Typing of 81 S. epidermidis samples (Luise)

1. prepare the bacto environment

   cd ~/DATA/Data_Luise_Sepi_STKN
   cp /home/jhuang/Tools/bacto/bacto-0.1.json .
   cp /home/jhuang/Tools/bacto/cluster.json .
   cp /home/jhuang/Tools/bacto/Snakefile .
   ln -s /home/jhuang/Tools/bacto/local .
   ln -s /home/jhuang/Tools/bacto/db .
   ln -s /home/jhuang/Tools/bacto/envs .
   

2. prepare raw_data

   mkdir raw_data; cd raw_data
   
   ln -s ../raw_data_batch2/mibi2312/Luise_1_S33_R1_001.fastq.gz mibi2312_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2312/Luise_1_S33_R2_001.fastq.gz mibi2312_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2379/Luise_2_S3_R1_001.fastq.gz  mibi2379_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2379/Luise_2_S3_R2_001.fastq.gz  mibi2379_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2313/Luise_3_S34_R1_001.fastq.gz mibi2313_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2313/Luise_3_S34_R2_001.fastq.gz mibi2313_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2380/Luise_4_S4_R1_001.fastq.gz  mibi2380_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2380/Luise_4_S4_R2_001.fastq.gz  mibi2380_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2314/Luise_5_S35_R1_001.fastq.gz mibi2314_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2314/Luise_5_S35_R2_001.fastq.gz mibi2314_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2315/Luise_6_S36_R1_001.fastq.gz mibi2315_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2315/Luise_6_S36_R2_001.fastq.gz mibi2315_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2381/Luise_7_S5_R1_001.fastq.gz  mibi2381_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2381/Luise_7_S5_R2_001.fastq.gz  mibi2381_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2316/Luise_8_S37_R1_001.fastq.gz mibi2316_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2316/Luise_8_S37_R2_001.fastq.gz mibi2316_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2317/Luise_9_S38_R1_001.fastq.gz mibi2317_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2317/Luise_9_S38_R2_001.fastq.gz mibi2317_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2318/Luise_10_S39_R1_001.fastq.gz mibi2318_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2318/Luise_10_S39_R2_001.fastq.gz mibi2318_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2319/Luise_11_S40_R1_001.fastq.gz mibi2319_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2319/Luise_11_S40_R2_001.fastq.gz mibi2319_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2320/Luise_12_S41_R1_001.fastq.gz mibi2320_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2320/Luise_12_S41_R2_001.fastq.gz mibi2320_R2.fastq.gz
   ln -s ../raw_data_batch2/mibi2321/Luise_13_S42_R1_001.fastq.gz mibi2321_R1.fastq.gz
   ln -s ../raw_data_batch2/mibi2321/Luise_13_S42_R2_001.fastq.gz mibi2321_R2.fastq.gz
   
   # raw_data_batch1: mibi1435 - mibi1506
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1435/S_epi_K_38_S1_R1_001.fastq.gz mibi1435_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1435/S_epi_K_38_S1_R2_001.fastq.gz mibi1435_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1436/S_epi_K_68_S2_R1_001.fastq.gz mibi1436_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1436/S_epi_K_68_S2_R2_001.fastq.gz mibi1436_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1437/S_epi_K_70_S3_R1_001.fastq.gz mibi1437_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1437/S_epi_K_70_S3_R2_001.fastq.gz mibi1437_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1438/S_epi_K_71_S4_R1_001.fastq.gz mibi1438_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1438/S_epi_K_71_S4_R2_001.fastq.gz mibi1438_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1439/S_epi_K_48_S5_R1_001.fastq.gz mibi1439_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1439/S_epi_K_48_S5_R2_001.fastq.gz mibi1439_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1440/S_epi_K_51_S6_R1_001.fastq.gz mibi1440_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1440/S_epi_K_51_S6_R2_001.fastq.gz mibi1440_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1441/S_epi_K_53_S7_R1_001.fastq.gz mibi1441_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1441/S_epi_K_53_S7_R2_001.fastq.gz mibi1441_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1442/S_epi_K_54_S8_R1_001.fastq.gz mibi1442_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1442/S_epi_K_54_S8_R2_001.fastq.gz mibi1442_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1443/S_epi_K_56_S9_R1_001.fastq.gz mibi1443_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1443/S_epi_K_56_S9_R2_001.fastq.gz mibi1443_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1444/S_epi_K_63_S10_R1_001.fastq.gz mibi1444_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1444/S_epi_K_63_S10_R2_001.fastq.gz mibi1444_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1445/S_epi_K_64_S11_R1_001.fastq.gz mibi1445_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1445/S_epi_K_64_S11_R2_001.fastq.gz mibi1445_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1446/S_epi_K_65_S12_R1_001.fastq.gz mibi1446_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1446/S_epi_K_65_S12_R2_001.fastq.gz mibi1446_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1447/S_epi_K_75_S13_R1_001.fastq.gz mibi1447_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1447/S_epi_K_75_S13_R2_001.fastq.gz mibi1447_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1448/S_epi_K_11_S14_R1_001.fastq.gz mibi1448_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1448/S_epi_K_11_S14_R2_001.fastq.gz mibi1448_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1449/S_epi_K_12_S15_R1_001.fastq.gz mibi1449_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1449/S_epi_K_12_S15_R2_001.fastq.gz mibi1449_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1450/S_epi_K_13_S16_R1_001.fastq.gz mibi1450_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1450/S_epi_K_13_S16_R2_001.fastq.gz mibi1450_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1451/S_epi_K_77_S17_R1_001.fastq.gz mibi1451_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1451/S_epi_K_77_S17_R2_001.fastq.gz mibi1451_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1452/S_epi_K_79_S18_R1_001.fastq.gz mibi1452_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1452/S_epi_K_79_S18_R2_001.fastq.gz mibi1452_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1453/S_epi_K_80_S19_R1_001.fastq.gz mibi1453_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1453/S_epi_K_80_S19_R2_001.fastq.gz mibi1453_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1454/S_epi_K_1_gross_S20_R1_001.fastq.gz mibi1454_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1454/S_epi_K_1_gross_S20_R2_001.fastq.gz mibi1454_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1455/S_epi_K_2_S21_R1_001.fastq.gz mibi1455_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1455/S_epi_K_2_S21_R2_001.fastq.gz mibi1455_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1456/S_epi_K_3_S22_R1_001.fastq.gz mibi1456_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1456/S_epi_K_3_S22_R2_001.fastq.gz mibi1456_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1457/S_epi_K_6_S23_R1_001.fastq.gz mibi1457_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1457/S_epi_K_6_S23_R2_001.fastq.gz mibi1457_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1458/S_epi_K_8_S24_R1_001.fastq.gz mibi1458_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1458/S_epi_K_8_S24_R2_001.fastq.gz mibi1458_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1459/S_epi_K_17_S25_R1_001.fastq.gz mibi1459_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1459/S_epi_K_17_S25_R2_001.fastq.gz mibi1459_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1460/S_epi_K_26_S26_R1_001.fastq.gz mibi1460_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1460/S_epi_K_26_S26_R2_001.fastq.gz mibi1460_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1461/S_epi_K_34_S27_R1_001.fastq.gz mibi1461_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1461/S_epi_K_34_S27_R2_001.fastq.gz mibi1461_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1462/S_epi_K_35_S28_R1_001.fastq.gz mibi1462_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1462/S_epi_K_35_S28_R2_001.fastq.gz mibi1462_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1463/S_epi_K_19_S29_R1_001.fastq.gz mibi1463_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1463/S_epi_K_19_S29_R2_001.fastq.gz mibi1463_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1464/S_epi_K_22_S30_R1_001.fastq.gz mibi1464_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1464/S_epi_K_22_S30_R2_001.fastq.gz mibi1464_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1465/S_epi_K_23_S31_R1_001.fastq.gz mibi1465_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1465/S_epi_K_23_S31_R2_001.fastq.gz mibi1465_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1466/S_epi_K_24_S32_R1_001.fastq.gz mibi1466_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1466/S_epi_K_24_S32_R2_001.fastq.gz mibi1466_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1467/S_epi_K_30_S33_R1_001.fastq.gz mibi1467_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1467/S_epi_K_30_S33_R2_001.fastq.gz mibi1467_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1468/S_epi_K_31_S34_R1_001.fastq.gz mibi1468_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1468/S_epi_K_31_S34_R2_001.fastq.gz mibi1468_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1469/S_epi_K_32_S35_R1_001.fastq.gz mibi1469_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1469/S_epi_K_32_S35_R2_001.fastq.gz mibi1469_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1470/S_epi_K_1_klein_S36_R1_001.fastq.gz mibi1470_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1470/S_epi_K_1_klein_S36_R2_001.fastq.gz mibi1470_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1471/S_epi_K_37_S37_R1_001.fastq.gz mibi1471_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1471/S_epi_K_37_S37_R2_001.fastq.gz mibi1471_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1472/S_epi_K_46_S38_R1_001.fastq.gz mibi1472_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1472/S_epi_K_46_S38_R2_001.fastq.gz mibi1472_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1473/S_epi_K_57_S39_R1_001.fastq.gz mibi1473_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1473/S_epi_K_57_S39_R2_001.fastq.gz mibi1473_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1474/S_epi_K_59_S40_R1_001.fastq.gz mibi1474_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1474/S_epi_K_59_S40_R2_001.fastq.gz mibi1474_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1475/S_epi_K_58_S41_R1_001.fastq.gz mibi1475_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1475/S_epi_K_58_S41_R2_001.fastq.gz mibi1475_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1476/S_epi_K_60_S42_R1_001.fastq.gz mibi1476_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1476/S_epi_K_60_S42_R2_001.fastq.gz mibi1476_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1477/S_epi_K_61_S43_R1_001.fastq.gz mibi1477_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1477/S_epi_K_61_S43_R2_001.fastq.gz mibi1477_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1478/S_epi_K_28_S44_R1_001.fastq.gz mibi1478_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1478/S_epi_K_28_S44_R2_001.fastq.gz mibi1478_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1479/S_epi_K_33_S45_R1_001.fastq.gz mibi1479_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1479/S_epi_K_33_S45_R2_001.fastq.gz mibi1479_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1480/S_epi_K_39_S46_R1_001.fastq.gz mibi1480_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1480/S_epi_K_39_S46_R2_001.fastq.gz mibi1480_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1481/S_epi_K_40_S47_R1_001.fastq.gz mibi1481_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1481/S_epi_K_40_S47_R2_001.fastq.gz mibi1481_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1482/S_epi_K_43_S48_R1_001.fastq.gz mibi1482_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1482/S_epi_K_43_S48_R2_001.fastq.gz mibi1482_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1483/S_epi_K_97_S49_R1_001.fastq.gz mibi1483_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1483/S_epi_K_97_S49_R2_001.fastq.gz mibi1483_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1484/S_epi_K_84_S50_R1_001.fastq.gz mibi1484_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1484/S_epi_K_84_S50_R2_001.fastq.gz mibi1484_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1485/S_epi_K_85_S51_R1_001.fastq.gz mibi1485_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1485/S_epi_K_85_S51_R2_001.fastq.gz mibi1485_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1486/S_epi_K_86_S52_R1_001.fastq.gz mibi1486_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1486/S_epi_K_86_S52_R2_001.fastq.gz mibi1486_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1487/S_epi_K_116_S53_R1_001.fastq.gz mibi1487_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1487/S_epi_K_116_S53_R2_001.fastq.gz mibi1487_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1488/S_epi_K_118_S54_R1_001.fastq.gz mibi1488_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1488/S_epi_K_118_S54_R2_001.fastq.gz mibi1488_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1489/S_epi_K_120_S55_R1_001.fastq.gz mibi1489_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1489/S_epi_K_120_S55_R2_001.fastq.gz mibi1489_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1490/S_epi_K_123_S56_R1_001.fastq.gz mibi1490_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1490/S_epi_K_123_S56_R2_001.fastq.gz mibi1490_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1491/S_epi_K_124_S57_R1_001.fastq.gz mibi1491_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1491/S_epi_K_124_S57_R2_001.fastq.gz mibi1491_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1492/S_epi_K_127_S58_R1_001.fastq.gz mibi1492_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1492/S_epi_K_127_S58_R2_001.fastq.gz mibi1492_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1493/S_epi_K_29_S59_R1_001.fastq.gz mibi1493_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1493/S_epi_K_29_S59_R2_001.fastq.gz mibi1493_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1494/S_epi_K_72_S60_R1_001.fastq.gz mibi1494_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1494/S_epi_K_72_S60_R2_001.fastq.gz mibi1494_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1495/S_epi_K_89_S61_R1_001.fastq.gz mibi1495_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1495/S_epi_K_89_S61_R2_001.fastq.gz mibi1495_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1496/S_epi_K_110_S62_R1_001.fastq.gz mibi1496_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1496/S_epi_K_110_S62_R2_001.fastq.gz mibi1496_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1497/S_epi_K_112_S63_R1_001.fastq.gz mibi1497_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1497/S_epi_K_112_S63_R2_001.fastq.gz mibi1497_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1498/S_epi_K_114_S64_R1_001.fastq.gz mibi1498_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1498/S_epi_K_114_S64_R2_001.fastq.gz mibi1498_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1499/S_epi_K_91_S65_R1_001.fastq.gz mibi1499_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1499/S_epi_K_91_S65_R2_001.fastq.gz mibi1499_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1500/S_epi_K_92_S66_R1_001.fastq.gz mibi1500_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1500/S_epi_K_92_S66_R2_001.fastq.gz mibi1500_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1501/S_epi_K_95_S67_R1_001.fastq.gz mibi1501_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1501/S_epi_K_95_S67_R2_001.fastq.gz mibi1501_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1502/S_epi_K_96_S68_R1_001.fastq.gz mibi1502_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1502/S_epi_K_96_S68_R2_001.fastq.gz mibi1502_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1503/S_epi_K_98_S69_R1_001.fastq.gz mibi1503_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1503/S_epi_K_98_S69_R2_001.fastq.gz mibi1503_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1504/S_epi_K_100_S70_R1_001.fastq.gz mibi1504_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1504/S_epi_K_100_S70_R2_001.fastq.gz mibi1504_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1505/S_epi_K_106_S71_R1_001.fastq.gz mibi1505_R1.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1505/S_epi_K_106_S71_R2_001.fastq.gz mibi1505_R2.fastq.gz
   ln -s ../200615_NB501882_0207_AH5YFGAFX2/mibi1506/S_epi_K_108_S72_R1_001.fastq.gz mibi1506_R1.fastq.gz
   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)

   (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

   find . -name "contigs.fa" -exec sh -c 'echo -n "{}: "; wc -c < "{}"; echo " contigs: $(grep -c ">" "{}")"' \;
   find . -name "contigs.fa" -exec sh -c 'wc -c < "{}" | tr -d "\n" | awk "{print \"{}: \" \$0 \" contigs: \" \$(grep -c \">\" \"{}\")} " ' \; | sort -k2,2n -k4,4n
   find . -name "contigs.fa" -exec sh -c 'size=$(wc -c < "{}"); contig_count=$(grep -c ">" "{}"); printf "%s: %d bytes, contigs: %d\n" "{}" "$size" "$contig_count"' \; | sort -t: -k4,4n
   
   grep -v '^>' contigs.fa | awk '{ total += length($0) } END { print total }'
   #2399339
   
   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
           ./mibi2381/contigs.fa: 1077606
           ./mibi1472/contigs.fa: 1145583
           ./mibi2380/contigs.fa: 1478149
           ./mibi1458/contigs.fa: 2345604
           ./mibi1466/contigs.fa: 2349339
           ./mibi1451/contigs.fa: 2375432
           ./mibi1441/contigs.fa: 2390897
           ./mibi1471/contigs.fa: 2399056
           ./mibi1435/contigs.fa: 2399339
           ./mibi1473/contigs.fa: 2416173
           ./mibi1474/contigs.fa: 2419849
           ./mibi1495/contigs.fa: 2423463
           ./mibi1497/contigs.fa: 2427317
           ./mibi1476/contigs.fa: 2428189
           ./mibi1463/contigs.fa: 2430568
           ./mibi2313/contigs.fa: 2434775
           ./mibi2321/contigs.fa: 2435584
           ./mibi1494/contigs.fa: 2436708
           ./mibi1481/contigs.fa: 2437976
           ./mibi1464/contigs.fa: 2438603
           ./mibi1450/contigs.fa: 2439465
           ./mibi1483/contigs.fa: 2440401
           ./mibi1506/contigs.fa: 2440413
           ./mibi1462/contigs.fa: 2441903
           ./mibi1443/contigs.fa: 2445186
           ./mibi1448/contigs.fa: 2447751
           ./mibi1439/contigs.fa: 2453223
           ./mibi1501/contigs.fa: 2454766
           ./mibi1505/contigs.fa: 2455113
           ./mibi1436/contigs.fa: 2457498
           ./mibi1499/contigs.fa: 2459216
           ./mibi1452/contigs.fa: 2467292
           ./mibi1500/contigs.fa: 2467976
           ./mibi1455/contigs.fa: 2468334
           ./mibi1445/contigs.fa: 2469433
           ./mibi1479/contigs.fa: 2471443
           ./mibi1482/contigs.fa: 2473012
           ./mibi1469/contigs.fa: 2475757
           ./mibi1468/contigs.fa: 2478455
           ./mibi1438/contigs.fa: 2482554
           ./mibi2379/contigs.fa: 2483292
           ./mibi1493/contigs.fa: 2483445
           ./mibi1488/contigs.fa: 2484950
           ./mibi1486/contigs.fa: 2485023
           ./mibi1442/contigs.fa: 2488933
           ./mibi1437/contigs.fa: 2489787
           ./mibi1460/contigs.fa: 2491014
           ./mibi2312/contigs.fa: 2494588
           ./mibi1489/contigs.fa: 2495771
           ./mibi1504/contigs.fa: 2501045
           ./mibi2317/contigs.fa: 2504746
           ./mibi1444/contigs.fa: 2504874
           ./mibi1446/contigs.fa: 2508952
           ./mibi1465/contigs.fa: 2509542
           ./mibi1467/contigs.fa: 2509571
           ./mibi2314/contigs.fa: 2510798
           ./mibi2315/contigs.fa: 2511464
           ./mibi1457/contigs.fa: 2513005
           ./mibi1490/contigs.fa: 2514271
           ./mibi1491/contigs.fa: 2519558
           ./mibi1449/contigs.fa: 2520352
           ./mibi1503/contigs.fa: 2521179
           ./mibi1475/contigs.fa: 2526469
           ./mibi1484/contigs.fa: 2530724
           ./mibi1447/contigs.fa: 2538610
           ./mibi1453/contigs.fa: 2543893
           ./mibi1477/contigs.fa: 2550922
           ./mibi1454/contigs.fa: 2553326
           ./mibi1498/contigs.fa: 2556315
           ./mibi2316/contigs.fa: 2556628
           ./mibi1492/contigs.fa: 2558492
           ./mibi1470/contigs.fa: 2563169
           ./mibi2320/contigs.fa: 2571421
           ./mibi1461/contigs.fa: 2582715
           ./mibi1478/contigs.fa: 2584524
           ./mibi2318/contigs.fa: 2594120
           ./mibi1459/contigs.fa: 2595990
           ./mibi1440/contigs.fa: 2604213
           ./mibi1456/contigs.fa: 2605647
           ./mibi1487/contigs.fa: 2614950
           ./mibi1496/contigs.fa: 2616533
           ./mibi2319/contigs.fa: 2621258
           ./mibi1480/contigs.fa: 2621312
           ./mibi1485/contigs.fa: 2665904
           ./mibi1502/contigs.fa: 2668891
   
   cd mibi1502
   awk '/^>/ {if(seen_header++) print "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"; next} {printf "%s", $0} END {print ""}' contigs.fa > concatenated_contigs.fasta
   awk '/^>/ {if(seen_header++) print ""; print $0; next} {printf "%s", $0} END {print ""}' concatenated_contigs.fasta > concatenated_contigs.fa
   sed -i '1s/^/>mibi1502\n/' concatenated_contigs.fa
   seqkit seq -i concatenated_contigs.fa -m 100 > ../mibi1502.fasta
   
   bakta --db /mnt/nvme0n1p1/bakta_db mibi1502.fasta
   
   ATCC 14990
   Genes (total)                     :: 2,368
           CDSs (total)                      :: 2,284
           Genes (coding)                    :: 2,231
           CDSs (with protein)               :: 2,231
           Genes (RNA)                       :: 84
           rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
           complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
           tRNAs                             :: 61
           ncRNAs                            :: 4
           Pseudo Genes (total)              :: 53
           CDSs (without protein)            :: 53
           Pseudo Genes (ambiguous residues) :: 0 of 53
           Pseudo Genes (frameshifted)       :: 34 of 53
           Pseudo Genes (incomplete)         :: 31 of 53
           Pseudo Genes (internal stop)      :: 24 of 53
   
