798
    2093. SE0760_on_mibi2314.blastn: 798
    2094. SE0760_on_mibi2315.blastn: 798
    2095. SE0760_on_mibi2316.blastn: 798
    2096. SE0760_on_mibi2317.blastn: 798
    2097. SE0760_on_mibi2318.blastn: 798
    2098. SE0760_on_mibi2319.blastn: 798
    2099. SE0760_on_mibi2320.blastn: 798
    2100. SE0760_on_mibi2321.blastn: 798
    2101. SE0760_on_mibi2379.blastn: 798
    2103. # -lenth(MT880870)=34053
    2104. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2105. blastn -db ../shovill/${sample}/contigs.fa -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./MT880870_on_${sample}.blastn
    2106. done
    2107. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2108. python3 analyze_blastn_res.py MT880870_on_${sample}.blastn
    2109. done
    2111. MT880870_on_mibi1435.blastn: 2366
    2112. MT880870_on_mibi1436.blastn: 3198
    2113. MT880870_on_mibi1437.blastn: 3198
    2114. MT880870_on_mibi1438.blastn: 2366
    2115. MT880870_on_mibi1439.blastn: 3198
    2116. MT880870_on_mibi1440.blastn: 34177
    2117. MT880870_on_mibi1441.blastn: 2372
    2118. MT880870_on_mibi1442.blastn: 3470
    2119. MT880870_on_mibi1443.blastn: 2366
    2120. MT880870_on_mibi1444.blastn: 2372
    2121. MT880870_on_mibi1445.blastn: 3198
    2122. MT880870_on_mibi1446.blastn: 3198
    2123. MT880870_on_mibi1447.blastn: 3198
    2124. MT880870_on_mibi1448.blastn: 3198
    2125. MT880870_on_mibi1449.blastn: 2366
    2126. MT880870_on_mibi1450.blastn: 3198
    2127. MT880870_on_mibi1451.blastn: 1085
    2128. MT880870_on_mibi1452.blastn: 1832
    2129. MT880870_on_mibi1453.blastn: 2366
    2130. MT880870_on_mibi1454.blastn: 34177
    2131. MT880870_on_mibi1455.blastn: 3198
    2132. MT880870_on_mibi1456.blastn: 34177
    2133. MT880870_on_mibi1457.blastn: 3198
    2134. MT880870_on_mibi1458.blastn: 835
    2135. MT880870_on_mibi1459.blastn: 34177
    2136. MT880870_on_mibi1460.blastn: 3198
    2137. MT880870_on_mibi1461.blastn: 34177
    2138. MT880870_on_mibi1462.blastn: 2372
    2139. MT880870_on_mibi1463.blastn: 2372
    2140. MT880870_on_mibi1464.blastn: 2311
    2141. MT880870_on_mibi1465.blastn: 3198
    2142. MT880870_on_mibi1466.blastn: 1264
    2143. MT880870_on_mibi1467.blastn: 3470
    2144. MT880870_on_mibi1468.blastn: 2372
    2145. MT880870_on_mibi1469.blastn: 2372
    2146. MT880870_on_mibi1471.blastn: 2366
    2147. MT880870_on_mibi1473.blastn: 3198
    2148. MT880870_on_mibi1474.blastn: 3198
    2149. MT880870_on_mibi1475.blastn: 3198
    2150. MT880870_on_mibi1476.blastn: 3198
    2151. MT880870_on_mibi1477.blastn: 2372
    2152. MT880870_on_mibi1478.blastn: 5918
    2153. MT880870_on_mibi1479.blastn: 3198
    2154. MT880870_on_mibi1480.blastn: 34177
    2155. MT880870_on_mibi1481.blastn: 3198
    2156. MT880870_on_mibi1482.blastn: 3198
    2157. MT880870_on_mibi1483.blastn: 3198
    2158. MT880870_on_mibi1484.blastn: 3198
    2159. MT880870_on_mibi1485.blastn: 20038
    2160. MT880870_on_mibi1486.blastn: 3198
    2161. MT880870_on_mibi1487.blastn: 28520
    2162. MT880870_on_mibi1488.blastn: 2366
    2163. MT880870_on_mibi1489.blastn: 2366
    2164. MT880870_on_mibi1490.blastn: 3198
    2165. MT880870_on_mibi1491.blastn: 3198
    2166. MT880870_on_mibi1492.blastn: 3198
    2167. MT880870_on_mibi1493.blastn: 2233
    2168. MT880870_on_mibi1494.blastn: 3198
    2169. MT880870_on_mibi1495.blastn: 3198
    2170. MT880870_on_mibi1496.blastn: 25135
    2171. MT880870_on_mibi1497.blastn: 3198
    2172. MT880870_on_mibi1498.blastn: 28012
    2173. MT880870_on_mibi1499.blastn: 3198
    2174. MT880870_on_mibi1500.blastn: 2366
    2175. MT880870_on_mibi1501.blastn: 2366
