user: Translate the below assembly code into C programming language:

```asm
<main>:
  endbr64
  push   %rbp
  mov    %rsp,%rbp
  push   %r15
  push   %r14
  push   %r13
  push   %r12
  push   %rbx
  mov    %rsi,%rbx
  sub    $0x78,%rsp
  mov    %fs:0x28,%rax
  mov    %rax,-0x38(%rbp)
  mov    %rsp,%rax
  cmp    %rax,%rsp
  je     L550
L556:
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  cmp    %rax,%rsp
  jne    L556
L550:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    0x8(%rbx),%rsi
  mov    %rsp,%rdi
  mov    %rsp,-0x98(%rbp)
  call   <strcpy@plt>
L365:
  cmp    -0x98(%rbp),%rsp
  je     L477
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L365
L477:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    0x10(%rbx),%rsi
  mov    %rsp,%rdi
  mov    %rsp,%r14
  call   <strcpy@plt>
L419:
  cmp    %r14,%rsp
  je     L210
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L419
L210:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    0x18(%rbx),%rsi
  mov    %rsp,%rdi
  mov    %rsp,-0x48(%rbp)
  call   <strcpy@plt>
L524:
  cmp    -0x48(%rbp),%rsp
  je     L196
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L524
L196:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    -0x48(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  lea    D87(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D257(%rip),%rsi
  mov    %rsp,%rdi
  call   <fopen@plt>
  mov    %rax,-0xa0(%rbp)
  mov    %rsp,%rax
L116:
  cmp    %rax,%rsp
  je     L563
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L116
L563:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    -0x48(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  lea    D182(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D226(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    -0x98(%rbp),%rbx
  mov    %rsp,%rdi
  mov    %rbx,%rsi
  call   <strcat@plt>
  lea    D231(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D226(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %rbx,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D107(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D64(%rip),%rsi
  mov    %rsp,%rdi
  call   <fopen@plt>
  mov    $0x2a,%edx
  mov    $0x1,%esi
  lea    D85(%rip),%rdi
  mov    %rax,%rcx
  mov    %rax,-0x60(%rbp)
  call   <fwrite@plt>
  mov    %rsp,%rax
L491:
  cmp    %rax,%rsp
  je     L406
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L491
L406:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    -0x48(%rbp),%rsi
  mov    %rsp,%rdi
  mov    %rsp,%r13
  call   <strcpy@plt>
  lea    D182(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D226(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    -0x98(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D231(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D226(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D139(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
L251:
  cmp    %r13,%rsp
  je     L163
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L251
L163:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  lea    D199(%rip),%rsi
  xor    %r12d,%r12d
  mov    %r13,%rdi
  mov    %rsp,%rbx
  call   <fopen@plt>
  mov    %rax,%r15
  test   %rax,%rax
  jne    L490
  jmp    L252
  nopl   0x0(%rax)
L531:
  add    $0x1,%r12d
L490:
  mov    %r15,%rdx
  mov    $0x3e8,%esi
  mov    %rbx,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L531
  mov    %r15,%rdi
  call   <fclose@plt>
L313:
  movslq %r12d,%rax
  mov    %rsp,%rcx
  imul   $0x3e8,%rax,%rax
  add    $0xf,%rax
  mov    %rax,%rsi
  mov    %rax,%rdx
  and    $0xfffffffffffff000,%rsi
  and    $0xfffffffffffffff0,%rdx
  sub    %rsi,%rcx
  cmp    %rcx,%rsp
  je     L322
L256:
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  cmp    %rcx,%rsp
  jne    L256
L322:
  and    $0xfff,%edx
  sub    %rdx,%rsp
  test   %rdx,%rdx
  je     L26
  orq    $0x0,-0x8(%rsp,%rdx,1)
L26:
  mov    %rsp,-0x90(%rbp)
  mov    %rax,%rdx
  mov    %rsp,%rcx
  and    $0xfffffffffffff000,%rax
  and    $0xfffffffffffffff0,%rdx
  sub    %rax,%rcx
L141:
  cmp    %rcx,%rsp
  je     L586
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L141
L252:
  mov    %r13,%rdi
  call   <perror@plt>
  jmp    L313
L586:
  mov    %rdx,%rax
  and    $0xfff,%eax
  sub    %rax,%rsp
  test   %rax,%rax
  je     L84
  orq    $0x0,-0x8(%rsp,%rax,1)
L84:
  lea    D199(%rip),%rsi
  mov    %r13,%rdi
  call   <fopen@plt>
  mov    %rax,%r15
  test   %rax,%rax
  je     L69
  mov    %rsp,-0x78(%rbp)
  mov    -0x90(%rbp),%r13
  mov    %rsp,%r12
  movl   $0x0,-0x68(%rbp)