   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.
   
   predict tRNAs...
           found: 61
   predict tmRNAs...
           found: 1
   predict rRNAs...
           found: 12
   predict ncRNAs...
           found: 55
   predict ncRNA regions...
           found: 26
   predict CRISPR arrays...
           found: 0
   predict & annotate CDSs...
           predicted: 2529
           discarded spurious: 0
           revised translational exceptions: 0
           detected IPSs: 2369
           found PSCs: 117
           found PSCCs: 26
           lookup annotations...
           conduct expert systems...
                   amrfinder: 20
                   protein sequences: 54
           combine annotations and mark hypotheticals...
           detect pseudogenes...
                   pseudogene candidates: 15
                   found pseudogenes: 7
   analyze hypothetical proteins: 96
           detected Pfam hits: 1
           calculated proteins statistics
           revise special cases...
   extract sORF...
           potential: 46973
           discarded due to overlaps: 37990
           discarded spurious: 0
           detected IPSs: 9
           found PSCs: 2
           lookup annotations...
           filter and combine annotations...
           filtered sORFs: 9
   detect gaps...
           found: 113
   detect oriCs/oriVs...
           found: 1
   detect oriTs...
           found: 0
   apply feature overlap filters...
   select features and create locus tags...
   selected: 2801
   improve annotations...
           revised gene symbols: 9
   

5. generate genebank in snpEff and run spandx

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

6. filter out 4 samples for downstream analyses

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

7. SCCmec typing and drawing with clinker

   #https://www.genomicepidemiology.org/
   #https://cge.food.dtu.dk/services/SCCmecFinder/
   mkdir contigs; cd contigs
   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
   cp ../${sample}/contigs.fa ${sample}_contigs.fa
   done
   
   #Predicted SCCmec element
   grep "Predicted SCCmec element" *.txt
   grep "2 SCCmec" *.txt
   grep "ccr class" *.txt
   grep "mec class" *.txt
   
   mibi1435_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVb(2B)
   mibi1436_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1437_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1438_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
   mibi1439_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
   
   mibi1440_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1441_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1442_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1443_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
   mibi1444_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
   mibi1445_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
   mibi1446_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   mibi1447_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   mibi1448_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1449_SCCmec_out.txt:Predicted SCCmec element: none
   
   mibi1450_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
   mibi1451_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
   mibi1452_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1453_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1454_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1455_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1456_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
   mibi1457_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   mibi1458_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1459_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
   
   mibi1460_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
   mibi1461_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1462_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
   mibi1463_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1464_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1465_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
   mibi1466_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   mibi1467_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1468_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1469_SCCmec_out.txt:Predicted SCCmec element: none
   
   mibi1471_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1473_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
   mibi1474_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1475_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   mibi1476_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1477_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1478_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
   mibi1479_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   
   mibi1480_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
   mibi1481_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_II(2A)
   mibi1482_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1483_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1484_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
   mibi1485_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1486_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1487_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
   mibi1488_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
   mibi1489_SCCmec_out.txt:Predicted SCCmec element: none
   
   mibi1490_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   mibi1491_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   mibi1492_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1493_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1494_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1495_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
   mibi1496_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1497_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1498_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1499_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
   
   mibi1500_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
   mibi1501_SCCmec_out.txt: SCCmec_type_IV(2B) and SCCmec_type_VI(4B)
   mibi1502_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
   mibi1503_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1504_SCCmec_out.txt:Predicted SCCmec element: none
   mibi1505_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
   mibi1506_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVg(2B)
   
   mibi2312_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
   mibi2313_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
   mibi2314_SCCmec_out.txt:Predicted SCCmec element: none
   mibi2315_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IVa(2B)
   mibi2316_SCCmec_out.txt:Predicted SCCmec element: none
   mibi2317_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
   mibi2318_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_III(3A)
   mibi2319_SCCmec_out.txt: SCCmec_type_III(3A) and SCCmec_type_VIII(4A)
   mibi2320_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
   mibi2321_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B)
   mibi2379_SCCmec_out.txt:Predicted SCCmec element: SCCmec_type_IV(2B&5)
   
   mibi1441_SCCmec_out.txt:ccr class 2
   mibi1446_SCCmec_out.txt:ccr class 2
   mibi1446_SCCmec_out.txt:ccr class 4
   mibi1447_SCCmec_out.txt:ccr class 2
   mibi1447_SCCmec_out.txt:ccr class 4
   mibi1452_SCCmec_out.txt:ccr class 5
   mibi1455_SCCmec_out.txt:ccr class 2
   
   mibi1457_SCCmec_out.txt:ccr class 2
   mibi1457_SCCmec_out.txt:ccr class 4
   
   mibi1464_SCCmec_out.txt:ccr class 2
   mibi1466_SCCmec_out.txt:ccr class 2
   mibi1466_SCCmec_out.txt:ccr class 4
   mibi1467_SCCmec_out.txt:ccr class 5
   mibi1475_SCCmec_out.txt:ccr class 2
   mibi1475_SCCmec_out.txt:ccr class 4
   
   mibi1477_SCCmec_out.txt:ccr class 9
   mibi1478_SCCmec_out.txt:ccr class 3
   mibi1478_SCCmec_out.txt:ccr class 4
   
   mibi1479_SCCmec_out.txt:ccr class 2
   mibi1479_SCCmec_out.txt:ccr class 4
   
   mibi1480_SCCmec_out.txt:ccr class 3
   mibi1480_SCCmec_out.txt:ccr class 4
   
   mibi1482_SCCmec_out.txt:ccr class 5
   mibi1483_SCCmec_out.txt:ccr class 5
   mibi1486_SCCmec_out.txt:ccr class 2
   
   mibi1487_SCCmec_out.txt:ccr class 3
   mibi1487_SCCmec_out.txt:ccr class 4
   
   mibi1489_SCCmec_out.txt:ccr class 2
   
   mibi1490_SCCmec_out.txt:ccr class 2
   mibi1490_SCCmec_out.txt:ccr class 4
   
   mibi1491_SCCmec_out.txt:ccr class 2
   mibi1491_SCCmec_out.txt:ccr class 4
   
   mibi1492_SCCmec_out.txt:ccr class 2
   mibi1494_SCCmec_out.txt:ccr class 5
   
   mibi1501_SCCmec_out.txt:ccr class 2
   mibi1501_SCCmec_out.txt:ccr class 4
   
   mibi1504_SCCmec_out.txt:ccr class 2
   mibi1504_SCCmec_out.txt:ccr class 5&5
   
   mibi2316_SCCmec_out.txt:ccr class 2
   mibi2319_SCCmec_out.txt:ccr class 3
   mibi2319_SCCmec_out.txt:ccr class 4
   
   mibi1446_SCCmec_out.txt:mec class B
   mibi1447_SCCmec_out.txt:mec class B
   
   mibi1457_SCCmec_out.txt:mec class B
   mibi1463_SCCmec_out.txt:mec class B
   mibi1466_SCCmec_out.txt:mec class B
   mibi1475_SCCmec_out.txt:mec class B
   mibi1478_SCCmec_out.txt:mec class A
   mibi1479_SCCmec_out.txt:mec class B
   mibi1480_SCCmec_out.txt:mec class A
   
   mibi1483_SCCmec_out.txt:mec class A
   mibi1487_SCCmec_out.txt:mec class A
   mibi1490_SCCmec_out.txt:mec class B
   mibi1491_SCCmec_out.txt:mec class B
   mibi1501_SCCmec_out.txt:mec class B
   mibi2319_SCCmec_out.txt:mec class A
   

8. agr typing

   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
   bakta --db /mnt/nvme0n1p1/bakta_db shovill/${sample}/contigs.fa --prefix ${sample}
   done
   
   grep "agrD" mibi1436.gbff
   mibi1435    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1436    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1437    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1438    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1439    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1440    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1441    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
   mibi1442    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1443    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1444    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1445    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1446    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1447    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1448    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1449    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
   mibi1450    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1451    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1452    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
   mibi1453    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1454    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1455    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1456    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1457    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1458    MENIFNLFIK I FTTILEF V GTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I* (with a 2-codon difference)
   mibi1459    MENIFNLFIK F FTTILEF I GTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1460    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1461    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1462    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1463    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1464    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
   mibi1465    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1466    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1467    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1468    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1469    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1471    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1473    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1474    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1475    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1476    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1477    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1478    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1479    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1480    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1481    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1482    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1483    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1484    none
   mibi1485    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1486    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1487    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1488    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1489    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1490    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1491    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1492    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1493    MNLLGGL F LK I FSNFMAVIGNA A KYNPC AS YLDEPQVPEELTKLDE  AgrD III* (with a 2-codon difference)
   mibi1494    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1495    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1496    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1497    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1498    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1499    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi1500    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1501    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1502    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1503    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
   mibi1504    MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE    AgrD III
   mibi1505    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi1506    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi2312    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi2313    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi2314    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi2315    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi2316    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi2317    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi2318    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi2319    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi2320    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   mibi2321    MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE    AgrD I
   mibi2379    MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE    AgrD II
   
       #MNLLGGL L LK L FSNFMAVIGNA A KYNPC AS YLDEPQVPEELTKLDE  AgrD III (2)
       #MNLLGGL L LK I FSNFMAVIGNA S KYNPC SN YLDEPQVPEELTKLDE  AgrD II  (4)
   
   -- AgrD I --
   Query  1       MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE  46
           M  +  L +K F+  +  IG  +  + C  Y DEP+VPEELTKL E
   Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688
   -- AgrD II --
   Query  1       MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE  46
           MNLLGGLLLKIFSNFMAVIGNASKYNPC  YLDEPQVPEELTKLDE
   Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688
   -- AgrD III --
   Query  1       MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE  46
           MNLLGGLLLK+FSNFMAVIGNA+KYNPC  YLDEPQVPEELTKLDE
   Sbjct  926825  MNLLGGLLLKIFSNFMAVIGNASKYNPCVMYLDEPQVPEELTKLDE  926688
   

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

   cut -d',' -f1 plotTreeHeatmap/typing.csv > all_isolate_names.txt
   grep "gene=gyrB" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   
   grep "gene=fumC" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   
   grep "gene=gltA" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   
   grep "gene=icd" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   
   grep "gene=apsS" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "gene=sigB" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   #27d26
   #< mibi1461
   
   grep "gene=sarA" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   #17d16
   #< mibi1451
   #32d30
   #< mibi1466
   #45d42
   #< mibi1481
   
   grep "gene=agrC" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "gene=yycG" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "PSM-beta" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "PSM-delta" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   #9d8
   #< mibi1443
   
   grep "hlb" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "atlE" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "gene=atl" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   #19d18
   #< mibi1453
   
   grep "gene=sdrG" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   #2d1
   < mibi1436
   5d3
   < mibi1439
   8,9d5
   < mibi1442
   < mibi1443
   11,12d6
   < mibi1445
   < mibi1446
   14d7
   < mibi1448
   18,19d10
   < mibi1452
   < mibi1453
   30,32d20
   < mibi1464
   < mibi1465
   < mibi1466
   34,35d21
   < mibi1468
   < mibi1469
   37d22
   < mibi1473
   39d23
   < mibi1475
   41d24
   < mibi1477
   43d25
   < mibi1479
   47d28
   < mibi1483
   50d30
   < mibi1486
   52d31
   < mibi1488
   55d33
   < mibi1491
   63,64d40
   < mibi1499
   < mibi1500
   67d42
   < mibi1503
   76d50
   < mibi2317
   79d52
   < mibi2320
   81d53
   < mibi2379
   
   grep "gene=sdrH" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   #24d23
   #< mibi1458
   #57d55
   #< mibi1493
   
   grep "gene=ebh" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   #1d0
   #< mibi1435
   6d4
   < mibi1440
   11,13d8
   < mibi1445
   < mibi1446
   < mibi1447
   16,18d10
   < mibi1450
   < mibi1451
   < mibi1452
   20d11
   < mibi1454
   22,23d12
   < mibi1456
   < mibi1457
   25,27d13
   < mibi1459
   < mibi1460
   < mibi1461
   29d14
   < mibi1463
   31,32d15
   < mibi1465
   < mibi1466
   37d19
   < mibi1473
   39d20
   < mibi1475
   41,44d21
   < mibi1477
   < mibi1478
   < mibi1479
   < mibi1480
   47d23
   < mibi1483
   49d24
   < mibi1485
   51,52d25
   < mibi1487
   < mibi1488
   54,55d26
   < mibi1490
   < mibi1491
   59,60d29
   < mibi1495
   < mibi1496
   62,63d30
   < mibi1498
   < mibi1499
   66d32
   < mibi1502
   71d36
   < mibi2312
   74d38
   < mibi2315
   76,79d39
   < mibi2317
   < mibi2318
   < mibi2319
   < mibi2320
   81d40
   < mibi2379
   
   grep "gene=ebpS" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   
   grep "gene=tagB" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   uniq temp1 > temp2    # 3 copies for each isolate
   diff all_isolate_names.txt temp2
   
   grep "gene=capC" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "gene=sepA" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   uniq temp1 > temp2
   diff all_isolate_names.txt temp2
   
   grep "gene=dltA" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   
   grep "gene=fmtC" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "gene=lipA" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   
   grep "gene=sceD" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   
   #TODO: check the sdrG more detailed with sequence alignments, since SE0760 is not standard gene name.
   grep "gene=SE0760" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "gene=esp" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1 | wc -l
   #TODO, using sequence comparisons for one record!
   
   grep "gene=ecpA" *.gff3 > temp
   cut -d'.' -f1 temp > temp1
   diff all_isolate_names.txt temp1
   17d16
   < mibi1451
   37d35
   < mibi1473
   

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

    (Optional online search) https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes
    #Title:Refseq prokaryote representative genomes (contains refseq assembly)
    #Molecule Type:mixed DNA
    #Update date:2024/10/16
    #Number of sequences:1038672
    
    #cat gyrB_revcomp.fasta fumC_revcomp.fasta gltA.fasta icd_revcomp.fasta apsS.fasta sigB_revcomp.fasta sarA_revcomp.fasta ...
    
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/apsS.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/agrC.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/yycG.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/psm-beta.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/hlb_.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/atlE.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/capC.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/fmtC.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/SE0760.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/esp.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880870.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880871.fasta .
    cp ~/DATA/Data_Patricia_Sepi_5Samples/presence_absence_matrix_on_gene_list/MT880872.fasta .
    