    2176. MT880870_on_mibi1502.blastn: 34177
    2177. MT880870_on_mibi1503.blastn: 2366
    2178. MT880870_on_mibi1504.blastn: 3198
    2179. MT880870_on_mibi1505.blastn: 3198
    2180. MT880870_on_mibi1506.blastn: 2372
    2181. MT880870_on_mibi2312.blastn: 3198
    2182. MT880870_on_mibi2313.blastn: 3198
    2183. MT880870_on_mibi2314.blastn: 3198
    2184. MT880870_on_mibi2315.blastn: 2366
    2185. MT880870_on_mibi2316.blastn: 3198
    2186. MT880870_on_mibi2317.blastn: 3198
    2187. MT880870_on_mibi2318.blastn: 20006
    2188. MT880870_on_mibi2319.blastn: 17544
    2189. MT880870_on_mibi2320.blastn: 3198
    2190. MT880870_on_mibi2321.blastn: 3198
    2191. MT880870_on_mibi2379.blastn: 3198
    2193. #len=36164
    2194. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2195. blastn -db ../shovill/${sample}/contigs.fa -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./MT880871_on_${sample}.blastn
    2196. done
    2197. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2198. python3 analyze_blastn_res.py MT880871_on_${sample}.blastn
    2199. done
    2200. MT880871_on_mibi1435.blastn: 270
    2201. MT880871_on_mibi1436.blastn: 35580
    2202. MT880871_on_mibi1437.blastn: 518
    2203. MT880871_on_mibi1438.blastn: 518
    2204. MT880871_on_mibi1439.blastn: 518
    2205. MT880871_on_mibi1440.blastn: 36682
    2206. MT880871_on_mibi1441.blastn: 519
    2207. MT880871_on_mibi1442.blastn: 514
    2208. MT880871_on_mibi1443.blastn: 0
    2209. MT880871_on_mibi1444.blastn: 0
    2210. MT880871_on_mibi1445.blastn: 518
    2211. MT880871_on_mibi1446.blastn: 518
    2212. MT880871_on_mibi1447.blastn: 518
    2213. MT880871_on_mibi1448.blastn: 518
    2214. MT880871_on_mibi1449.blastn: 518
    2215. MT880871_on_mibi1450.blastn: 518
    2216. MT880871_on_mibi1451.blastn: 0
    2217. MT880871_on_mibi1452.blastn: 30418
    2218. MT880871_on_mibi1453.blastn: 518
    2219. MT880871_on_mibi1454.blastn: 982
    2220. MT880871_on_mibi1455.blastn: 518
    2221. MT880871_on_mibi1456.blastn: 982
    2222. MT880871_on_mibi1457.blastn: 518
    2223. MT880871_on_mibi1458.blastn: 0
    2224. MT880871_on_mibi1459.blastn: 34965
    2225. MT880871_on_mibi1460.blastn: 518
    2226. MT880871_on_mibi1461.blastn: 16296
    2227. MT880871_on_mibi1462.blastn: 0
    2228. MT880871_on_mibi1463.blastn: 518
    2229. MT880871_on_mibi1464.blastn: 947
    2230. MT880871_on_mibi1465.blastn: 518
    2231. MT880871_on_mibi1466.blastn: 0
    2232. MT880871_on_mibi1467.blastn: 514
    2233. MT880871_on_mibi1468.blastn: 518
    2234. MT880871_on_mibi1469.blastn: 518
    2235. MT880871_on_mibi1471.blastn: 518
    2236. MT880871_on_mibi1473.blastn: 518
    2237. MT880871_on_mibi1474.blastn: 518
    2238. MT880871_on_mibi1475.blastn: 518
    2239. MT880871_on_mibi1476.blastn: 518
    2240. MT880871_on_mibi1477.blastn: 518
    2241. MT880871_on_mibi1478.blastn: 18607
    2242. MT880871_on_mibi1479.blastn: 518
    2243. MT880871_on_mibi1480.blastn: 36682
    2244. MT880871_on_mibi1481.blastn: 0
    2245. MT880871_on_mibi1482.blastn: 518
    2246. MT880871_on_mibi1483.blastn: 32395
    2247. MT880871_on_mibi1484.blastn: 0
    2248. MT880871_on_mibi1485.blastn: 36164
    2249. MT880871_on_mibi1486.blastn: 31072
    2250. MT880871_on_mibi1487.blastn: 36682
    2251. MT880871_on_mibi1488.blastn: 0
    2252. MT880871_on_mibi1489.blastn: 0
    2253. MT880871_on_mibi1490.blastn: 518
    2254. MT880871_on_mibi1491.blastn: 518
    2255. MT880871_on_mibi1492.blastn: 518
    2256. MT880871_on_mibi1493.blastn: 740
    2257. MT880871_on_mibi1494.blastn: 518