    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
    cd ../shovill/${sample}/
    makeblastdb -in contigs.fa -dbtype nucl
    cd ../../presence_absence_matrix_on_gene_list
    done
    
    # -length(apsS.fasta)=1041
    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
    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
    done
    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
    python3 analyze_blastn_res.py apsS_on_${sample}.blastn
    done
    apsS_on_mibi1435.blastn: 1041
    apsS_on_mibi1436.blastn: 1041
    apsS_on_mibi1437.blastn: 1041
    apsS_on_mibi1438.blastn: 1041
    apsS_on_mibi1439.blastn: 1041
    apsS_on_mibi1440.blastn: 1041
    apsS_on_mibi1441.blastn: 1041
    apsS_on_mibi1442.blastn: 1041
    apsS_on_mibi1443.blastn: 1041
    apsS_on_mibi1444.blastn: 1041
    apsS_on_mibi1445.blastn: 1041
    apsS_on_mibi1446.blastn: 1041
    apsS_on_mibi1447.blastn: 1041
    apsS_on_mibi1448.blastn: 1041
    apsS_on_mibi1449.blastn: 1041
    apsS_on_mibi1450.blastn: 1041
    apsS_on_mibi1451.blastn: 1041
    apsS_on_mibi1452.blastn: 1041
    apsS_on_mibi1453.blastn: 1041
    apsS_on_mibi1454.blastn: 1041
    apsS_on_mibi1455.blastn: 1041
    apsS_on_mibi1456.blastn: 1041
    apsS_on_mibi1457.blastn: 1041
    apsS_on_mibi1458.blastn: 1041
    apsS_on_mibi1459.blastn: 1041
    apsS_on_mibi1460.blastn: 1041
    apsS_on_mibi1461.blastn: 1041
    apsS_on_mibi1462.blastn: 1041
    apsS_on_mibi1463.blastn: 1041
    apsS_on_mibi1464.blastn: 1041
    apsS_on_mibi1465.blastn: 1041
    apsS_on_mibi1466.blastn: 1041
    apsS_on_mibi1467.blastn: 1041
    apsS_on_mibi1468.blastn: 1041
    apsS_on_mibi1469.blastn: 1041
    apsS_on_mibi1471.blastn: 1041
    apsS_on_mibi1473.blastn: 1041
    apsS_on_mibi1474.blastn: 1041
    apsS_on_mibi1475.blastn: 1041
    apsS_on_mibi1476.blastn: 1041
    apsS_on_mibi1477.blastn: 1041
    apsS_on_mibi1478.blastn: 1041
    apsS_on_mibi1479.blastn: 1041
    apsS_on_mibi1480.blastn: 1041
    apsS_on_mibi1481.blastn: 1041
    apsS_on_mibi1482.blastn: 1041
    apsS_on_mibi1483.blastn: 1041
    apsS_on_mibi1484.blastn: 1041
    apsS_on_mibi1485.blastn: 1041
    apsS_on_mibi1486.blastn: 1041
    apsS_on_mibi1487.blastn: 1041
    apsS_on_mibi1488.blastn: 1041
    apsS_on_mibi1489.blastn: 1041
    apsS_on_mibi1490.blastn: 1041
    apsS_on_mibi1491.blastn: 1041
    apsS_on_mibi1492.blastn: 1041
    apsS_on_mibi1493.blastn: 1041
    apsS_on_mibi1494.blastn: 1041
    apsS_on_mibi1495.blastn: 1041
    apsS_on_mibi1496.blastn: 1041
    apsS_on_mibi1497.blastn: 1041
    apsS_on_mibi1498.blastn: 1041
    apsS_on_mibi1499.blastn: 1041
    apsS_on_mibi1500.blastn: 1041
    apsS_on_mibi1501.blastn: 1041
    apsS_on_mibi1502.blastn: 1041
    apsS_on_mibi1503.blastn: 1041
    apsS_on_mibi1504.blastn: 1041
    apsS_on_mibi1505.blastn: 1041
    apsS_on_mibi1506.blastn: 1041
    apsS_on_mibi2312.blastn: 1041
    apsS_on_mibi2313.blastn: 1041
    apsS_on_mibi2314.blastn: 1041
    apsS_on_mibi2315.blastn: 1041
    apsS_on_mibi2316.blastn: 1041
    apsS_on_mibi2317.blastn: 1041
    apsS_on_mibi2318.blastn: 1041
    apsS_on_mibi2319.blastn: 1041
    apsS_on_mibi2320.blastn: 1041
    apsS_on_mibi2321.blastn: 1041
    apsS_on_mibi2379.blastn: 1041
    
    # -length(sigB_revcomp.fasta)=771
    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
    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
    done
    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
    python3 analyze_blastn_res.py sigB_on_${sample}.blastn
    done
    sigB_on_mibi1435.blastn: 771
    sigB_on_mibi1436.blastn: 771
    sigB_on_mibi1437.blastn: 771
    sigB_on_mibi1438.blastn: 771
    sigB_on_mibi1439.blastn: 771
    sigB_on_mibi1440.blastn: 771
    sigB_on_mibi1441.blastn: 771
    sigB_on_mibi1442.blastn: 771
    sigB_on_mibi1443.blastn: 771
    sigB_on_mibi1444.blastn: 771
    sigB_on_mibi1445.blastn: 771
    sigB_on_mibi1446.blastn: 771
    sigB_on_mibi1447.blastn: 771
    sigB_on_mibi1448.blastn: 771
    sigB_on_mibi1449.blastn: 771
    sigB_on_mibi1450.blastn: 771
    sigB_on_mibi1451.blastn: 771
    sigB_on_mibi1452.blastn: 771
    sigB_on_mibi1453.blastn: 771
    sigB_on_mibi1454.blastn: 771
    sigB_on_mibi1455.blastn: 771
    sigB_on_mibi1456.blastn: 771
    sigB_on_mibi1457.blastn: 771
    sigB_on_mibi1458.blastn: 771
    sigB_on_mibi1459.blastn: 771
    sigB_on_mibi1460.blastn: 771
    sigB_on_mibi1461.blastn: 0 *
    sigB_on_mibi1462.blastn: 771
    sigB_on_mibi1463.blastn: 771
    sigB_on_mibi1464.blastn: 771
    sigB_on_mibi1465.blastn: 771
    sigB_on_mibi1466.blastn: 771
    sigB_on_mibi1467.blastn: 771
    sigB_on_mibi1468.blastn: 771
    sigB_on_mibi1469.blastn: 771
    sigB_on_mibi1471.blastn: 771
    sigB_on_mibi1473.blastn: 771
    sigB_on_mibi1474.blastn: 771
    sigB_on_mibi1475.blastn: 771
    sigB_on_mibi1476.blastn: 771
    sigB_on_mibi1477.blastn: 771
    sigB_on_mibi1478.blastn: 771
    sigB_on_mibi1479.blastn: 771
    sigB_on_mibi1480.blastn: 771
    sigB_on_mibi1481.blastn: 771
    sigB_on_mibi1482.blastn: 771
    sigB_on_mibi1483.blastn: 771
    sigB_on_mibi1484.blastn: 771
    sigB_on_mibi1485.blastn: 771
    sigB_on_mibi1486.blastn: 771
    sigB_on_mibi1487.blastn: 771
    sigB_on_mibi1488.blastn: 771
    sigB_on_mibi1489.blastn: 771
    sigB_on_mibi1490.blastn: 771
    sigB_on_mibi1491.blastn: 771
    sigB_on_mibi1492.blastn: 771
    sigB_on_mibi1493.blastn: 771
    sigB_on_mibi1494.blastn: 771
    sigB_on_mibi1495.blastn: 771
    sigB_on_mibi1496.blastn: 771
    sigB_on_mibi1497.blastn: 771
    sigB_on_mibi1498.blastn: 771
    sigB_on_mibi1499.blastn: 771
    sigB_on_mibi1500.blastn: 771
    sigB_on_mibi1501.blastn: 771
    sigB_on_mibi1502.blastn: 771
    sigB_on_mibi1503.blastn: 771
    sigB_on_mibi1504.blastn: 771
    sigB_on_mibi1505.blastn: 771
    sigB_on_mibi1506.blastn: 771
    sigB_on_mibi2312.blastn: 771
    sigB_on_mibi2313.blastn: 771
    sigB_on_mibi2314.blastn: 771
    sigB_on_mibi2315.blastn: 771
    sigB_on_mibi2316.blastn: 771
    sigB_on_mibi2317.blastn: 771
    sigB_on_mibi2318.blastn: 771
    sigB_on_mibi2319.blastn: 771
    sigB_on_mibi2320.blastn: 771
    sigB_on_mibi2321.blastn: 771
    sigB_on_mibi2379.blastn: 771
    
    # - length(sarA_revcomp.fasta)=375
    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
    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
    done
    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
    python3 analyze_blastn_res.py sarA_on_${sample}.blastn
    done
    sarA_on_mibi1435.blastn: 375
    sarA_on_mibi1436.blastn: 375
    sarA_on_mibi1437.blastn: 375
    sarA_on_mibi1438.blastn: 375
    sarA_on_mibi1439.blastn: 375
    sarA_on_mibi1440.blastn: 375
    sarA_on_mibi1441.blastn: 375
    sarA_on_mibi1442.blastn: 375
    sarA_on_mibi1443.blastn: 375
    sarA_on_mibi1444.blastn: 375
    sarA_on_mibi1445.blastn: 375
    sarA_on_mibi1446.blastn: 375
    sarA_on_mibi1447.blastn: 375
    sarA_on_mibi1448.blastn: 375
    sarA_on_mibi1449.blastn: 375
    sarA_on_mibi1450.blastn: 375
    sarA_on_mibi1451.blastn: 0 *
    sarA_on_mibi1452.blastn: 375
    sarA_on_mibi1453.blastn: 375
    sarA_on_mibi1454.blastn: 375
    sarA_on_mibi1455.blastn: 375
    sarA_on_mibi1456.blastn: 375
    sarA_on_mibi1457.blastn: 375
    sarA_on_mibi1458.blastn: 375
    sarA_on_mibi1459.blastn: 375
    sarA_on_mibi1460.blastn: 375
    sarA_on_mibi1461.blastn: 375
    sarA_on_mibi1462.blastn: 375
    sarA_on_mibi1463.blastn: 375
    sarA_on_mibi1464.blastn: 375
    sarA_on_mibi1465.blastn: 375
    sarA_on_mibi1466.blastn: 208 *
    sarA_on_mibi1467.blastn: 375
    sarA_on_mibi1468.blastn: 375
    sarA_on_mibi1469.blastn: 375
    sarA_on_mibi1471.blastn: 375
    sarA_on_mibi1473.blastn: 375
    sarA_on_mibi1474.blastn: 375
    sarA_on_mibi1475.blastn: 375
    sarA_on_mibi1476.blastn: 375
    sarA_on_mibi1477.blastn: 375
    sarA_on_mibi1478.blastn: 375
    sarA_on_mibi1479.blastn: 375
    sarA_on_mibi1480.blastn: 375
    sarA_on_mibi1481.blastn: 248 *
    sarA_on_mibi1482.blastn: 375
    sarA_on_mibi1483.blastn: 375
    sarA_on_mibi1484.blastn: 375
    sarA_on_mibi1485.blastn: 375
    sarA_on_mibi1486.blastn: 375
    sarA_on_mibi1487.blastn: 375
    sarA_on_mibi1488.blastn: 375
    sarA_on_mibi1489.blastn: 375
    sarA_on_mibi1490.blastn: 375
    sarA_on_mibi1491.blastn: 375
    sarA_on_mibi1492.blastn: 375
    sarA_on_mibi1493.blastn: 375
    sarA_on_mibi1494.blastn: 375
    sarA_on_mibi1495.blastn: 375
    sarA_on_mibi1496.blastn: 375
    sarA_on_mibi1497.blastn: 375
    sarA_on_mibi1498.blastn: 375
    sarA_on_mibi1499.blastn: 375
    sarA_on_mibi1500.blastn: 375
    sarA_on_mibi1501.blastn: 375
    sarA_on_mibi1502.blastn: 375
    sarA_on_mibi1503.blastn: 375
    sarA_on_mibi1504.blastn: 375
    sarA_on_mibi1505.blastn: 375
    sarA_on_mibi1506.blastn: 357
    sarA_on_mibi2312.blastn: 375
    sarA_on_mibi2313.blastn: 375
    sarA_on_mibi2314.blastn: 375
    sarA_on_mibi2315.blastn: 375
    sarA_on_mibi2316.blastn: 375
    sarA_on_mibi2317.blastn: 375
    sarA_on_mibi2318.blastn: 375
    sarA_on_mibi2319.blastn: 375
    sarA_on_mibi2320.blastn: 375
    sarA_on_mibi2321.blastn: 375
    sarA_on_mibi2379.blastn: 375
    
    # -length(agrC.fasta)=1290
    samtools faidx agrABCD_hld.fasta "gi|3320006|emb|Z49220.1|":1494-2783
    
    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
    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
    done
    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
    python3 analyze_blastn_res.py agrC_on_${sample}.blastn
    done
    agrC_on_mibi1435.blastn: 1002
    agrC_on_mibi1436.blastn: 1290
    agrC_on_mibi1437.blastn: 688
    agrC_on_mibi1438.blastn: 1290
    agrC_on_mibi1439.blastn: 688
    agrC_on_mibi1440.blastn: 1290
    agrC_on_mibi1441.blastn: 861
    agrC_on_mibi1442.blastn: 688
    agrC_on_mibi1443.blastn: 1290
    agrC_on_mibi1444.blastn: 1290
    agrC_on_mibi1445.blastn: 688
    agrC_on_mibi1446.blastn: 688
    agrC_on_mibi1447.blastn: 688
    agrC_on_mibi1448.blastn: 1290
    agrC_on_mibi1449.blastn: 861
    agrC_on_mibi1450.blastn: 1290
    agrC_on_mibi1451.blastn: 688
    agrC_on_mibi1452.blastn: 818
    agrC_on_mibi1453.blastn: 1290
    agrC_on_mibi1454.blastn: 1290
    agrC_on_mibi1455.blastn: 1290
    agrC_on_mibi1456.blastn: 1290
    agrC_on_mibi1457.blastn: 688
    agrC_on_mibi1458.blastn: 1290
    agrC_on_mibi1459.blastn: 1290
    agrC_on_mibi1460.blastn: 688
    agrC_on_mibi1461.blastn: 1290
    agrC_on_mibi1462.blastn: 1290
    agrC_on_mibi1463.blastn: 1290
    agrC_on_mibi1464.blastn: 861
    agrC_on_mibi1465.blastn: 688
    agrC_on_mibi1466.blastn: 541
    agrC_on_mibi1467.blastn: 688
    agrC_on_mibi1468.blastn: 1290
    agrC_on_mibi1469.blastn: 1290
    agrC_on_mibi1471.blastn: 1165
    agrC_on_mibi1473.blastn: 688
    agrC_on_mibi1474.blastn: 1290
    agrC_on_mibi1475.blastn: 688
    agrC_on_mibi1476.blastn: 1290
    agrC_on_mibi1477.blastn: 688
    agrC_on_mibi1478.blastn: 442
    agrC_on_mibi1479.blastn: 688
    agrC_on_mibi1480.blastn: 1290
    agrC_on_mibi1481.blastn: 862
    agrC_on_mibi1482.blastn: 1290
    agrC_on_mibi1483.blastn: 1290
    agrC_on_mibi1484.blastn: 491
    agrC_on_mibi1485.blastn: 1290
    agrC_on_mibi1486.blastn: 1290
    agrC_on_mibi1487.blastn: 1290
    agrC_on_mibi1488.blastn: 1290
    agrC_on_mibi1489.blastn: 688
    agrC_on_mibi1490.blastn: 688
    agrC_on_mibi1491.blastn: 688
    agrC_on_mibi1492.blastn: 688
    agrC_on_mibi1493.blastn: 818
    agrC_on_mibi1494.blastn: 1290
    agrC_on_mibi1495.blastn: 688
    agrC_on_mibi1496.blastn: 1290
    agrC_on_mibi1497.blastn: 911
    agrC_on_mibi1498.blastn: 1290
    agrC_on_mibi1499.blastn: 688
    agrC_on_mibi1500.blastn: 1290
    agrC_on_mibi1501.blastn: 1290
    agrC_on_mibi1502.blastn: 1094
    agrC_on_mibi1503.blastn: 818
    agrC_on_mibi1504.blastn: 861
    agrC_on_mibi1505.blastn: 1290
    agrC_on_mibi1506.blastn: 1290
    agrC_on_mibi2312.blastn: 688
    agrC_on_mibi2313.blastn: 1290
    agrC_on_mibi2314.blastn: 1290
    agrC_on_mibi2315.blastn: 1290
    agrC_on_mibi2316.blastn: 688
    agrC_on_mibi2317.blastn: 688
    agrC_on_mibi2318.blastn: 1290
    agrC_on_mibi2319.blastn: 1290
    agrC_on_mibi2320.blastn: 688
    agrC_on_mibi2321.blastn: 1290
    agrC_on_mibi2379.blastn: 688
    
    partial, 1002/1290 nt present
    +
    partial, 688/1290 nt present
    +
    partial, 688/1290 nt present
    +
    partial, 861/1290 nt present
    partial, 688/1290 nt present
    +
    +
    partial, 688/1290 nt present
    partial, 688/1290 nt present
    partial, 688/1290 nt present
    +
    partial, 861/1290 nt present
    +
    partial, 688/1290 nt present
    partial, 818/1290 nt present
    +
    +
    +
    +
    partial, 688/1290 nt present
    +
    +
    partial, 688/1290 nt present
    +
    +
    +
    partial, 861/1290 nt present
    partial, 688/1290 nt present
    partial, 541/1290 nt present
    partial, 688/1290 nt present
    +
    +
    partial, 1165/1290 nt present
    partial, 688/1290 nt present
    +
    partial, 688/1290 nt present
    +
    partial, 688/1290 nt present
    partial, 442/1290 nt present
    partial, 688/1290 nt present
    +
    partial, 862/1290 nt present
    +
    +
    partial, 491/1290 nt present
    +
    +
    +
    +
    partial, 688/1290 nt present
    partial, 688/1290 nt present
    partial, 688/1290 nt present
    partial, 688/1290 nt present
    partial, 818/1290 nt present
    +
    partial, 688/1290 nt present
    +
    partial, 911/1290 nt present
    +
    partial, 688/1290 nt present
    +
    +
    partial, 1094/1290 nt present
    partial, 818/1290 nt present
    partial, 861/1290 nt present
    +
    +
    partial, 688/1290 nt present
    +
    +
    +
    partial, 688/1290 nt present
    partial, 688/1290 nt present
    +
    +
    partial, 688/1290 nt present
    +
    partial, 688/1290 nt present
    
    # - length(yycG.fasta)=1827
    gene            complement(2589240..2591072)
                    /gene="yycG"
    samtools faidx CP000029.fasta "gi|57636010|gb|CP000029.1|":2589240-2591072 > yycG.fasta
    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
    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
    done
    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
    python3 analyze_blastn_res.py yycG_on_${sample}.blastn
    done
    #-->WARNING: Only 80% similarity, not the same gene!
    yycG_on_mibi1435.blastn: 1833
    yycG_on_mibi1436.blastn: 1833
    yycG_on_mibi1437.blastn: 1833
    yycG_on_mibi1438.blastn: 1833
    yycG_on_mibi1439.blastn: 1833
    yycG_on_mibi1440.blastn: 1833
    yycG_on_mibi1441.blastn: 1833
    yycG_on_mibi1442.blastn: 1833
    yycG_on_mibi1443.blastn: 1833
    yycG_on_mibi1444.blastn: 1833
    yycG_on_mibi1445.blastn: 1833
    yycG_on_mibi1446.blastn: 1833
    yycG_on_mibi1447.blastn: 1833
    yycG_on_mibi1448.blastn: 1833
    yycG_on_mibi1449.blastn: 1833
    yycG_on_mibi1450.blastn: 1833
    yycG_on_mibi1451.blastn: 1833
    yycG_on_mibi1452.blastn: 1833
    yycG_on_mibi1453.blastn: 1833
    yycG_on_mibi1454.blastn: 1833
    yycG_on_mibi1455.blastn: 1833
    yycG_on_mibi1456.blastn: 1833
    yycG_on_mibi1457.blastn: 1833
    yycG_on_mibi1458.blastn: 1833
    yycG_on_mibi1459.blastn: 1833
    yycG_on_mibi1460.blastn: 1833
    yycG_on_mibi1461.blastn: 1833
    yycG_on_mibi1462.blastn: 1833
    yycG_on_mibi1463.blastn: 1833
    yycG_on_mibi1464.blastn: 1833
    yycG_on_mibi1465.blastn: 1833
    yycG_on_mibi1466.blastn: 1833
    yycG_on_mibi1467.blastn: 1833
    yycG_on_mibi1468.blastn: 1833
    yycG_on_mibi1469.blastn: 1833
    yycG_on_mibi1471.blastn: 1833
    yycG_on_mibi1473.blastn: 1833
    yycG_on_mibi1474.blastn: 1833
    yycG_on_mibi1475.blastn: 1833
    yycG_on_mibi1476.blastn: 1833
    yycG_on_mibi1477.blastn: 1833
    yycG_on_mibi1478.blastn: 1833
    yycG_on_mibi1479.blastn: 1833
    yycG_on_mibi1480.blastn: 1833
    yycG_on_mibi1481.blastn: 1833
    yycG_on_mibi1482.blastn: 1833
    yycG_on_mibi1483.blastn: 1833
    yycG_on_mibi1484.blastn: 1833
    yycG_on_mibi1485.blastn: 1833
    yycG_on_mibi1486.blastn: 1833
    yycG_on_mibi1487.blastn: 1833
    yycG_on_mibi1488.blastn: 1833
    yycG_on_mibi1489.blastn: 1833
    yycG_on_mibi1490.blastn: 1833
    yycG_on_mibi1491.blastn: 1833
    yycG_on_mibi1492.blastn: 1833
    yycG_on_mibi1493.blastn: 1833
    yycG_on_mibi1494.blastn: 1833
    yycG_on_mibi1495.blastn: 1833
    yycG_on_mibi1496.blastn: 1833
    yycG_on_mibi1497.blastn: 1833
    yycG_on_mibi1498.blastn: 1833
    yycG_on_mibi1499.blastn: 1833
    yycG_on_mibi1500.blastn: 1833
    yycG_on_mibi1501.blastn: 1833
    yycG_on_mibi1502.blastn: 1833
    yycG_on_mibi1503.blastn: 1833
    yycG_on_mibi1504.blastn: 1833
    yycG_on_mibi1505.blastn: 1833
    yycG_on_mibi1506.blastn: 1833
    yycG_on_mibi2312.blastn: 1833
    yycG_on_mibi2313.blastn: 1833
    yycG_on_mibi2314.blastn: 1833
    yycG_on_mibi2315.blastn: 1833
    yycG_on_mibi2316.blastn: 1833
    yycG_on_mibi2317.blastn: 1833
    yycG_on_mibi2318.blastn: 1833
    yycG_on_mibi2319.blastn: 1833
    yycG_on_mibi2320.blastn: 1833
    yycG_on_mibi2321.blastn: 1833
    yycG_on_mibi2379.blastn: 1833
    
    #TODOs: exact the gene sequence for psm-delta and atl
    #https://www.ncbi.nlm.nih.gov/nuccore    (psm gene) AND "Staphylococcus aureus"[porgn:__txid1280]
    #grep "PSM-delta" mibi1435.gbff
    #                     /product="Phenol-soluble modulin PSM-delta"
    #grep "atl" mibi1435.gbff
    #                     /gene="atl"
    #                     /gene="atl"
    
    https://www.ncbi.nlm.nih.gov/nuccore/JQ066320.1
    # -length(psm-beta1.fasta)=135
    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
    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
    done
    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
    python3 analyze_blastn_res.py psm-beta1_on_${sample}.blastn
    done
    psm-beta1_on_mibi1435.blastn: 0
    psm-beta1_on_mibi1436.blastn: 0
    psm-beta1_on_mibi1437.blastn: 0
    psm-beta1_on_mibi1438.blastn: 0
    psm-beta1_on_mibi1439.blastn: 0
    psm-beta1_on_mibi1440.blastn: 0
    psm-beta1_on_mibi1441.blastn: 0
    psm-beta1_on_mibi1442.blastn: 0
    psm-beta1_on_mibi1443.blastn: 0
    psm-beta1_on_mibi1444.blastn: 0
    psm-beta1_on_mibi1445.blastn: 0
    psm-beta1_on_mibi1446.blastn: 0
    psm-beta1_on_mibi1447.blastn: 0
    psm-beta1_on_mibi1448.blastn: 0
    psm-beta1_on_mibi1449.blastn: 0
    psm-beta1_on_mibi1450.blastn: 0
    psm-beta1_on_mibi1451.blastn: 0
    psm-beta1_on_mibi1452.blastn: 0
    psm-beta1_on_mibi1453.blastn: 0
    psm-beta1_on_mibi1454.blastn: 0
    psm-beta1_on_mibi1455.blastn: 0
    psm-beta1_on_mibi1456.blastn: 0
    psm-beta1_on_mibi1457.blastn: 0
    psm-beta1_on_mibi1458.blastn: 0
    psm-beta1_on_mibi1459.blastn: 0
    psm-beta1_on_mibi1460.blastn: 0
    psm-beta1_on_mibi1461.blastn: 0
    psm-beta1_on_mibi1462.blastn: 0
    psm-beta1_on_mibi1463.blastn: 0
    psm-beta1_on_mibi1464.blastn: 0
    psm-beta1_on_mibi1465.blastn: 0
    psm-beta1_on_mibi1466.blastn: 0
    psm-beta1_on_mibi1467.blastn: 0
    psm-beta1_on_mibi1468.blastn: 0
    psm-beta1_on_mibi1469.blastn: 0
    psm-beta1_on_mibi1471.blastn: 0
    psm-beta1_on_mibi1473.blastn: 0
    psm-beta1_on_mibi1474.blastn: 0
    psm-beta1_on_mibi1475.blastn: 0
    psm-beta1_on_mibi1476.blastn: 0
    psm-beta1_on_mibi1477.blastn: 0
    psm-beta1_on_mibi1478.blastn: 0
    psm-beta1_on_mibi1479.blastn: 0
    psm-beta1_on_mibi1480.blastn: 0
    psm-beta1_on_mibi1481.blastn: 0
    psm-beta1_on_mibi1482.blastn: 0
    psm-beta1_on_mibi1483.blastn: 0
    psm-beta1_on_mibi1484.blastn: 0
    psm-beta1_on_mibi1485.blastn: 0
    psm-beta1_on_mibi1486.blastn: 0
    psm-beta1_on_mibi1487.blastn: 0
    psm-beta1_on_mibi1488.blastn: 0
    psm-beta1_on_mibi1489.blastn: 0
    psm-beta1_on_mibi1490.blastn: 0
    psm-beta1_on_mibi1491.blastn: 0
    psm-beta1_on_mibi1492.blastn: 0
    psm-beta1_on_mibi1493.blastn: 0
    psm-beta1_on_mibi1494.blastn: 0
    psm-beta1_on_mibi1495.blastn: 0
    psm-beta1_on_mibi1496.blastn: 0
    psm-beta1_on_mibi1497.blastn: 0
    psm-beta1_on_mibi1498.blastn: 0
    psm-beta1_on_mibi1499.blastn: 0
    psm-beta1_on_mibi1500.blastn: 0
    psm-beta1_on_mibi1501.blastn: 0
    psm-beta1_on_mibi1502.blastn: 0
    psm-beta1_on_mibi1503.blastn: 0
    psm-beta1_on_mibi1504.blastn: 0
    psm-beta1_on_mibi1505.blastn: 0
    psm-beta1_on_mibi1506.blastn: 0
    psm-beta1_on_mibi2312.blastn: 0
    psm-beta1_on_mibi2313.blastn: 0
    psm-beta1_on_mibi2314.blastn: 0
    psm-beta1_on_mibi2315.blastn: 0
    psm-beta1_on_mibi2316.blastn: 0
    psm-beta1_on_mibi2317.blastn: 0
    psm-beta1_on_mibi2318.blastn: 0
    psm-beta1_on_mibi2319.blastn: 0
    psm-beta1_on_mibi2320.blastn: 0
    psm-beta1_on_mibi2321.blastn: 0
    psm-beta1_on_mibi2379.blastn: 0
    
    # -length(hlb.fasta)=993
    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
    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
    done
    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
    python3 analyze_blastn_res.py hlb_on_${sample}.blastn
    done
    hlb_on_mibi1435.blastn: 0
    hlb_on_mibi1436.blastn: 0
    hlb_on_mibi1437.blastn: 0
    hlb_on_mibi1438.blastn: 0
    hlb_on_mibi1439.blastn: 0
    hlb_on_mibi1440.blastn: 0
    hlb_on_mibi1441.blastn: 0
    hlb_on_mibi1442.blastn: 0
    hlb_on_mibi1443.blastn: 0
    hlb_on_mibi1444.blastn: 0
    hlb_on_mibi1445.blastn: 0
    hlb_on_mibi1446.blastn: 0
    hlb_on_mibi1447.blastn: 0
    hlb_on_mibi1448.blastn: 0
    hlb_on_mibi1449.blastn: 0
    hlb_on_mibi1450.blastn: 0
    hlb_on_mibi1451.blastn: 0
    hlb_on_mibi1452.blastn: 0
    hlb_on_mibi1453.blastn: 0
    hlb_on_mibi1454.blastn: 0
    hlb_on_mibi1455.blastn: 0
    hlb_on_mibi1456.blastn: 0
    hlb_on_mibi1457.blastn: 0
    hlb_on_mibi1458.blastn: 0
    hlb_on_mibi1459.blastn: 0
    hlb_on_mibi1460.blastn: 0
    hlb_on_mibi1461.blastn: 0
    hlb_on_mibi1462.blastn: 0
    hlb_on_mibi1463.blastn: 0
    hlb_on_mibi1464.blastn: 0
    hlb_on_mibi1465.blastn: 0
    hlb_on_mibi1466.blastn: 0
    hlb_on_mibi1467.blastn: 0
    hlb_on_mibi1468.blastn: 0
    hlb_on_mibi1469.blastn: 0
    hlb_on_mibi1471.blastn: 0
    hlb_on_mibi1473.blastn: 0
    hlb_on_mibi1474.blastn: 0
    hlb_on_mibi1475.blastn: 0
    hlb_on_mibi1476.blastn: 0
    hlb_on_mibi1477.blastn: 0
    hlb_on_mibi1478.blastn: 0
    hlb_on_mibi1479.blastn: 0
    hlb_on_mibi1480.blastn: 0
    hlb_on_mibi1481.blastn: 0
    hlb_on_mibi1482.blastn: 0
    hlb_on_mibi1483.blastn: 0
    hlb_on_mibi1484.blastn: 0
    hlb_on_mibi1485.blastn: 0
    hlb_on_mibi1486.blastn: 0
    hlb_on_mibi1487.blastn: 0
    hlb_on_mibi1488.blastn: 0
    hlb_on_mibi1489.blastn: 0
    hlb_on_mibi1490.blastn: 0
    hlb_on_mibi1491.blastn: 0
    hlb_on_mibi1492.blastn: 0
    hlb_on_mibi1493.blastn: 0
    hlb_on_mibi1494.blastn: 0
    hlb_on_mibi1495.blastn: 0
    hlb_on_mibi1496.blastn: 0
    hlb_on_mibi1497.blastn: 0
    hlb_on_mibi1498.blastn: 0
    hlb_on_mibi1499.blastn: 0
    hlb_on_mibi1500.blastn: 0
    hlb_on_mibi1501.blastn: 0
    hlb_on_mibi1502.blastn: 0
    hlb_on_mibi1503.blastn: 0
    hlb_on_mibi1504.blastn: 0
    hlb_on_mibi1505.blastn: 0
    hlb_on_mibi1506.blastn: 0
    hlb_on_mibi2312.blastn: 0
    hlb_on_mibi2313.blastn: 0
    hlb_on_mibi2314.blastn: 0
    hlb_on_mibi2315.blastn: 0
    hlb_on_mibi2316.blastn: 0
    hlb_on_mibi2317.blastn: 0
    hlb_on_mibi2318.blastn: 0
    hlb_on_mibi2319.blastn: 0
    hlb_on_mibi2320.blastn: 0
    hlb_on_mibi2321.blastn: 0
    hlb_on_mibi2379.blastn: 0
    
    ## -length(altE_revcomp.fasta)=4008
    #gene            complement(627656..631663)
    #                     /gene="atlE"
    #samtools faidx CP000029.fasta gi|57636010|gb|CP000029.1|
    samtools faidx CP000029.fasta "gi|57636010|gb|CP000029.1|":627656-631663 > atlE.fasta
    revcomp atlE.fasta > atlE_revcomp.fasta
    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
    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
    done
    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
    python3 analyze_blastn_res.py atlE_on_${sample}.blastn
    done
    atlE_on_mibi1435.blastn: 4008
    atlE_on_mibi1436.blastn: 4008
    atlE_on_mibi1437.blastn: 4465
    atlE_on_mibi1438.blastn: 4008
    atlE_on_mibi1439.blastn: 4008
    atlE_on_mibi1440.blastn: 4008
    atlE_on_mibi1441.blastn: 4450
    atlE_on_mibi1442.blastn: 4450
    atlE_on_mibi1443.blastn: 4008
    atlE_on_mibi1444.blastn: 4008
    atlE_on_mibi1445.blastn: 4008
    atlE_on_mibi1446.blastn: 4008
    atlE_on_mibi1447.blastn: 4008
    atlE_on_mibi1448.blastn: 4008
    atlE_on_mibi1449.blastn: 4008
    atlE_on_mibi1450.blastn: 4008
    atlE_on_mibi1451.blastn: 4008
    atlE_on_mibi1452.blastn: 4450
    atlE_on_mibi1453.blastn: 4008
    atlE_on_mibi1454.blastn: 4008
    atlE_on_mibi1455.blastn: 4008
    atlE_on_mibi1456.blastn: 4008
    atlE_on_mibi1457.blastn: 4008
    atlE_on_mibi1458.blastn: 4450
    atlE_on_mibi1459.blastn: 4008
    atlE_on_mibi1460.blastn: 4008
    atlE_on_mibi1461.blastn: 4008
    atlE_on_mibi1462.blastn: 4008
    atlE_on_mibi1463.blastn: 4450
    atlE_on_mibi1464.blastn: 4450
    atlE_on_mibi1465.blastn: 4008
    atlE_on_mibi1466.blastn: 4008
    atlE_on_mibi1467.blastn: 4450
    atlE_on_mibi1468.blastn: 4465
    atlE_on_mibi1469.blastn: 4465
    atlE_on_mibi1471.blastn: 4008
    atlE_on_mibi1473.blastn: 4008
    atlE_on_mibi1474.blastn: 4008
    atlE_on_mibi1475.blastn: 4008
    atlE_on_mibi1476.blastn: 4008
    atlE_on_mibi1477.blastn: 4008
    atlE_on_mibi1478.blastn: 4008
    atlE_on_mibi1479.blastn: 4008
    atlE_on_mibi1480.blastn: 4008
    atlE_on_mibi1481.blastn: 4008
    atlE_on_mibi1482.blastn: 4008
    atlE_on_mibi1483.blastn: 4450
    atlE_on_mibi1484.blastn: 4008
    atlE_on_mibi1485.blastn: 4008
    atlE_on_mibi1486.blastn: 4450
    atlE_on_mibi1487.blastn: 4008
    atlE_on_mibi1488.blastn: 4008
    atlE_on_mibi1489.blastn: 4450
    atlE_on_mibi1490.blastn: 4008
    atlE_on_mibi1491.blastn: 4008
    atlE_on_mibi1492.blastn: 4008
    atlE_on_mibi1493.blastn: 4450
    atlE_on_mibi1494.blastn: 4008
    atlE_on_mibi1495.blastn: 4008
    atlE_on_mibi1496.blastn: 4008
    atlE_on_mibi1497.blastn: 4008
    atlE_on_mibi1498.blastn: 4008
    atlE_on_mibi1499.blastn: 4008
    atlE_on_mibi1500.blastn: 4008
    atlE_on_mibi1501.blastn: 4008
    atlE_on_mibi1502.blastn: 4008
    atlE_on_mibi1503.blastn: 4008
    atlE_on_mibi1504.blastn: 4450
    atlE_on_mibi1505.blastn: 4008
    atlE_on_mibi1506.blastn: 4008
    atlE_on_mibi2312.blastn: 4008
    atlE_on_mibi2313.blastn: 4008
    atlE_on_mibi2314.blastn: 4008
    atlE_on_mibi2315.blastn: 4008
    atlE_on_mibi2316.blastn: 4008
    atlE_on_mibi2317.blastn: 4008
    atlE_on_mibi2318.blastn: 4008
    atlE_on_mibi2319.blastn: 4008
    atlE_on_mibi2320.blastn: 4008
    atlE_on_mibi2321.blastn: 4008
    atlE_on_mibi2379.blastn: 4008
    
    # -length(sdrG)=2796
    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
    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
    done
    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
    python3 analyze_blastn_res.py sdrG_on_${sample}.blastn
    done
    sdrG_on_mibi1435.blastn: 2973
    sdrG_on_mibi1436.blastn: 2967
    sdrG_on_mibi1437.blastn: 2821
    sdrG_on_mibi1438.blastn: 2796
    sdrG_on_mibi1439.blastn: 3155
    sdrG_on_mibi1440.blastn: 2967
    sdrG_on_mibi1441.blastn: 2797
    sdrG_on_mibi1442.blastn: 2801
    sdrG_on_mibi1443.blastn: 2966
    sdrG_on_mibi1444.blastn: 2796
    sdrG_on_mibi1445.blastn: 3158
    sdrG_on_mibi1446.blastn: 3155
    sdrG_on_mibi1447.blastn: 2966
    sdrG_on_mibi1448.blastn: 2797
    sdrG_on_mibi1449.blastn: 2712
    sdrG_on_mibi1450.blastn: 2794
    sdrG_on_mibi1451.blastn: 2946
    sdrG_on_mibi1452.blastn: 3166
    sdrG_on_mibi1453.blastn: 2970
    sdrG_on_mibi1454.blastn: 2976
    sdrG_on_mibi1455.blastn: 2797
    sdrG_on_mibi1456.blastn: 2967
    sdrG_on_mibi1457.blastn: 2963
    sdrG_on_mibi1458.blastn: 2794
    sdrG_on_mibi1459.blastn: 3153
    sdrG_on_mibi1460.blastn: 2566
    sdrG_on_mibi1461.blastn: 2500
    sdrG_on_mibi1462.blastn: 2966
    sdrG_on_mibi1463.blastn: 2971
    sdrG_on_mibi1464.blastn: 2530
    sdrG_on_mibi1465.blastn: 2981
    sdrG_on_mibi1466.blastn: 1547 *
    sdrG_on_mibi1467.blastn: 2794
    sdrG_on_mibi1468.blastn: 2967
    sdrG_on_mibi1469.blastn: 2967
    sdrG_on_mibi1471.blastn: 2796
    sdrG_on_mibi1473.blastn: 2976
    sdrG_on_mibi1474.blastn: 2797
    sdrG_on_mibi1475.blastn: 2981
    sdrG_on_mibi1476.blastn: 2794
    sdrG_on_mibi1477.blastn: 2967
    sdrG_on_mibi1478.blastn: 1511 *
    sdrG_on_mibi1479.blastn: 2966
    sdrG_on_mibi1480.blastn: 2976
    sdrG_on_mibi1481.blastn: 2797
    sdrG_on_mibi1482.blastn: 2797
    sdrG_on_mibi1483.blastn: 2797
    sdrG_on_mibi1484.blastn: 2976
    sdrG_on_mibi1485.blastn: 3001
    sdrG_on_mibi1486.blastn: 2797
    sdrG_on_mibi1487.blastn: 2976
    sdrG_on_mibi1488.blastn: 2963
    sdrG_on_mibi1489.blastn: 2797
    sdrG_on_mibi1490.blastn: 2981
    sdrG_on_mibi1491.blastn: 3155
    sdrG_on_mibi1492.blastn: 2982
    sdrG_on_mibi1493.blastn: 2904
    sdrG_on_mibi1494.blastn: 2980
    sdrG_on_mibi1495.blastn: 2976
    sdrG_on_mibi1496.blastn: 2994
    sdrG_on_mibi1497.blastn: 2797
    sdrG_on_mibi1498.blastn: 2967
    sdrG_on_mibi1499.blastn: 2976
    sdrG_on_mibi1500.blastn: 2797
    sdrG_on_mibi1501.blastn: 2797
    sdrG_on_mibi1502.blastn: 2976
    sdrG_on_mibi1503.blastn: 2976
    sdrG_on_mibi1504.blastn: 2634
    sdrG_on_mibi1505.blastn: 2970
    sdrG_on_mibi1506.blastn: 2985
    sdrG_on_mibi2312.blastn: 2866
    sdrG_on_mibi2313.blastn: 2794
    sdrG_on_mibi2314.blastn: 3171
    sdrG_on_mibi2315.blastn: 2797
    sdrG_on_mibi2316.blastn: 3158
    sdrG_on_mibi2317.blastn: 2975
    sdrG_on_mibi2318.blastn: 2976
    sdrG_on_mibi2319.blastn: 2613
    sdrG_on_mibi2320.blastn: 2972
    sdrG_on_mibi2321.blastn: 2794
    sdrG_on_mibi2379.blastn: 2975
    