    2258. MT880871_on_mibi1495.blastn: 0
    2259. MT880871_on_mibi1496.blastn: 24187
    2260. MT880871_on_mibi1497.blastn: 31069
    2261. MT880871_on_mibi1498.blastn: 36682
    2262. MT880871_on_mibi1499.blastn: 518
    2263. MT880871_on_mibi1500.blastn: 0
    2264. MT880871_on_mibi1501.blastn: 0
    2265. MT880871_on_mibi1502.blastn: 36682
    2266. MT880871_on_mibi1503.blastn: 518
    2267. MT880871_on_mibi1504.blastn: 518
    2268. MT880871_on_mibi1505.blastn: 518
    2269. MT880871_on_mibi1506.blastn: 0
    2270. MT880871_on_mibi2312.blastn: 316
    2271. MT880871_on_mibi2313.blastn: 518
    2272. MT880871_on_mibi2314.blastn: 518
    2273. MT880871_on_mibi2315.blastn: 0
    2274. MT880871_on_mibi2316.blastn: 518
    2275. MT880871_on_mibi2317.blastn: 518
    2276. MT880871_on_mibi2318.blastn: 36682
    2277. MT880871_on_mibi2319.blastn: 36164
    2278. MT880871_on_mibi2320.blastn: 518
    2279. MT880871_on_mibi2321.blastn: 518
    2280. MT880871_on_mibi2379.blastn: 518
    2282. #len=147057
    2283. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2284. blastn -db ../shovill/${sample}/contigs.fa -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_${sample}.blastn
    2285. done
    2286. for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
    2287. python3 analyze_blastn_res.py MT880872_on_${sample}.blastn
    2288. done
    2289. MT880872_on_mibi1435.blastn: 19155
    2290. MT880872_on_mibi1436.blastn: 19049
    2291. MT880872_on_mibi1437.blastn: 19049
    2292. MT880872_on_mibi1438.blastn: 19045
    2293. MT880872_on_mibi1439.blastn: 19042
    2294. MT880872_on_mibi1440.blastn: 77536 *
    2295. MT880872_on_mibi1441.blastn: 19041
    2296. MT880872_on_mibi1442.blastn: 19044
    2297. MT880872_on_mibi1443.blastn: 19049
    2298. MT880872_on_mibi1444.blastn: 19049
    2299. MT880872_on_mibi1445.blastn: 19042
    2300. MT880872_on_mibi1446.blastn: 19042
    2301. MT880872_on_mibi1447.blastn: 19042
    2302. MT880872_on_mibi1448.blastn: 19049
    2303. MT880872_on_mibi1449.blastn: 19041
    2304. MT880872_on_mibi1450.blastn: 19049
    2305. MT880872_on_mibi1451.blastn: 19043
    2306. MT880872_on_mibi1452.blastn: 19047
    2307. MT880872_on_mibi1453.blastn: 19165
    2308. MT880872_on_mibi1454.blastn: 52122 *
    2309. MT880872_on_mibi1455.blastn: 20996
    2310. MT880872_on_mibi1456.blastn: 52122 *
    2311. MT880872_on_mibi1457.blastn: 19042
    2312. MT880872_on_mibi1458.blastn: 19048
    2313. MT880872_on_mibi1459.blastn: 77366 *
    2314. MT880872_on_mibi1460.blastn: 19042
    2315. MT880872_on_mibi1461.blastn: 84536 *
    2316. MT880872_on_mibi1462.blastn: 19048
    2317. MT880872_on_mibi1463.blastn: 19042
    2318. MT880872_on_mibi1464.blastn: 19049
    2319. MT880872_on_mibi1465.blastn: 19045
    2320. MT880872_on_mibi1466.blastn: 6525
    2321. MT880872_on_mibi1467.blastn: 19044
    2322. MT880872_on_mibi1468.blastn: 19037
    2323. MT880872_on_mibi1469.blastn: 19039
    2324. MT880872_on_mibi1471.blastn: 19045
    2325. MT880872_on_mibi1473.blastn: 19043
    2326. MT880872_on_mibi1474.blastn: 19052
    2327. MT880872_on_mibi1475.blastn: 19264
    2328. MT880872_on_mibi1476.blastn: 19052
    2329. MT880872_on_mibi1477.blastn: 19041
    2330. MT880872_on_mibi1478.blastn: 26492 *
    2331. MT880872_on_mibi1479.blastn: 19042
    2332. MT880872_on_mibi1480.blastn: 45789 *
    2333. MT880872_on_mibi1481.blastn: 19036
    2334. MT880872_on_mibi1482.blastn: 19036
    2335. MT880872_on_mibi1483.blastn: 19036
    2336. MT880872_on_mibi1484.blastn: 19045
    2337. MT880872_on_mibi1485.blastn: 52124 *
    2338. MT880872_on_mibi1486.blastn: 19052
    2339. MT880872_on_mibi1487.blastn: 56847 *
    2340. MT880872_on_mibi1488.blastn: 19049
    2341. MT880872_on_mibi1489.blastn: 19053
    2342. MT880872_on_mibi1490.blastn: 19045
    2343. MT880872_on_mibi1491.blastn: 19042
    2344. MT880872_on_mibi1492.blastn: 19049
    2345. MT880872_on_mibi1493.blastn: 19046
    2346. MT880872_on_mibi1494.blastn: 19049
    2347. MT880872_on_mibi1495.blastn: 19046
    2348. MT880872_on_mibi1496.blastn: 92504 *
    2349. MT880872_on_mibi1497.blastn: 19052
    2350. MT880872_on_mibi1498.blastn: 58985 *
    2351. MT880872_on_mibi1499.blastn: 19043
    2352. MT880872_on_mibi1500.blastn: 19052
    2353. MT880872_on_mibi1501.blastn: 19049
    2354. MT880872_on_mibi1502.blastn: 46101 *
    2355. MT880872_on_mibi1503.blastn: 19044
    2356. MT880872_on_mibi1504.blastn: 19041
    2357. MT880872_on_mibi1505.blastn: 19052
    2358. MT880872_on_mibi1506.blastn: 19049
    2359. MT880872_on_mibi2312.blastn: 19045
    2360. MT880872_on_mibi2313.blastn: 19049
    2361. MT880872_on_mibi2314.blastn: 19052
    2362. MT880872_on_mibi2315.blastn: 19049
    2363. MT880872_on_mibi2316.blastn: 19052
    2364. MT880872_on_mibi2317.blastn: 19042
    2365. MT880872_on_mibi2318.blastn: 78246 *
    2366. MT880872_on_mibi2319.blastn: 77512 *
    2367. MT880872_on_mibi2320.blastn: 19045
    2368. MT880872_on_mibi2321.blastn: 19052
    2369. MT880872_on_mibi2379.blastn: 19156

  11. yycG has only 80% similarity, but it still belongs to the gene family.

    1. Based on the provided BLASTN result summary, determining whether it's the same gene depends on multiple factors, including sequence similarity, alignment length, and expected value (E-value).
    3. Let’s break down the results:
    5. Query ID: gi|49240382|emb|BX571856.1|:25617-27443
    6. Subject ID: contig00005
    7. Percentage Identity: 80.338%
    8. Alignment Length: 1836 (out of 1827 in the subject sequence)
    9. Mismatches: 349
    10. Gap Openings: 7
    11. E-value: 0.0 (this indicates a highly significant alignment)
    12. Bit Score: 1380
    14. Key Points to Consider:
    16. Percentage Identity (80.34%): While 80% identity is relatively high, it’s not close enough to the 90-100% typically expected for identical or highly similar genes. However, the threshold for considering sequences as "the same gene" depends on the organism, type of gene, and biological context. For some genes or species, this might still be acceptable.
    18. Alignment Length (1836 bp): The alignment covers a large portion of both sequences (1827 in the subject sequence and 1836 in the query). This is a good indication that the sequences are largely aligned.
    20. Mismatches and Gaps: There are 349 mismatches and 7 gap openings, which suggests there are differences between the two sequences. The number of differences is significant, and the biological impact of these differences would depend on whether they occur in coding regions or regulatory elements.
    22. E-value (0.0): The E-value of 0.0 indicates that the alignment is highly significant and not due to chance.
    24. Conclusion:
    26. Based on the 80.34% identity and the number of mismatches, it is unlikely that this is exactly the same gene, but it could still be a closely related gene variant, allele, or paralog. If you are looking for an exact match, this result would not qualify. However, if you are investigating gene families or variants, this sequence could be considered closely related. Further functional or experimental validation might be necessary to determine the biological significance of these differences.