    ##length(sdrH)=1446
    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
    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
    done
    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
    python3 analyze_blastn_res.py sdrH_on_${sample}.blastn
    done
    sdrH_on_mibi1435.blastn: 1647
    sdrH_on_mibi1436.blastn: 1683
    sdrH_on_mibi1437.blastn: 1482
    sdrH_on_mibi1438.blastn: 1608
    sdrH_on_mibi1439.blastn: 1739
    sdrH_on_mibi1440.blastn: 1644
    sdrH_on_mibi1441.blastn: 1446
    sdrH_on_mibi1442.blastn: 1482
    sdrH_on_mibi1443.blastn: 1683
    sdrH_on_mibi1444.blastn: 1683
    sdrH_on_mibi1445.blastn: 1482
    sdrH_on_mibi1446.blastn: 1482
    sdrH_on_mibi1447.blastn: 1482
    sdrH_on_mibi1448.blastn: 1446
    sdrH_on_mibi1449.blastn: 1450
    sdrH_on_mibi1450.blastn: 1446
    sdrH_on_mibi1451.blastn: 1487
    sdrH_on_mibi1452.blastn: 1446
    sdrH_on_mibi1453.blastn: 1464
    sdrH_on_mibi1454.blastn: 1647
    sdrH_on_mibi1455.blastn: 1644
    sdrH_on_mibi1456.blastn: 1647
    sdrH_on_mibi1457.blastn: 1572
    sdrH_on_mibi1458.blastn: 1632
    sdrH_on_mibi1459.blastn: 1647
    sdrH_on_mibi1460.blastn: 1482
    sdrH_on_mibi1461.blastn: 1647
    sdrH_on_mibi1462.blastn: 1683
    sdrH_on_mibi1463.blastn: 1647
    sdrH_on_mibi1464.blastn: 1739
    sdrH_on_mibi1465.blastn: 1464
    sdrH_on_mibi1466.blastn: 1305
    sdrH_on_mibi1467.blastn: 1482
    sdrH_on_mibi1468.blastn: 1559
    sdrH_on_mibi1469.blastn: 1556
    sdrH_on_mibi1471.blastn: 1572
    sdrH_on_mibi1473.blastn: 1482
    sdrH_on_mibi1474.blastn: 1446
    sdrH_on_mibi1475.blastn: 1482
    sdrH_on_mibi1476.blastn: 1458
    sdrH_on_mibi1477.blastn: 1647
    sdrH_on_mibi1478.blastn: 710 *
    sdrH_on_mibi1479.blastn: 1482
    sdrH_on_mibi1480.blastn: 1647
    sdrH_on_mibi1481.blastn: 1412
    sdrH_on_mibi1482.blastn: 1647
    sdrH_on_mibi1483.blastn: 1647
    sdrH_on_mibi1484.blastn: 1448
    sdrH_on_mibi1485.blastn: 1647
    sdrH_on_mibi1486.blastn: 1827
    sdrH_on_mibi1487.blastn: 1647
    sdrH_on_mibi1488.blastn: 1683
    sdrH_on_mibi1489.blastn: 1739
    sdrH_on_mibi1490.blastn: 1482
    sdrH_on_mibi1491.blastn: 1482
    sdrH_on_mibi1492.blastn: 1482
    sdrH_on_mibi1493.blastn: 1440
    sdrH_on_mibi1494.blastn: 1458
    sdrH_on_mibi1495.blastn: 1482
    sdrH_on_mibi1496.blastn: 1644
    sdrH_on_mibi1497.blastn: 1736
    sdrH_on_mibi1498.blastn: 1647
    sdrH_on_mibi1499.blastn: 1482
    sdrH_on_mibi1500.blastn: 1683
    sdrH_on_mibi1501.blastn: 1647
    sdrH_on_mibi1502.blastn: 1647
    sdrH_on_mibi1503.blastn: 1745
    sdrH_on_mibi1504.blastn: 1683
    sdrH_on_mibi1505.blastn: 1736
    sdrH_on_mibi1506.blastn: 1683
    sdrH_on_mibi2312.blastn: 1556
    sdrH_on_mibi2313.blastn: 1464
    sdrH_on_mibi2314.blastn: 1464
    sdrH_on_mibi2315.blastn: 1683
    sdrH_on_mibi2316.blastn: 1482
    sdrH_on_mibi2317.blastn: 1464
    sdrH_on_mibi2318.blastn: 1647
    sdrH_on_mibi2319.blastn: 1644
    sdrH_on_mibi2320.blastn: 1464
    sdrH_on_mibi2321.blastn: 1464
    sdrH_on_mibi2379.blastn: 1647
    
    # -length(ebh_revcomp.fasta)=30450
    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
    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
    done
    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
    python3 analyze_blastn_res.py ebh_on_${sample}.blastn
    done
    
    ebh_on_mibi1435.blastn: 30450
    ebh_on_mibi1436.blastn: 30450
    ebh_on_mibi1437.blastn: 29490
    ebh_on_mibi1438.blastn: 25428
    ebh_on_mibi1439.blastn: 30452
    ebh_on_mibi1440.blastn: 11933
    ebh_on_mibi1441.blastn: 30450
    ebh_on_mibi1442.blastn: 30463
    ebh_on_mibi1443.blastn: 30450
    ebh_on_mibi1444.blastn: 30450
    ebh_on_mibi1445.blastn: 30450
    ebh_on_mibi1446.blastn: 30450
    ebh_on_mibi1447.blastn: 30450
    ebh_on_mibi1448.blastn: 30450
    ebh_on_mibi1449.blastn: 30450
    ebh_on_mibi1450.blastn: 30450
    ebh_on_mibi1451.blastn: 30450
    ebh_on_mibi1452.blastn: 21401
    ebh_on_mibi1453.blastn: 30450
    ebh_on_mibi1454.blastn: 11933
    ebh_on_mibi1455.blastn: 30450
    ebh_on_mibi1456.blastn: 11933
    ebh_on_mibi1457.blastn: 30450
    ebh_on_mibi1458.blastn: 29955
    ebh_on_mibi1459.blastn: 11933
    ebh_on_mibi1460.blastn: 30450
    ebh_on_mibi1461.blastn: 11933
    ebh_on_mibi1462.blastn: 30450
    ebh_on_mibi1463.blastn: 20602
    ebh_on_mibi1464.blastn: 30450
    ebh_on_mibi1465.blastn: 30450
    ebh_on_mibi1466.blastn: 14964
    ebh_on_mibi1467.blastn: 30463
    ebh_on_mibi1468.blastn: 30450
    ebh_on_mibi1469.blastn: 30450
    ebh_on_mibi1471.blastn: 25428
    ebh_on_mibi1473.blastn: 30450
    ebh_on_mibi1474.blastn: 30450
    ebh_on_mibi1475.blastn: 30450
    ebh_on_mibi1476.blastn: 30450
    ebh_on_mibi1477.blastn: 30384
    ebh_on_mibi1478.blastn: 11933
    ebh_on_mibi1479.blastn: 30450
    ebh_on_mibi1480.blastn: 11933
    ebh_on_mibi1481.blastn: 25694
    ebh_on_mibi1482.blastn: 30450
    ebh_on_mibi1483.blastn: 30450
    ebh_on_mibi1484.blastn: 30450
    ebh_on_mibi1485.blastn: 11933
    ebh_on_mibi1486.blastn: 30450
    ebh_on_mibi1487.blastn: 11933
    ebh_on_mibi1488.blastn: 30450
    ebh_on_mibi1489.blastn: 30450
    ebh_on_mibi1490.blastn: 30450
    ebh_on_mibi1491.blastn: 30450
    ebh_on_mibi1492.blastn: 30450
    ebh_on_mibi1493.blastn: 30465
    ebh_on_mibi1494.blastn: 30450
    ebh_on_mibi1495.blastn: 30450
    ebh_on_mibi1496.blastn: 11933
    ebh_on_mibi1497.blastn: 30450
    ebh_on_mibi1498.blastn: 11933
    ebh_on_mibi1499.blastn: 30450
    ebh_on_mibi1500.blastn: 30450
    ebh_on_mibi1501.blastn: 30450
    ebh_on_mibi1502.blastn: 11933
    ebh_on_mibi1503.blastn: 30450
    ebh_on_mibi1504.blastn: 30450
    ebh_on_mibi1505.blastn: 30450
    ebh_on_mibi1506.blastn: 30450
    ebh_on_mibi2312.blastn: 30450
    ebh_on_mibi2313.blastn: 30450
    ebh_on_mibi2314.blastn: 30450
    ebh_on_mibi2315.blastn: 30461
    ebh_on_mibi2316.blastn: 30450
    ebh_on_mibi2317.blastn: 30450
    ebh_on_mibi2318.blastn: 11933
    ebh_on_mibi2319.blastn: 11933
    ebh_on_mibi2320.blastn: 30110
    ebh_on_mibi2321.blastn: 30450
    ebh_on_mibi2379.blastn: 30450
    
    #For gene: ebpS, tagB, capC, sepA, dltA, fmtC
    # -length(SE0760)=1383
    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
    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
    done
    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
    python3 analyze_blastn_res.py ebpS_on_${sample}.blastn
    done
    ebpS_on_mibi1435.blastn: 1383
    ebpS_on_mibi1436.blastn: 1383
    ebpS_on_mibi1437.blastn: 1383
    ebpS_on_mibi1438.blastn: 1383
    ebpS_on_mibi1439.blastn: 1383
    ebpS_on_mibi1440.blastn: 1383
    ebpS_on_mibi1441.blastn: 1383
    ebpS_on_mibi1442.blastn: 1408
    ebpS_on_mibi1443.blastn: 1383
    ebpS_on_mibi1444.blastn: 1383
    ebpS_on_mibi1445.blastn: 1383
    ebpS_on_mibi1446.blastn: 1383
    ebpS_on_mibi1447.blastn: 1383
    ebpS_on_mibi1448.blastn: 1383
    ebpS_on_mibi1449.blastn: 1383
    ebpS_on_mibi1450.blastn: 1383
    ebpS_on_mibi1451.blastn: 1383
    ebpS_on_mibi1452.blastn: 1408
    ebpS_on_mibi1453.blastn: 1383
    ebpS_on_mibi1454.blastn: 1383
    ebpS_on_mibi1455.blastn: 1383
    ebpS_on_mibi1456.blastn: 1383
    ebpS_on_mibi1457.blastn: 1383
    ebpS_on_mibi1458.blastn: 1408
    ebpS_on_mibi1459.blastn: 1383
    ebpS_on_mibi1460.blastn: 1383
    ebpS_on_mibi1461.blastn: 1383
    ebpS_on_mibi1462.blastn: 1383
    ebpS_on_mibi1463.blastn: 1383
    ebpS_on_mibi1464.blastn: 1392
    ebpS_on_mibi1465.blastn: 1383
    ebpS_on_mibi1466.blastn: 1383
    ebpS_on_mibi1467.blastn: 1420
    ebpS_on_mibi1468.blastn: 1383
    ebpS_on_mibi1469.blastn: 1383
    ebpS_on_mibi1471.blastn: 1383
    ebpS_on_mibi1473.blastn: 1383
    ebpS_on_mibi1474.blastn: 1383
    ebpS_on_mibi1475.blastn: 1383
    ebpS_on_mibi1476.blastn: 1383
    ebpS_on_mibi1477.blastn: 1275
    ebpS_on_mibi1478.blastn: 1383
    ebpS_on_mibi1479.blastn: 1383
    ebpS_on_mibi1480.blastn: 1383
    ebpS_on_mibi1481.blastn: 1383
    ebpS_on_mibi1482.blastn: 1383
    ebpS_on_mibi1483.blastn: 1383
    ebpS_on_mibi1484.blastn: 1383
    ebpS_on_mibi1485.blastn: 1383
    ebpS_on_mibi1486.blastn: 1383
    ebpS_on_mibi1487.blastn: 1383
    ebpS_on_mibi1488.blastn: 1383
    ebpS_on_mibi1489.blastn: 1383
    ebpS_on_mibi1490.blastn: 1383
    ebpS_on_mibi1491.blastn: 1383
    ebpS_on_mibi1492.blastn: 1383
    ebpS_on_mibi1493.blastn: 1420
    ebpS_on_mibi1494.blastn: 1383
    ebpS_on_mibi1495.blastn: 1383
    ebpS_on_mibi1496.blastn: 1383
    ebpS_on_mibi1497.blastn: 1383
    ebpS_on_mibi1498.blastn: 1383
    ebpS_on_mibi1499.blastn: 1383
    ebpS_on_mibi1500.blastn: 1383
    ebpS_on_mibi1501.blastn: 1383
    ebpS_on_mibi1502.blastn: 1383
    ebpS_on_mibi1503.blastn: 1383
    ebpS_on_mibi1504.blastn: 1408
    ebpS_on_mibi1505.blastn: 1383
    ebpS_on_mibi1506.blastn: 1383
    ebpS_on_mibi2312.blastn: 1383
    ebpS_on_mibi2313.blastn: 1383
    ebpS_on_mibi2314.blastn: 1383
    ebpS_on_mibi2315.blastn: 1383
    ebpS_on_mibi2316.blastn: 1383
    ebpS_on_mibi2317.blastn: 1383
    ebpS_on_mibi2318.blastn: 1383
    ebpS_on_mibi2319.blastn: 1383
    ebpS_on_mibi2320.blastn: 1383
    ebpS_on_mibi2321.blastn: 1383
    ebpS_on_mibi2379.blastn: 1383
    
    # -length(tagB)=1680
    #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
    samtools faidx mibi1435.fna contig_2:146190-147869 > tagB_mibi1435.fasta
    revcomp tagB_mibi1435.fasta > tagB_mibi1435_revcomp.fasta
    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
    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
    done
    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
    python3 analyze_blastn_res.py tagB_on_${sample}.blastn
    done
    tagB_on_mibi1435.blastn: 1680
    tagB_on_mibi1436.blastn: 1680
    tagB_on_mibi1437.blastn: 1680
    tagB_on_mibi1438.blastn: 1680
    tagB_on_mibi1439.blastn: 1680
    tagB_on_mibi1440.blastn: 1680
    tagB_on_mibi1441.blastn: 1680
    tagB_on_mibi1442.blastn: 1680
    tagB_on_mibi1443.blastn: 1680
    tagB_on_mibi1444.blastn: 1680
    tagB_on_mibi1445.blastn: 1680
    tagB_on_mibi1446.blastn: 1680
    tagB_on_mibi1447.blastn: 1680
    tagB_on_mibi1448.blastn: 1680
    tagB_on_mibi1449.blastn: 1680
    tagB_on_mibi1450.blastn: 1680
    tagB_on_mibi1451.blastn: 1680
    tagB_on_mibi1452.blastn: 1680
    tagB_on_mibi1453.blastn: 1680
    tagB_on_mibi1454.blastn: 1680
    tagB_on_mibi1455.blastn: 1680
    tagB_on_mibi1456.blastn: 1680
    tagB_on_mibi1457.blastn: 1680
    tagB_on_mibi1458.blastn: 1680
    tagB_on_mibi1459.blastn: 1680
    tagB_on_mibi1460.blastn: 1680
    tagB_on_mibi1461.blastn: 1680
    tagB_on_mibi1462.blastn: 1680
    tagB_on_mibi1463.blastn: 1680
    tagB_on_mibi1464.blastn: 1680
    tagB_on_mibi1465.blastn: 1680
    tagB_on_mibi1466.blastn: 1680
    tagB_on_mibi1467.blastn: 1680
    tagB_on_mibi1468.blastn: 1680
    tagB_on_mibi1469.blastn: 1680
    tagB_on_mibi1471.blastn: 1680
    tagB_on_mibi1473.blastn: 1680
    tagB_on_mibi1474.blastn: 1680
    tagB_on_mibi1475.blastn: 1680
    tagB_on_mibi1476.blastn: 1680
    tagB_on_mibi1477.blastn: 1680
    tagB_on_mibi1478.blastn: 1680
    tagB_on_mibi1479.blastn: 1680
    tagB_on_mibi1480.blastn: 1680
    tagB_on_mibi1481.blastn: 1680
    tagB_on_mibi1482.blastn: 1680
    tagB_on_mibi1483.blastn: 1680
    tagB_on_mibi1484.blastn: 1680
    tagB_on_mibi1485.blastn: 1680
    tagB_on_mibi1486.blastn: 1680
    tagB_on_mibi1487.blastn: 1680
    tagB_on_mibi1488.blastn: 1680
    tagB_on_mibi1489.blastn: 1680
    tagB_on_mibi1490.blastn: 1680
    tagB_on_mibi1491.blastn: 1680
    tagB_on_mibi1492.blastn: 1680
    tagB_on_mibi1493.blastn: 1680
    tagB_on_mibi1494.blastn: 1680
    tagB_on_mibi1495.blastn: 1680
    tagB_on_mibi1496.blastn: 1680
    tagB_on_mibi1497.blastn: 1680
    tagB_on_mibi1498.blastn: 1680
    tagB_on_mibi1499.blastn: 1680
    tagB_on_mibi1500.blastn: 1680
    tagB_on_mibi1501.blastn: 1680
    tagB_on_mibi1502.blastn: 1680
    tagB_on_mibi1503.blastn: 1680
    tagB_on_mibi1504.blastn: 1680
    tagB_on_mibi1505.blastn: 1680
    tagB_on_mibi1506.blastn: 1680
    tagB_on_mibi2312.blastn: 1680
    tagB_on_mibi2313.blastn: 1680
    tagB_on_mibi2314.blastn: 1680
    tagB_on_mibi2315.blastn: 1680
    tagB_on_mibi2316.blastn: 1680
    tagB_on_mibi2317.blastn: 1680
    tagB_on_mibi2318.blastn: 1680
    tagB_on_mibi2319.blastn: 1680
    tagB_on_mibi2320.blastn: 1680
    tagB_on_mibi2321.blastn: 1680
    tagB_on_mibi2379.blastn: 1680
    