  12. plotTreeHeatmap

    1. FastTree -gtr -nt variants/snippy.core_without_reference.aln > plotTreeHeatmap/snippy.core.tree
    3. library(ggtree)
    4. library(ggplot2)
    5. library(dplyr)
    6. setwd("/home/jhuang/DATA/Data_Luise_Sepi_STKN/plotTreeHeatmap/")
    7. # -- edit tree --
    8. info <- read.csv("typing.csv", sep="\t")
    9. info$name <- info$Isolate
    10. tree <- read.tree("990_backup.tree")
    11. #cols <- c(infection='purple2', commensalism='skyblue2')
    13. #heatmapData2 <- info %>% select(Isolate, ST, SCCmec, agr.typing)
    14. heatmapData2 <- info %>% select(Isolate, ST)
    15. rn <- heatmapData2$Isolate
    16. heatmapData2$Isolate <- NULL
    17. heatmapData2 <- as.data.frame(sapply(heatmapData2, as.character))
    18. rownames(heatmapData2) <- rn
    20. #https://bookdown.org/hneth/ds4psy/D-3-apx-colors-basics.html
    21. #"blueviolet","darkgoldenrod",  "tomato","mediumpurple4","indianred",
    22. #"lightcyan3","azure3",
    23. #"magenta",
    24. #"tan","brown",
    25. heatmap.colours <- c("cornflowerblue","darkgreen","seagreen3","tan","red",  "navyblue", "gold",     "green","orange","pink","purple","magenta","brown", "darksalmon","chocolate4","darkkhaki", "azure3", "maroon","lightgreen",     "blue","cyan", "skyblue2", "blueviolet","darkgrey")
    26.                         #"cornflowerblue","darkgreen","seagreen3","tan","red","green","orange","pink","brown","darkgrey",  #"cornflowerblue","darkgreen","red",     "darkgrey")
    27. names(heatmap.colours) <- c("2","5","7","9","14", "17","23",   "35","59","73", "81","86","87","89","130","190","290", "297","325",    "454","487","558","766","-")
    28. #"SCCmec_type_II(2A)","SCCmec_type_III(3A)","SCCmec_type_III(3A) and #SCCmec_type_VIII(4A)","SCCmec_type_IV(2B)","SCCmec_type_IV(2B&5)","SCCmec_type_IV(2B) and #SCCmec_type_VI(4B)","SCCmec_type_IVa(2B)","SCCmec_type_IVb(2B)","SCCmec_type_IVg(2B)","none",    "I","II","III", "none")
    30. #circular
    31. #scale_color_manual(values=cols) +
    32. #geom_tippoint(aes(color=Type)) +
    33. p <- ggtree(tree, layout='circular', branch.length='none') %<+% info +
    34. geom_tiplab2(aes(label=name), offset=1, size=6.0)
    35. #, geom='text', align=TRUE,  linetype=NA, hjust=1.8,check.overlap=TRUE
    36. #difference between geom_tiplab and geom_tiplab2?
    37. #+ theme(axis.text.x = element_text(angle = 30, vjust = 0.5)) + theme(axis.text = element_text(size = 20))  + scale_size(range = c(1, 20))
    38. #font.size=10,
    39. png("ggtree.png", width=1260, height=1260)
    40. #svg("ggtree.svg", width=1260, height=1260)
    41. p
    42. dev.off()
    43. png("ggtree_and_gheatmap.png", width=1290, height=1000)
    44. #svg("ggtree_and_gheatmap.svg", width=17, height=15)
    45. gheatmap(p, heatmapData2, width=0.1,colnames_position="top", colnames_angle=90, colnames_offset_y = 0.1, hjust=0.5, font.size=6, offset = 5) + scale_fill_manual(values=heatmap.colours) +  theme(legend.text = element_text(size = 14)) + theme(legend.title = element_text(size = 14)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))
    46. dev.off()

  13. Response

    1. I’ve reviewed the 85 genomes as discussed. Four samples were filtered out due to insufficient coverage: mibi2381, mibi2380, and mibi1472. Additionally, the sample mibi1470 was excluded as it could not be identified as S. epidermidis based on its MLST type.
    3. This leaves us with a total of 81 samples for downstream analysis.
    5. Attached, you’ll find:
    7. * The graphic ggtree_and_gheatmap.png
    8. * A table, presence_absence_matrix_on_genes, providing an overview of gene presence/absence and relevant typing information
    9. * FASTA files for all 81 genomes

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