    # -length(capC)=450
    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
    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
    done
    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
    python3 analyze_blastn_res.py capC_on_${sample}.blastn
    done
    capC_on_mibi1435.blastn: 0
    capC_on_mibi1436.blastn: 0
    capC_on_mibi1437.blastn: 0
    capC_on_mibi1438.blastn: 0
    capC_on_mibi1439.blastn: 0
    capC_on_mibi1440.blastn: 0
    capC_on_mibi1441.blastn: 0
    capC_on_mibi1442.blastn: 0
    capC_on_mibi1443.blastn: 0
    capC_on_mibi1444.blastn: 0
    capC_on_mibi1445.blastn: 0
    capC_on_mibi1446.blastn: 0
    capC_on_mibi1447.blastn: 0
    capC_on_mibi1448.blastn: 0
    capC_on_mibi1449.blastn: 0
    capC_on_mibi1450.blastn: 0
    capC_on_mibi1451.blastn: 0
    capC_on_mibi1452.blastn: 0
    capC_on_mibi1453.blastn: 0
    capC_on_mibi1454.blastn: 0
    capC_on_mibi1455.blastn: 0
    capC_on_mibi1456.blastn: 0
    capC_on_mibi1457.blastn: 0
    capC_on_mibi1458.blastn: 0
    capC_on_mibi1459.blastn: 0
    capC_on_mibi1460.blastn: 0
    capC_on_mibi1461.blastn: 0
    capC_on_mibi1462.blastn: 0
    capC_on_mibi1463.blastn: 0
    capC_on_mibi1464.blastn: 0
    capC_on_mibi1465.blastn: 0
    capC_on_mibi1466.blastn: 0
    capC_on_mibi1467.blastn: 0
    capC_on_mibi1468.blastn: 0
    capC_on_mibi1469.blastn: 0
    capC_on_mibi1471.blastn: 0
    capC_on_mibi1473.blastn: 0
    capC_on_mibi1474.blastn: 0
    capC_on_mibi1475.blastn: 0
    capC_on_mibi1476.blastn: 0
    capC_on_mibi1477.blastn: 0
    capC_on_mibi1478.blastn: 0
    capC_on_mibi1479.blastn: 0
    capC_on_mibi1480.blastn: 0
    capC_on_mibi1481.blastn: 0
    capC_on_mibi1482.blastn: 0
    capC_on_mibi1483.blastn: 0
    capC_on_mibi1484.blastn: 0
    capC_on_mibi1485.blastn: 0
    capC_on_mibi1486.blastn: 0
    capC_on_mibi1487.blastn: 0
    capC_on_mibi1488.blastn: 0
    capC_on_mibi1489.blastn: 0
    capC_on_mibi1490.blastn: 0
    capC_on_mibi1491.blastn: 0
    capC_on_mibi1492.blastn: 0
    capC_on_mibi1493.blastn: 0
    capC_on_mibi1494.blastn: 0
    capC_on_mibi1495.blastn: 0
    capC_on_mibi1496.blastn: 0
    capC_on_mibi1497.blastn: 0
    capC_on_mibi1498.blastn: 0
    capC_on_mibi1499.blastn: 0
    capC_on_mibi1500.blastn: 0
    capC_on_mibi1501.blastn: 0
    capC_on_mibi1502.blastn: 0
    capC_on_mibi1503.blastn: 0
    capC_on_mibi1504.blastn: 0
    capC_on_mibi1505.blastn: 0
    capC_on_mibi1506.blastn: 0
    capC_on_mibi2312.blastn: 0
    capC_on_mibi2313.blastn: 0
    capC_on_mibi2314.blastn: 0
    capC_on_mibi2315.blastn: 0
    capC_on_mibi2316.blastn: 0
    capC_on_mibi2317.blastn: 0
    capC_on_mibi2318.blastn: 0
    capC_on_mibi2319.blastn: 0
    capC_on_mibi2320.blastn: 0
    capC_on_mibi2321.blastn: 0
    capC_on_mibi2379.blastn: 0
    
    # -length(sepA_mibi1435.fasta)=1524
    #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
    samtools faidx mibi1435.fna contig_7:52151-53674 > sepA_mibi1435.fasta
    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
    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
    done
    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
    python3 analyze_blastn_res.py sepA_on_${sample}.blastn
    done
    sepA_on_mibi1435.blastn: 1524
    sepA_on_mibi1436.blastn: 1524
    sepA_on_mibi1437.blastn: 1523
    sepA_on_mibi1438.blastn: 1524
    sepA_on_mibi1439.blastn: 1523
    sepA_on_mibi1440.blastn: 1523
    sepA_on_mibi1441.blastn: 1523
    sepA_on_mibi1442.blastn: 1523
    sepA_on_mibi1443.blastn: 1523
    sepA_on_mibi1444.blastn: 1523
    sepA_on_mibi1445.blastn: 1523
    sepA_on_mibi1446.blastn: 1523
    sepA_on_mibi1447.blastn: 1523
    sepA_on_mibi1448.blastn: 1524
    sepA_on_mibi1449.blastn: 1523
    sepA_on_mibi1450.blastn: 1523
    sepA_on_mibi1451.blastn: 1523
    sepA_on_mibi1452.blastn: 1523
    sepA_on_mibi1453.blastn: 1523
    sepA_on_mibi1454.blastn: 1523
    sepA_on_mibi1455.blastn: 1524
    sepA_on_mibi1456.blastn: 1523
    sepA_on_mibi1457.blastn: 1523
    sepA_on_mibi1458.blastn: 1523
    sepA_on_mibi1459.blastn: 1523
    sepA_on_mibi1460.blastn: 1523
    sepA_on_mibi1461.blastn: 1523
    sepA_on_mibi1462.blastn: 1523
    sepA_on_mibi1463.blastn: 1523
    sepA_on_mibi1464.blastn: 1523
    sepA_on_mibi1465.blastn: 1523
    sepA_on_mibi1466.blastn: 1523
    sepA_on_mibi1467.blastn: 1524
    sepA_on_mibi1468.blastn: 1523
    sepA_on_mibi1469.blastn: 1523
    sepA_on_mibi1471.blastn: 1524
    sepA_on_mibi1473.blastn: 1523
    sepA_on_mibi1474.blastn: 1524
    sepA_on_mibi1475.blastn: 1523
    sepA_on_mibi1476.blastn: 1523
    sepA_on_mibi1477.blastn: 1524
    sepA_on_mibi1478.blastn: 1523
    sepA_on_mibi1479.blastn: 1523
    sepA_on_mibi1480.blastn: 1523
    sepA_on_mibi1481.blastn: 1524
    sepA_on_mibi1482.blastn: 1524
    sepA_on_mibi1483.blastn: 1523
    sepA_on_mibi1484.blastn: 1523
    sepA_on_mibi1485.blastn: 1523
    sepA_on_mibi1486.blastn: 1523
    sepA_on_mibi1487.blastn: 1523
    sepA_on_mibi1488.blastn: 1523
    sepA_on_mibi1489.blastn: 1523
    sepA_on_mibi1490.blastn: 1523
    sepA_on_mibi1491.blastn: 1523
    sepA_on_mibi1492.blastn: 1523
    sepA_on_mibi1493.blastn: 1523
    sepA_on_mibi1494.blastn: 1523
    sepA_on_mibi1495.blastn: 1523
    sepA_on_mibi1496.blastn: 1523
    sepA_on_mibi1497.blastn: 1523
    sepA_on_mibi1498.blastn: 1523
    sepA_on_mibi1499.blastn: 1523
    sepA_on_mibi1500.blastn: 1523
    sepA_on_mibi1501.blastn: 1523
    sepA_on_mibi1502.blastn: 1523
    sepA_on_mibi1503.blastn: 1523
    sepA_on_mibi1504.blastn: 1523
    sepA_on_mibi1505.blastn: 1523
    sepA_on_mibi1506.blastn: 1523
    sepA_on_mibi2312.blastn: 1523
    sepA_on_mibi2313.blastn: 1523
    sepA_on_mibi2314.blastn: 1523
    sepA_on_mibi2315.blastn: 1523
    sepA_on_mibi2316.blastn: 1523
    sepA_on_mibi2317.blastn: 1523
    sepA_on_mibi2318.blastn: 1523
    sepA_on_mibi2319.blastn: 1523
    sepA_on_mibi2320.blastn: 1523
    sepA_on_mibi2321.blastn: 1523
    sepA_on_mibi2379.blastn: 1523
    
    # -length(dltA.fasta)=1458
    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
    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
    done
    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
    python3 analyze_blastn_res.py dltA_on_${sample}.blastn
    done
    dltA_on_mibi1435.blastn: 1458
    dltA_on_mibi1436.blastn: 1458
    dltA_on_mibi1437.blastn: 1458
    dltA_on_mibi1438.blastn: 1458
    dltA_on_mibi1439.blastn: 1458
    dltA_on_mibi1440.blastn: 1458
    dltA_on_mibi1441.blastn: 1458
    dltA_on_mibi1442.blastn: 1458
    dltA_on_mibi1443.blastn: 1458
    dltA_on_mibi1444.blastn: 1458
    dltA_on_mibi1445.blastn: 1458
    dltA_on_mibi1446.blastn: 1458
    dltA_on_mibi1447.blastn: 1458
    dltA_on_mibi1448.blastn: 1464
    dltA_on_mibi1449.blastn: 1458
    dltA_on_mibi1450.blastn: 1458
    dltA_on_mibi1451.blastn: 1458
    dltA_on_mibi1452.blastn: 1458
    dltA_on_mibi1453.blastn: 1458
    dltA_on_mibi1454.blastn: 1458
    dltA_on_mibi1455.blastn: 1458
    dltA_on_mibi1456.blastn: 1458
    dltA_on_mibi1457.blastn: 1458
    dltA_on_mibi1458.blastn: 1458
    dltA_on_mibi1459.blastn: 1458
    dltA_on_mibi1460.blastn: 1458
    dltA_on_mibi1461.blastn: 1458
    dltA_on_mibi1462.blastn: 1458
    dltA_on_mibi1463.blastn: 1458
    dltA_on_mibi1464.blastn: 1458
    dltA_on_mibi1465.blastn: 1458
    dltA_on_mibi1466.blastn: 1458
    dltA_on_mibi1467.blastn: 1458
    dltA_on_mibi1468.blastn: 1458
    dltA_on_mibi1469.blastn: 1458
    dltA_on_mibi1471.blastn: 1458
    dltA_on_mibi1473.blastn: 1458
    dltA_on_mibi1474.blastn: 1458
    dltA_on_mibi1475.blastn: 1458
    dltA_on_mibi1476.blastn: 1458
    dltA_on_mibi1477.blastn: 1458
    dltA_on_mibi1478.blastn: 1458
    dltA_on_mibi1479.blastn: 1458
    dltA_on_mibi1480.blastn: 1458
    dltA_on_mibi1481.blastn: 1458
    dltA_on_mibi1482.blastn: 1458
    dltA_on_mibi1483.blastn: 1458
    dltA_on_mibi1484.blastn: 1458
    dltA_on_mibi1485.blastn: 1458
    dltA_on_mibi1486.blastn: 1458
    dltA_on_mibi1487.blastn: 1458
    dltA_on_mibi1488.blastn: 1458
    dltA_on_mibi1489.blastn: 1458
    dltA_on_mibi1490.blastn: 1458
    dltA_on_mibi1491.blastn: 1458
    dltA_on_mibi1492.blastn: 1458
    dltA_on_mibi1493.blastn: 1458
    dltA_on_mibi1494.blastn: 1458
    dltA_on_mibi1495.blastn: 1458
    dltA_on_mibi1496.blastn: 1458
    dltA_on_mibi1497.blastn: 1458
    dltA_on_mibi1498.blastn: 1458
    dltA_on_mibi1499.blastn: 1458
    dltA_on_mibi1500.blastn: 1458
    dltA_on_mibi1501.blastn: 1458
    dltA_on_mibi1502.blastn: 1458
    dltA_on_mibi1503.blastn: 1458
    dltA_on_mibi1504.blastn: 1458
    dltA_on_mibi1505.blastn: 1458
    dltA_on_mibi1506.blastn: 1458
    dltA_on_mibi2312.blastn: 1458
    dltA_on_mibi2313.blastn: 1458
    dltA_on_mibi2314.blastn: 1458
    dltA_on_mibi2315.blastn: 1458
    dltA_on_mibi2316.blastn: 1458
    dltA_on_mibi2317.blastn: 1458
    dltA_on_mibi2318.blastn: 1458
    dltA_on_mibi2319.blastn: 1458
    dltA_on_mibi2320.blastn: 1458
    dltA_on_mibi2321.blastn: 1458
    dltA_on_mibi2379.blastn: 1458
    
    # -length(fmtC.fasta)=2523
    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
    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
    done
    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
    python3 analyze_blastn_res.py fmtC_on_${sample}.blastn
    done
    fmtC_on_mibi1435.blastn: 0
    fmtC_on_mibi1436.blastn: 0
    fmtC_on_mibi1437.blastn: 0
    fmtC_on_mibi1438.blastn: 0
    fmtC_on_mibi1439.blastn: 0
    fmtC_on_mibi1440.blastn: 0
    fmtC_on_mibi1441.blastn: 0
    fmtC_on_mibi1442.blastn: 0
    fmtC_on_mibi1443.blastn: 0
    fmtC_on_mibi1444.blastn: 0
    fmtC_on_mibi1445.blastn: 0
    fmtC_on_mibi1446.blastn: 0
    fmtC_on_mibi1447.blastn: 0
    fmtC_on_mibi1448.blastn: 0
    fmtC_on_mibi1449.blastn: 0
    fmtC_on_mibi1450.blastn: 0
    fmtC_on_mibi1451.blastn: 0
    fmtC_on_mibi1452.blastn: 0
    fmtC_on_mibi1453.blastn: 0
    fmtC_on_mibi1454.blastn: 0
    fmtC_on_mibi1455.blastn: 0
    fmtC_on_mibi1456.blastn: 0
    fmtC_on_mibi1457.blastn: 0
    fmtC_on_mibi1458.blastn: 0
    fmtC_on_mibi1459.blastn: 0
    fmtC_on_mibi1460.blastn: 0
    fmtC_on_mibi1461.blastn: 0
    fmtC_on_mibi1462.blastn: 0
    fmtC_on_mibi1463.blastn: 0
    fmtC_on_mibi1464.blastn: 0
    fmtC_on_mibi1465.blastn: 0
    fmtC_on_mibi1466.blastn: 0
    fmtC_on_mibi1467.blastn: 0
    fmtC_on_mibi1468.blastn: 0
    fmtC_on_mibi1469.blastn: 0
    fmtC_on_mibi1471.blastn: 0
    fmtC_on_mibi1473.blastn: 0
    fmtC_on_mibi1474.blastn: 0
    fmtC_on_mibi1475.blastn: 0
    fmtC_on_mibi1476.blastn: 0
    fmtC_on_mibi1477.blastn: 0
    fmtC_on_mibi1478.blastn: 0
    fmtC_on_mibi1479.blastn: 0
    fmtC_on_mibi1480.blastn: 0
    fmtC_on_mibi1481.blastn: 0
    fmtC_on_mibi1482.blastn: 0
    fmtC_on_mibi1483.blastn: 0
    fmtC_on_mibi1484.blastn: 0
    fmtC_on_mibi1485.blastn: 0
    fmtC_on_mibi1486.blastn: 0
    fmtC_on_mibi1487.blastn: 0
    fmtC_on_mibi1488.blastn: 0
    fmtC_on_mibi1489.blastn: 0
    fmtC_on_mibi1490.blastn: 0
    fmtC_on_mibi1491.blastn: 0
    fmtC_on_mibi1492.blastn: 0
    fmtC_on_mibi1493.blastn: 0
    fmtC_on_mibi1494.blastn: 0
    fmtC_on_mibi1495.blastn: 0
    fmtC_on_mibi1496.blastn: 0
    fmtC_on_mibi1497.blastn: 0
    fmtC_on_mibi1498.blastn: 0
    fmtC_on_mibi1499.blastn: 0
    fmtC_on_mibi1500.blastn: 0
    fmtC_on_mibi1501.blastn: 0
    fmtC_on_mibi1502.blastn: 0
    fmtC_on_mibi1503.blastn: 0
    fmtC_on_mibi1504.blastn: 0
    fmtC_on_mibi1505.blastn: 0
    fmtC_on_mibi1506.blastn: 0
    fmtC_on_mibi2312.blastn: 0
    fmtC_on_mibi2313.blastn: 0
    fmtC_on_mibi2314.blastn: 0
    fmtC_on_mibi2315.blastn: 0
    fmtC_on_mibi2316.blastn: 0
    fmtC_on_mibi2317.blastn: 0
    fmtC_on_mibi2318.blastn: 0
    fmtC_on_mibi2319.blastn: 0
    fmtC_on_mibi2320.blastn: 0
    fmtC_on_mibi2321.blastn: 0
    fmtC_on_mibi2379.blastn: 0
    
    #-- For genes: lipA (915), sceD (699), esp (660), ecpA (1188)
    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
    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
    done
    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
    python3 analyze_blastn_res.py lipA_on_${sample}.blastn
    done
    lipA_on_mibi1435.blastn: 915
    lipA_on_mibi1436.blastn: 915
    lipA_on_mibi1437.blastn: 915
    lipA_on_mibi1438.blastn: 915
    lipA_on_mibi1439.blastn: 915
    lipA_on_mibi1440.blastn: 915
    lipA_on_mibi1441.blastn: 915
    lipA_on_mibi1442.blastn: 915
    lipA_on_mibi1443.blastn: 915
    lipA_on_mibi1444.blastn: 915
    lipA_on_mibi1445.blastn: 915
    lipA_on_mibi1446.blastn: 915
    lipA_on_mibi1447.blastn: 915
    lipA_on_mibi1448.blastn: 915
    lipA_on_mibi1449.blastn: 915
    lipA_on_mibi1450.blastn: 915
    lipA_on_mibi1451.blastn: 915
    lipA_on_mibi1452.blastn: 915
    lipA_on_mibi1453.blastn: 915
    lipA_on_mibi1454.blastn: 915
    lipA_on_mibi1455.blastn: 915
    lipA_on_mibi1456.blastn: 915
    lipA_on_mibi1457.blastn: 915
    lipA_on_mibi1458.blastn: 915
    lipA_on_mibi1459.blastn: 915
    lipA_on_mibi1460.blastn: 915
    lipA_on_mibi1461.blastn: 915
    lipA_on_mibi1462.blastn: 915
    lipA_on_mibi1463.blastn: 915
    lipA_on_mibi1464.blastn: 915
    lipA_on_mibi1465.blastn: 915
    lipA_on_mibi1466.blastn: 915
    lipA_on_mibi1467.blastn: 915
    lipA_on_mibi1468.blastn: 915
    lipA_on_mibi1469.blastn: 915
    lipA_on_mibi1471.blastn: 915
    lipA_on_mibi1473.blastn: 915
    lipA_on_mibi1474.blastn: 915
    lipA_on_mibi1475.blastn: 915
    lipA_on_mibi1476.blastn: 915
    lipA_on_mibi1477.blastn: 915
    lipA_on_mibi1478.blastn: 915
    lipA_on_mibi1479.blastn: 915
    lipA_on_mibi1480.blastn: 915
    lipA_on_mibi1481.blastn: 915
    lipA_on_mibi1482.blastn: 915
    lipA_on_mibi1483.blastn: 915
    lipA_on_mibi1484.blastn: 915
    lipA_on_mibi1485.blastn: 915
    lipA_on_mibi1486.blastn: 915
    lipA_on_mibi1487.blastn: 915
    lipA_on_mibi1488.blastn: 915
    lipA_on_mibi1489.blastn: 915
    lipA_on_mibi1490.blastn: 915
    lipA_on_mibi1491.blastn: 915
    lipA_on_mibi1492.blastn: 915
    lipA_on_mibi1493.blastn: 915
    lipA_on_mibi1494.blastn: 915
    lipA_on_mibi1495.blastn: 915
    lipA_on_mibi1496.blastn: 915
    lipA_on_mibi1497.blastn: 915
    lipA_on_mibi1498.blastn: 915
    lipA_on_mibi1499.blastn: 915
    lipA_on_mibi1500.blastn: 915
    lipA_on_mibi1501.blastn: 915
    lipA_on_mibi1502.blastn: 915
    lipA_on_mibi1503.blastn: 915
    lipA_on_mibi1504.blastn: 915
    lipA_on_mibi1505.blastn: 915
    lipA_on_mibi1506.blastn: 915
    lipA_on_mibi2312.blastn: 915
    lipA_on_mibi2313.blastn: 915
    lipA_on_mibi2314.blastn: 915
    lipA_on_mibi2315.blastn: 915
    lipA_on_mibi2316.blastn: 915
    lipA_on_mibi2317.blastn: 915
    lipA_on_mibi2318.blastn: 915
    lipA_on_mibi2319.blastn: 915
    lipA_on_mibi2320.blastn: 915
    lipA_on_mibi2321.blastn: 915
    lipA_on_mibi2379.blastn: 915
    
    #grep "gene=sceD" mibi1435.gff3
    #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
    samtools faidx mibi1435.fna contig_11:25537-26196 > sceD_mibi1435.fasta
    revcomp sceD_mibi1435.fasta > sceD_mibi1435_revcomp.fasta
    cp sceD_mibi1435_revcomp.fasta ../presence_absence_matrix_on_gene_list/
    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
    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
    done
    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
    python3 analyze_blastn_res.py sceD_on_${sample}.blastn
    done
    sceD_on_mibi1435.blastn: 660
    sceD_on_mibi1436.blastn: 660
    sceD_on_mibi1437.blastn: 660
    sceD_on_mibi1438.blastn: 660
    sceD_on_mibi1439.blastn: 660
    sceD_on_mibi1440.blastn: 660
    sceD_on_mibi1441.blastn: 660
    sceD_on_mibi1442.blastn: 660
    sceD_on_mibi1443.blastn: 660
    sceD_on_mibi1444.blastn: 660
    sceD_on_mibi1445.blastn: 660
    sceD_on_mibi1446.blastn: 660
    sceD_on_mibi1447.blastn: 660
    sceD_on_mibi1448.blastn: 660
    sceD_on_mibi1449.blastn: 660
    sceD_on_mibi1450.blastn: 660
    sceD_on_mibi1451.blastn: 660
    sceD_on_mibi1452.blastn: 660
    sceD_on_mibi1453.blastn: 660
    sceD_on_mibi1454.blastn: 660
    sceD_on_mibi1455.blastn: 660
    sceD_on_mibi1456.blastn: 660
    sceD_on_mibi1457.blastn: 660
    sceD_on_mibi1458.blastn: 660
    sceD_on_mibi1459.blastn: 660
    sceD_on_mibi1460.blastn: 660
    sceD_on_mibi1461.blastn: 660
    sceD_on_mibi1462.blastn: 660
    sceD_on_mibi1463.blastn: 660
    sceD_on_mibi1464.blastn: 660
    sceD_on_mibi1465.blastn: 660
    sceD_on_mibi1466.blastn: 660
    sceD_on_mibi1467.blastn: 660
    sceD_on_mibi1468.blastn: 660
    sceD_on_mibi1469.blastn: 660
    sceD_on_mibi1471.blastn: 660
    sceD_on_mibi1473.blastn: 660
    sceD_on_mibi1474.blastn: 660
    sceD_on_mibi1475.blastn: 660
    sceD_on_mibi1476.blastn: 660
    sceD_on_mibi1477.blastn: 660
    sceD_on_mibi1478.blastn: 660
    sceD_on_mibi1479.blastn: 660
    sceD_on_mibi1480.blastn: 660
    sceD_on_mibi1481.blastn: 660
    sceD_on_mibi1482.blastn: 660
    sceD_on_mibi1483.blastn: 660
    sceD_on_mibi1484.blastn: 660
    sceD_on_mibi1485.blastn: 660
    sceD_on_mibi1486.blastn: 660
    sceD_on_mibi1487.blastn: 660
    sceD_on_mibi1488.blastn: 660
    sceD_on_mibi1489.blastn: 660
    sceD_on_mibi1490.blastn: 660
    sceD_on_mibi1491.blastn: 660
    sceD_on_mibi1492.blastn: 660
    sceD_on_mibi1493.blastn: 660
    sceD_on_mibi1494.blastn: 660
    sceD_on_mibi1495.blastn: 660
    sceD_on_mibi1496.blastn: 660
    sceD_on_mibi1497.blastn: 660
    sceD_on_mibi1498.blastn: 660
    sceD_on_mibi1499.blastn: 660
    sceD_on_mibi1500.blastn: 660
    sceD_on_mibi1501.blastn: 660
    sceD_on_mibi1502.blastn: 660
    sceD_on_mibi1503.blastn: 660
    sceD_on_mibi1504.blastn: 660
    sceD_on_mibi1505.blastn: 660
    sceD_on_mibi1506.blastn: 660
    sceD_on_mibi2312.blastn: 660
    sceD_on_mibi2313.blastn: 660
    sceD_on_mibi2314.blastn: 660
    sceD_on_mibi2315.blastn: 660
    sceD_on_mibi2316.blastn: 660
    sceD_on_mibi2317.blastn: 660
    sceD_on_mibi2318.blastn: 660
    sceD_on_mibi2319.blastn: 660
    sceD_on_mibi2320.blastn: 660
    sceD_on_mibi2321.blastn: 660
    sceD_on_mibi2379.blastn: 660
    
    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
    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
    done
    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
    python3 analyze_blastn_res.py esp_on_${sample}.blastn
    done
    esp_on_mibi1435.blastn: 0
    esp_on_mibi1436.blastn: 0
    esp_on_mibi1437.blastn: 0
    esp_on_mibi1438.blastn: 0
    esp_on_mibi1439.blastn: 0
    esp_on_mibi1440.blastn: 0
    esp_on_mibi1441.blastn: 0
    esp_on_mibi1442.blastn: 0
    esp_on_mibi1443.blastn: 0
    esp_on_mibi1444.blastn: 0
    esp_on_mibi1445.blastn: 0
    esp_on_mibi1446.blastn: 0
    esp_on_mibi1447.blastn: 0
    esp_on_mibi1448.blastn: 0
    esp_on_mibi1449.blastn: 0
    esp_on_mibi1450.blastn: 0
    esp_on_mibi1451.blastn: 0
    esp_on_mibi1452.blastn: 0
    esp_on_mibi1453.blastn: 0
    esp_on_mibi1454.blastn: 0
    esp_on_mibi1455.blastn: 0
    esp_on_mibi1456.blastn: 0
    esp_on_mibi1457.blastn: 0
    esp_on_mibi1458.blastn: 0
    esp_on_mibi1459.blastn: 0
    esp_on_mibi1460.blastn: 0
    esp_on_mibi1461.blastn: 0
    esp_on_mibi1462.blastn: 0
    esp_on_mibi1463.blastn: 0
    esp_on_mibi1464.blastn: 0
    esp_on_mibi1465.blastn: 0
    esp_on_mibi1466.blastn: 0
    esp_on_mibi1467.blastn: 0
    esp_on_mibi1468.blastn: 0
    esp_on_mibi1469.blastn: 0
    esp_on_mibi1471.blastn: 0
    esp_on_mibi1473.blastn: 0
    esp_on_mibi1474.blastn: 0
    esp_on_mibi1475.blastn: 0
    esp_on_mibi1476.blastn: 0
    esp_on_mibi1477.blastn: 0
    esp_on_mibi1478.blastn: 0
    esp_on_mibi1479.blastn: 0
    esp_on_mibi1480.blastn: 0
    esp_on_mibi1481.blastn: 0
    esp_on_mibi1482.blastn: 0
    esp_on_mibi1483.blastn: 0
    esp_on_mibi1484.blastn: 0
    esp_on_mibi1485.blastn: 0
    esp_on_mibi1486.blastn: 0
    esp_on_mibi1487.blastn: 0
    esp_on_mibi1488.blastn: 0
    esp_on_mibi1489.blastn: 0
    esp_on_mibi1490.blastn: 0
    esp_on_mibi1491.blastn: 0
    esp_on_mibi1492.blastn: 0
    esp_on_mibi1493.blastn: 0
    esp_on_mibi1494.blastn: 0
    esp_on_mibi1495.blastn: 0
    esp_on_mibi1496.blastn: 0
    esp_on_mibi1497.blastn: 0
    esp_on_mibi1498.blastn: 0
    esp_on_mibi1499.blastn: 0
    esp_on_mibi1500.blastn: 0
    esp_on_mibi1501.blastn: 0
    esp_on_mibi1502.blastn: 0
    esp_on_mibi1503.blastn: 0
    esp_on_mibi1504.blastn: 0
    esp_on_mibi1505.blastn: 0
    esp_on_mibi1506.blastn: 0
    esp_on_mibi2312.blastn: 0
    esp_on_mibi2313.blastn: 0
    esp_on_mibi2314.blastn: 0
    esp_on_mibi2315.blastn: 0
    esp_on_mibi2316.blastn: 0
    esp_on_mibi2317.blastn: 0
    esp_on_mibi2318.blastn: 0
    esp_on_mibi2319.blastn: 0
    esp_on_mibi2320.blastn: 0
    esp_on_mibi2321.blastn: 0
    esp_on_mibi2379.blastn: 0
    
    #grep "gene=ecpA" mibi1435.gff3
    #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
    samtools faidx mibi1435.fna contig_9:6382-7569 > ecpA_mibi1435.fasta
    revcomp ecpA_mibi1435.fasta > ecpA_mibi1435_revcomp.fasta
    cp ecpA_mibi1435_revcomp.fasta ../presence_absence_matrix_on_gene_list/
    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
    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
    done
    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
    python3 analyze_blastn_res.py ecpA_on_${sample}.blastn
    done
    ecpA_on_mibi1435.blastn: 1188
    ecpA_on_mibi1436.blastn: 1188
    ecpA_on_mibi1437.blastn: 1188
    ecpA_on_mibi1438.blastn: 1188
    ecpA_on_mibi1439.blastn: 1188
    ecpA_on_mibi1440.blastn: 1188
    ecpA_on_mibi1441.blastn: 1188
    ecpA_on_mibi1442.blastn: 1188
    ecpA_on_mibi1443.blastn: 1188
    ecpA_on_mibi1444.blastn: 1188
    ecpA_on_mibi1445.blastn: 1188
    ecpA_on_mibi1446.blastn: 1188
    ecpA_on_mibi1447.blastn: 1188
    ecpA_on_mibi1448.blastn: 1188
    ecpA_on_mibi1449.blastn: 1188
    ecpA_on_mibi1450.blastn: 1188
    ecpA_on_mibi1451.blastn: 1188
    ecpA_on_mibi1452.blastn: 1188
    ecpA_on_mibi1453.blastn: 1188
    ecpA_on_mibi1454.blastn: 1188
    ecpA_on_mibi1455.blastn: 1188
    ecpA_on_mibi1456.blastn: 1188
    ecpA_on_mibi1457.blastn: 1188
    ecpA_on_mibi1458.blastn: 1188
    ecpA_on_mibi1459.blastn: 1188
    ecpA_on_mibi1460.blastn: 1188
    ecpA_on_mibi1461.blastn: 1188
    ecpA_on_mibi1462.blastn: 1188
    ecpA_on_mibi1463.blastn: 1188
    ecpA_on_mibi1464.blastn: 1188
    ecpA_on_mibi1465.blastn: 1188
    ecpA_on_mibi1466.blastn: 1188
    ecpA_on_mibi1467.blastn: 1188
    ecpA_on_mibi1468.blastn: 1188
    ecpA_on_mibi1469.blastn: 1188
    ecpA_on_mibi1471.blastn: 1188
    ecpA_on_mibi1473.blastn: 1188
    ecpA_on_mibi1474.blastn: 1188
    ecpA_on_mibi1475.blastn: 1188
    ecpA_on_mibi1476.blastn: 1188
    ecpA_on_mibi1477.blastn: 1188
    ecpA_on_mibi1478.blastn: 1188
    ecpA_on_mibi1479.blastn: 1188
    ecpA_on_mibi1480.blastn: 1188
    ecpA_on_mibi1481.blastn: 1188
    ecpA_on_mibi1482.blastn: 1188
    ecpA_on_mibi1483.blastn: 1188
    ecpA_on_mibi1484.blastn: 1188
    ecpA_on_mibi1485.blastn: 1188
    ecpA_on_mibi1486.blastn: 1188
    ecpA_on_mibi1487.blastn: 1188
    ecpA_on_mibi1488.blastn: 1188
    ecpA_on_mibi1489.blastn: 1188
    ecpA_on_mibi1490.blastn: 1188
    ecpA_on_mibi1491.blastn: 1188
    ecpA_on_mibi1492.blastn: 1188
    ecpA_on_mibi1493.blastn: 1188
    ecpA_on_mibi1494.blastn: 1188
    ecpA_on_mibi1495.blastn: 1188
    ecpA_on_mibi1496.blastn: 1188
    ecpA_on_mibi1497.blastn: 1188
    ecpA_on_mibi1498.blastn: 1188
    ecpA_on_mibi1499.blastn: 1188
    ecpA_on_mibi1500.blastn: 1188
    ecpA_on_mibi1501.blastn: 1188
    ecpA_on_mibi1502.blastn: 1188
    ecpA_on_mibi1503.blastn: 1188
    ecpA_on_mibi1504.blastn: 1188
    ecpA_on_mibi1505.blastn: 1188
    ecpA_on_mibi1506.blastn: 1188
    ecpA_on_mibi2312.blastn: 1188
    ecpA_on_mibi2313.blastn: 1188
    ecpA_on_mibi2314.blastn: 1188
    ecpA_on_mibi2315.blastn: 1188
    ecpA_on_mibi2316.blastn: 1188
    ecpA_on_mibi2317.blastn: 1188
    ecpA_on_mibi2318.blastn: 1188
    ecpA_on_mibi2319.blastn: 1188
    ecpA_on_mibi2320.blastn: 1188
    ecpA_on_mibi2321.blastn: 1188
    ecpA_on_mibi2379.blastn: 1188
    
    # -length(SE0760)=798
    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
    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
    done
    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
    python3 analyze_blastn_res.py SE0760_on_${sample}.blastn
    done
    SE0760_on_mibi1435.blastn: 798
    SE0760_on_mibi1436.blastn: 798
    SE0760_on_mibi1437.blastn: 798
    SE0760_on_mibi1438.blastn: 798
    SE0760_on_mibi1439.blastn: 798
    SE0760_on_mibi1440.blastn: 798
    SE0760_on_mibi1441.blastn: 798
    SE0760_on_mibi1442.blastn: 798
    SE0760_on_mibi1443.blastn: 798
    SE0760_on_mibi1444.blastn: 798
    SE0760_on_mibi1445.blastn: 798
    SE0760_on_mibi1446.blastn: 798
    SE0760_on_mibi1447.blastn: 798
    SE0760_on_mibi1448.blastn: 798
    SE0760_on_mibi1449.blastn: 798
    SE0760_on_mibi1450.blastn: 798
    SE0760_on_mibi1451.blastn: 798
    SE0760_on_mibi1452.blastn: 798
    SE0760_on_mibi1453.blastn: 798
    SE0760_on_mibi1454.blastn: 798
    SE0760_on_mibi1455.blastn: 798
    SE0760_on_mibi1456.blastn: 798
    SE0760_on_mibi1457.blastn: 798
    SE0760_on_mibi1458.blastn: 798
    SE0760_on_mibi1459.blastn: 798
    SE0760_on_mibi1460.blastn: 798
    SE0760_on_mibi1461.blastn: 798
    SE0760_on_mibi1462.blastn: 798
    SE0760_on_mibi1463.blastn: 798
    SE0760_on_mibi1464.blastn: 798
    SE0760_on_mibi1465.blastn: 798
    SE0760_on_mibi1466.blastn: 798
    SE0760_on_mibi1467.blastn: 799
    SE0760_on_mibi1468.blastn: 798
    SE0760_on_mibi1469.blastn: 798
    SE0760_on_mibi1471.blastn: 798
    SE0760_on_mibi1473.blastn: 798
    SE0760_on_mibi1474.blastn: 798
    SE0760_on_mibi1475.blastn: 798
    SE0760_on_mibi1476.blastn: 798
    SE0760_on_mibi1477.blastn: 798
    SE0760_on_mibi1478.blastn: 798
    SE0760_on_mibi1479.blastn: 798
    SE0760_on_mibi1480.blastn: 798
    SE0760_on_mibi1481.blastn: 798
    SE0760_on_mibi1482.blastn: 798
    SE0760_on_mibi1483.blastn: 798
    SE0760_on_mibi1484.blastn: 798
    SE0760_on_mibi1485.blastn: 798
    SE0760_on_mibi1486.blastn: 798
    SE0760_on_mibi1487.blastn: 798
    SE0760_on_mibi1488.blastn: 798
    SE0760_on_mibi1489.blastn: 798
    SE0760_on_mibi1490.blastn: 798
    SE0760_on_mibi1491.blastn: 798
    SE0760_on_mibi1492.blastn: 798
    SE0760_on_mibi1493.blastn: 798
    SE0760_on_mibi1494.blastn: 798
    SE0760_on_mibi1495.blastn: 798
    SE0760_on_mibi1496.blastn: 798
    SE0760_on_mibi1497.blastn: 798
    SE0760_on_mibi1498.blastn: 798
    SE0760_on_mibi1499.blastn: 798
    SE0760_on_mibi1500.blastn: 798
    SE0760_on_mibi1501.blastn: 798
    SE0760_on_mibi1502.blastn: 798
    SE0760_on_mibi1503.blastn: 798
    SE0760_on_mibi1504.blastn: 798
    SE0760_on_mibi1505.blastn: 798
    SE0760_on_mibi1506.blastn: 798
    SE0760_on_mibi2312.blastn: 798
    SE0760_on_mibi2313.blastn: 798
    SE0760_on_mibi2314.blastn: 798
    SE0760_on_mibi2315.blastn: 798
    SE0760_on_mibi2316.blastn: 798
    SE0760_on_mibi2317.blastn: 798
    SE0760_on_mibi2318.blastn: 798
    SE0760_on_mibi2319.blastn: 798
    SE0760_on_mibi2320.blastn: 798
    SE0760_on_mibi2321.blastn: 798
    SE0760_on_mibi2379.blastn: 798
    
    # -lenth(MT880870)=34053
    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
    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
    done
    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
    python3 analyze_blastn_res.py MT880870_on_${sample}.blastn
    done
    
    MT880870_on_mibi1435.blastn: 2366
    MT880870_on_mibi1436.blastn: 3198
    MT880870_on_mibi1437.blastn: 3198
    MT880870_on_mibi1438.blastn: 2366
    MT880870_on_mibi1439.blastn: 3198
    MT880870_on_mibi1440.blastn: 34177
    MT880870_on_mibi1441.blastn: 2372
    MT880870_on_mibi1442.blastn: 3470
    MT880870_on_mibi1443.blastn: 2366
    MT880870_on_mibi1444.blastn: 2372
    MT880870_on_mibi1445.blastn: 3198
    MT880870_on_mibi1446.blastn: 3198
    MT880870_on_mibi1447.blastn: 3198
    MT880870_on_mibi1448.blastn: 3198
    MT880870_on_mibi1449.blastn: 2366
    MT880870_on_mibi1450.blastn: 3198
    MT880870_on_mibi1451.blastn: 1085
    MT880870_on_mibi1452.blastn: 1832
    MT880870_on_mibi1453.blastn: 2366
    MT880870_on_mibi1454.blastn: 34177
    MT880870_on_mibi1455.blastn: 3198
    MT880870_on_mibi1456.blastn: 34177
    MT880870_on_mibi1457.blastn: 3198
    MT880870_on_mibi1458.blastn: 835
    MT880870_on_mibi1459.blastn: 34177
    MT880870_on_mibi1460.blastn: 3198
    MT880870_on_mibi1461.blastn: 34177
    MT880870_on_mibi1462.blastn: 2372
    MT880870_on_mibi1463.blastn: 2372
    MT880870_on_mibi1464.blastn: 2311
    MT880870_on_mibi1465.blastn: 3198
    MT880870_on_mibi1466.blastn: 1264
    MT880870_on_mibi1467.blastn: 3470
    MT880870_on_mibi1468.blastn: 2372
    MT880870_on_mibi1469.blastn: 2372
    MT880870_on_mibi1471.blastn: 2366
    MT880870_on_mibi1473.blastn: 3198
    MT880870_on_mibi1474.blastn: 3198
    MT880870_on_mibi1475.blastn: 3198
    MT880870_on_mibi1476.blastn: 3198
    MT880870_on_mibi1477.blastn: 2372
    MT880870_on_mibi1478.blastn: 5918
    MT880870_on_mibi1479.blastn: 3198
    MT880870_on_mibi1480.blastn: 34177
    MT880870_on_mibi1481.blastn: 3198
    MT880870_on_mibi1482.blastn: 3198
    MT880870_on_mibi1483.blastn: 3198
    MT880870_on_mibi1484.blastn: 3198
    MT880870_on_mibi1485.blastn: 20038
    MT880870_on_mibi1486.blastn: 3198
    MT880870_on_mibi1487.blastn: 28520
    MT880870_on_mibi1488.blastn: 2366
    MT880870_on_mibi1489.blastn: 2366
    MT880870_on_mibi1490.blastn: 3198
    MT880870_on_mibi1491.blastn: 3198
    MT880870_on_mibi1492.blastn: 3198
    MT880870_on_mibi1493.blastn: 2233
    MT880870_on_mibi1494.blastn: 3198
    MT880870_on_mibi1495.blastn: 3198
    MT880870_on_mibi1496.blastn: 25135
    MT880870_on_mibi1497.blastn: 3198
    MT880870_on_mibi1498.blastn: 28012
    MT880870_on_mibi1499.blastn: 3198
    MT880870_on_mibi1500.blastn: 2366
    MT880870_on_mibi1501.blastn: 2366
    MT880870_on_mibi1502.blastn: 34177
    MT880870_on_mibi1503.blastn: 2366
    MT880870_on_mibi1504.blastn: 3198
    MT880870_on_mibi1505.blastn: 3198
    MT880870_on_mibi1506.blastn: 2372
    MT880870_on_mibi2312.blastn: 3198
    MT880870_on_mibi2313.blastn: 3198
    MT880870_on_mibi2314.blastn: 3198
    MT880870_on_mibi2315.blastn: 2366
    MT880870_on_mibi2316.blastn: 3198
    MT880870_on_mibi2317.blastn: 3198
    MT880870_on_mibi2318.blastn: 20006
    MT880870_on_mibi2319.blastn: 17544
    MT880870_on_mibi2320.blastn: 3198
    MT880870_on_mibi2321.blastn: 3198
    MT880870_on_mibi2379.blastn: 3198
    
    #len=36164
    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
    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
    done
    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
    python3 analyze_blastn_res.py MT880871_on_${sample}.blastn
    done
    MT880871_on_mibi1435.blastn: 270
    MT880871_on_mibi1436.blastn: 35580
    MT880871_on_mibi1437.blastn: 518
    MT880871_on_mibi1438.blastn: 518
    MT880871_on_mibi1439.blastn: 518
    MT880871_on_mibi1440.blastn: 36682
    MT880871_on_mibi1441.blastn: 519
    MT880871_on_mibi1442.blastn: 514
    MT880871_on_mibi1443.blastn: 0
    MT880871_on_mibi1444.blastn: 0
    MT880871_on_mibi1445.blastn: 518
    MT880871_on_mibi1446.blastn: 518
    MT880871_on_mibi1447.blastn: 518
    MT880871_on_mibi1448.blastn: 518
    MT880871_on_mibi1449.blastn: 518
    MT880871_on_mibi1450.blastn: 518
    MT880871_on_mibi1451.blastn: 0
    MT880871_on_mibi1452.blastn: 30418
    MT880871_on_mibi1453.blastn: 518
    MT880871_on_mibi1454.blastn: 982
    MT880871_on_mibi1455.blastn: 518
    MT880871_on_mibi1456.blastn: 982
    MT880871_on_mibi1457.blastn: 518
    MT880871_on_mibi1458.blastn: 0
    MT880871_on_mibi1459.blastn: 34965
    MT880871_on_mibi1460.blastn: 518
    MT880871_on_mibi1461.blastn: 16296
    MT880871_on_mibi1462.blastn: 0
    MT880871_on_mibi1463.blastn: 518
    MT880871_on_mibi1464.blastn: 947
    MT880871_on_mibi1465.blastn: 518
    MT880871_on_mibi1466.blastn: 0
    MT880871_on_mibi1467.blastn: 514
    MT880871_on_mibi1468.blastn: 518
    MT880871_on_mibi1469.blastn: 518
    MT880871_on_mibi1471.blastn: 518
    MT880871_on_mibi1473.blastn: 518
    MT880871_on_mibi1474.blastn: 518
    MT880871_on_mibi1475.blastn: 518
    MT880871_on_mibi1476.blastn: 518
    MT880871_on_mibi1477.blastn: 518
    MT880871_on_mibi1478.blastn: 18607
    MT880871_on_mibi1479.blastn: 518
    MT880871_on_mibi1480.blastn: 36682
    MT880871_on_mibi1481.blastn: 0
    MT880871_on_mibi1482.blastn: 518
    MT880871_on_mibi1483.blastn: 32395
    MT880871_on_mibi1484.blastn: 0
    MT880871_on_mibi1485.blastn: 36164
    MT880871_on_mibi1486.blastn: 31072
    MT880871_on_mibi1487.blastn: 36682
    MT880871_on_mibi1488.blastn: 0
    MT880871_on_mibi1489.blastn: 0
    MT880871_on_mibi1490.blastn: 518
    MT880871_on_mibi1491.blastn: 518
    MT880871_on_mibi1492.blastn: 518
    MT880871_on_mibi1493.blastn: 740
    MT880871_on_mibi1494.blastn: 518
    MT880871_on_mibi1495.blastn: 0
    MT880871_on_mibi1496.blastn: 24187
    MT880871_on_mibi1497.blastn: 31069
    MT880871_on_mibi1498.blastn: 36682
    MT880871_on_mibi1499.blastn: 518
    MT880871_on_mibi1500.blastn: 0
    MT880871_on_mibi1501.blastn: 0
    MT880871_on_mibi1502.blastn: 36682
    MT880871_on_mibi1503.blastn: 518
    MT880871_on_mibi1504.blastn: 518
    MT880871_on_mibi1505.blastn: 518
    MT880871_on_mibi1506.blastn: 0
    MT880871_on_mibi2312.blastn: 316
    MT880871_on_mibi2313.blastn: 518
    MT880871_on_mibi2314.blastn: 518
    MT880871_on_mibi2315.blastn: 0
    MT880871_on_mibi2316.blastn: 518
    MT880871_on_mibi2317.blastn: 518
    MT880871_on_mibi2318.blastn: 36682
    MT880871_on_mibi2319.blastn: 36164
    MT880871_on_mibi2320.blastn: 518
    MT880871_on_mibi2321.blastn: 518
    MT880871_on_mibi2379.blastn: 518
    
    #len=147057
    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
    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
    done
    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
    python3 analyze_blastn_res.py MT880872_on_${sample}.blastn
    done
    MT880872_on_mibi1435.blastn: 19155
    MT880872_on_mibi1436.blastn: 19049
    MT880872_on_mibi1437.blastn: 19049
    MT880872_on_mibi1438.blastn: 19045
    MT880872_on_mibi1439.blastn: 19042
    MT880872_on_mibi1440.blastn: 77536 *
    MT880872_on_mibi1441.blastn: 19041
    MT880872_on_mibi1442.blastn: 19044
    MT880872_on_mibi1443.blastn: 19049
    MT880872_on_mibi1444.blastn: 19049
    MT880872_on_mibi1445.blastn: 19042
    MT880872_on_mibi1446.blastn: 19042
    MT880872_on_mibi1447.blastn: 19042
    MT880872_on_mibi1448.blastn: 19049
    MT880872_on_mibi1449.blastn: 19041
    MT880872_on_mibi1450.blastn: 19049
    MT880872_on_mibi1451.blastn: 19043
    MT880872_on_mibi1452.blastn: 19047
    MT880872_on_mibi1453.blastn: 19165
    MT880872_on_mibi1454.blastn: 52122 *
    MT880872_on_mibi1455.blastn: 20996
    MT880872_on_mibi1456.blastn: 52122 *
    MT880872_on_mibi1457.blastn: 19042
    MT880872_on_mibi1458.blastn: 19048
    MT880872_on_mibi1459.blastn: 77366 *
    MT880872_on_mibi1460.blastn: 19042
    MT880872_on_mibi1461.blastn: 84536 *
    MT880872_on_mibi1462.blastn: 19048
    MT880872_on_mibi1463.blastn: 19042
    MT880872_on_mibi1464.blastn: 19049
    MT880872_on_mibi1465.blastn: 19045
    MT880872_on_mibi1466.blastn: 6525
    MT880872_on_mibi1467.blastn: 19044
    MT880872_on_mibi1468.blastn: 19037
    MT880872_on_mibi1469.blastn: 19039
    MT880872_on_mibi1471.blastn: 19045
    MT880872_on_mibi1473.blastn: 19043
    MT880872_on_mibi1474.blastn: 19052
    MT880872_on_mibi1475.blastn: 19264
    MT880872_on_mibi1476.blastn: 19052
    MT880872_on_mibi1477.blastn: 19041
    MT880872_on_mibi1478.blastn: 26492 *
    MT880872_on_mibi1479.blastn: 19042
    MT880872_on_mibi1480.blastn: 45789 *
    MT880872_on_mibi1481.blastn: 19036
    MT880872_on_mibi1482.blastn: 19036
    MT880872_on_mibi1483.blastn: 19036
    MT880872_on_mibi1484.blastn: 19045
    MT880872_on_mibi1485.blastn: 52124 *
    MT880872_on_mibi1486.blastn: 19052
    MT880872_on_mibi1487.blastn: 56847 *
    MT880872_on_mibi1488.blastn: 19049
    MT880872_on_mibi1489.blastn: 19053
    MT880872_on_mibi1490.blastn: 19045
    MT880872_on_mibi1491.blastn: 19042
    MT880872_on_mibi1492.blastn: 19049
    MT880872_on_mibi1493.blastn: 19046
    MT880872_on_mibi1494.blastn: 19049
    MT880872_on_mibi1495.blastn: 19046
    MT880872_on_mibi1496.blastn: 92504 *
    MT880872_on_mibi1497.blastn: 19052
    MT880872_on_mibi1498.blastn: 58985 *
    MT880872_on_mibi1499.blastn: 19043
    MT880872_on_mibi1500.blastn: 19052
    MT880872_on_mibi1501.blastn: 19049
    MT880872_on_mibi1502.blastn: 46101 *
    MT880872_on_mibi1503.blastn: 19044
    MT880872_on_mibi1504.blastn: 19041
    MT880872_on_mibi1505.blastn: 19052
    MT880872_on_mibi1506.blastn: 19049
    MT880872_on_mibi2312.blastn: 19045
    MT880872_on_mibi2313.blastn: 19049
    MT880872_on_mibi2314.blastn: 19052
    MT880872_on_mibi2315.blastn: 19049
    MT880872_on_mibi2316.blastn: 19052
    MT880872_on_mibi2317.blastn: 19042
    MT880872_on_mibi2318.blastn: 78246 *
    MT880872_on_mibi2319.blastn: 77512 *
    MT880872_on_mibi2320.blastn: 19045
    MT880872_on_mibi2321.blastn: 19052
    MT880872_on_mibi2379.blastn: 19156
    

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

    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).
    
    Let’s break down the results:
    
    Query ID: gi|49240382|emb|BX571856.1|:25617-27443
    Subject ID: contig00005
    Percentage Identity: 80.338%
    Alignment Length: 1836 (out of 1827 in the subject sequence)
    Mismatches: 349
    Gap Openings: 7
    E-value: 0.0 (this indicates a highly significant alignment)
    Bit Score: 1380
    
    Key Points to Consider:
    
    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.
    
    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.
    
    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.
    
    E-value (0.0): The E-value of 0.0 indicates that the alignment is highly significant and not due to chance.
    
    Conclusion:
    
    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

    FastTree -gtr -nt variants/snippy.core_without_reference.aln > plotTreeHeatmap/snippy.core.tree
    
    library(ggtree)
    library(ggplot2)
    library(dplyr)
    setwd("/home/jhuang/DATA/Data_Luise_Sepi_STKN/plotTreeHeatmap/")
    # -- edit tree --
    info <- read.csv("typing.csv", sep="\t")
    info$name <- info$Isolate
    tree <- read.tree("990_backup.tree")
    #cols <- c(infection='purple2', commensalism='skyblue2')
    
    #heatmapData2 <- info %>% select(Isolate, ST, SCCmec, agr.typing)
    heatmapData2 <- info %>% select(Isolate, ST)
    rn <- heatmapData2$Isolate
    heatmapData2$Isolate <- NULL
    heatmapData2 <- as.data.frame(sapply(heatmapData2, as.character))
    rownames(heatmapData2) <- rn
    
    #https://bookdown.org/hneth/ds4psy/D-3-apx-colors-basics.html
    #"blueviolet","darkgoldenrod",  "tomato","mediumpurple4","indianred",
    #"lightcyan3","azure3",
    #"magenta",
    #"tan","brown",
    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")
                            #"cornflowerblue","darkgreen","seagreen3","tan","red","green","orange","pink","brown","darkgrey",  #"cornflowerblue","darkgreen","red",     "darkgrey")
    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","-")
    #"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")
    
    #circular
    #scale_color_manual(values=cols) +
    #geom_tippoint(aes(color=Type)) +
    p <- ggtree(tree, layout='circular', branch.length='none') %<+% info +
    geom_tiplab2(aes(label=name), offset=1, size=6.0)
    #, geom='text', align=TRUE,  linetype=NA, hjust=1.8,check.overlap=TRUE
    #difference between geom_tiplab and geom_tiplab2?
    #+ theme(axis.text.x = element_text(angle = 30, vjust = 0.5)) + theme(axis.text = element_text(size = 20))  + scale_size(range = c(1, 20))
    #font.size=10,
    png("ggtree.png", width=1260, height=1260)
    #svg("ggtree.svg", width=1260, height=1260)
    p
    dev.off()
    png("ggtree_and_gheatmap.png", width=1290, height=1000)
    #svg("ggtree_and_gheatmap.svg", width=17, height=15)
    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)))
    dev.off()
    

13. Response

    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.
    
    This leaves us with a total of 81 samples for downstream analysis.
    
    Attached, you’ll find:
    
    * The graphic ggtree_and_gheatmap.png
    * A table, presence_absence_matrix_on_genes, providing an overview of gene presence/absence and relevant typing information
    * FASTA files for all 81 genomes
    

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