  jmp    L30
  nopl   (%rax)
L404:
  mov    %rbx,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  cltq
  cmpb   $0xa,(%rbx,%rax,1)
  jne    L136
  movb   $0x0,(%rbx,%rax,1)
L136:
  mov    %r13,%rdi
  mov    %rbx,%rsi
  add    $0x3e8,%r13
  call   <strcpy@plt>
  mov    -0x48(%rbp),%rsi
  mov    %r12,%rdi
  call   <strcpy@plt>
  mov    %r12,%rdi
  lea    D182(%rip),%rsi
  call   <strcat@plt>
  mov    %r12,%rdi
  mov    %r14,%rsi
  call   <strcat@plt>
  mov    %r12,%rdi
  lea    D226(%rip),%rsi
  call   <strcat@plt>
  mov    -0x98(%rbp),%rsi
  mov    %r12,%rdi
  call   <strcat@plt>
  mov    %r12,%rdi
  lea    D231(%rip),%rsi
  call   <strcat@plt>
  mov    %r12,%rdi
  mov    %r14,%rsi
  call   <strcat@plt>
  mov    %r12,%rdi
  lea    D68(%rip),%rsi
  call   <strcat@plt>
  mov    %r12,%rdi
  mov    %rbx,%rsi
  call   <strcat@plt>
  mov    %r12,%rdi
  lea    D188(%rip),%rsi
  add    $0x3e8,%r12
  call   <strcat@plt>
  addl   $0x1,-0x68(%rbp)
L30:
  mov    %r15,%rdx
  mov    $0x3e8,%esi
  mov    %rbx,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L404
  mov    %r15,%rdi
  call   <fclose@plt>
  lea    -0xf4000(%rsp),%rax
L555:
  cmp    %rax,%rsp
  je     L273
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L555
L273:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,-0x80(%rbp)
  lea    -0xf4000(%rsp),%rax
L333:
  cmp    %rax,%rsp
  je     L342
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L333
L69:
  mov    %r13,%rdi
  call   <perror@plt>
L605:
  mov    -0x98(%rbp),%rbx
  lea    D206(%rip),%r12
  mov    %r12,%rdi
  mov    %rbx,%rsi
  call   <printf@plt>
  xor    %eax,%eax
  mov    %rbx,%rdx
  mov    %r12,%rsi
  mov    -0xa0(%rbp),%rdi
  call   <fprintf@plt>
  mov    -0x38(%rbp),%rax
  sub    %fs:0x28,%rax
  jne    L388
  lea    -0x28(%rbp),%rsp
  xor    %eax,%eax
  pop    %rbx
  pop    %r12
  pop    %r13
  pop    %r14
  pop    %r15
  pop    %rbp
  ret
L342:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  cmpl   $0x0,-0x68(%rbp)
  mov    %rsp,-0x88(%rbp)
  movq   $0x0,-0x70(%rbp)
  movl   $0x0,-0x64(%rbp)
  je     L605
  nopl   0x0(%rax,%rax,1)
L184:
  mov    -0x78(%rbp),%r12
  add    -0x70(%rbp),%r12
  lea    D199(%rip),%rsi
  mov    %r12,%rdi
  call   <fopen@plt>
  mov    %rax,%rbx
  test   %rax,%rax
  je     L144
  lea    -0xf4000(%rsp),%rax
  mov    %rsp,%r12
  cmp    %rax,%rsp
  je     L55
L250:
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  cmp    %rax,%rsp
  jne    L250
L55:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,%r13
  jmp    L73
  nopl   (%rax)
L182:
  cmpb   $0x3e,0x0(%r13)
  jne    L46
L73:
  mov    %rbx,%rdx
  mov    $0xf4240,%esi
  mov    %r13,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L182
  mov    %r12,%rsp
L87:
  mov    -0x90(%rbp),%r13
  mov    -0x70(%rbp),%rax
  add    %r13,%rax
  mov    %rax,-0x58(%rbp)
  mov    -0x64(%rbp),%eax
  test   %eax,%eax
  je     L383
  mov    -0x68(%rbp),%ecx
  mov    -0x78(%rbp),%rbx
  cmp    %eax,%ecx
  cmovle %ecx,%eax
  xor    %r12d,%r12d
  mov    %eax,-0x50(%rbp)
  nopw   0x0(%rax,%rax,1)
L331:
  lea    D199(%rip),%rsi
  mov    %rbx,%rdi
  call   <fopen@plt>
  mov    %rax,%r14
  test   %rax,%rax
  je     L105
  lea    -0xf4000(%rsp),%rax
  mov    %rsp,-0x48(%rbp)
  cmp    %rax,%rsp
  je     L527
L502:
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  cmp    %rax,%rsp
  jne    L502
L527:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,%r15
  jmp    L82
  xchg   %ax,%ax
L199:
  cmpb   $0x3e,(%r15)
  jne    L72
L82:
  mov    %r14,%rdx
  mov    $0xf4240,%esi
  mov    %r15,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L199
  mov    -0x48(%rbp),%rsp
L14:
  mov    -0x80(%rbp),%r15
  mov    %r15,%rdi
  call   <strlen@plt>
  mov    %eax,%r9d
  test   %eax,%eax
  jle    L372
  movslq %eax,%rdi
  mov    -0x88(%rbp),%r11
  xor    %eax,%eax
  xor    %esi,%esi
  xor    %r8d,%r8d
  mov    %r15,%r10
  jmp    L115
L275:
  movzbl (%r11,%rax,1),%ecx
  cmp    $0x4e,%cl
  je     L416
  cmp    %cl,%dl
  setne  %dl
  add    $0x1,%rax
  movzbl %dl,%edx
  add    %edx,%r8d
  cmp    %rax,%rdi
  je     L562
L115:
  movzbl (%r10,%rax,1),%edx
  cmp    $0x4e,%dl
  jne    L275
L416:
  add    $0x1,%rax
  add    $0x1,%esi
  cmp    %rax,%rdi
  jne    L115
L562:
  pxor   %xmm0,%xmm0
  sub    %esi,%r9d
  cvtsi2ss %r8d,%xmm0
L507:
  pxor   %xmm1,%xmm1
  mov    %r8d,-0x4c(%rbp)
  add    $0x1,%r12d
  add    $0x3e8,%rbx
  cvtsi2ss %r9d,%xmm1
  mov    %r9d,-0x48(%rbp)
  divss  %xmm1,%xmm0
  movss  D106(%rip),%xmm1
  mulss  D271(%rip),%xmm0
  subss  %xmm0,%xmm1
  cvttss2si %xmm1,%edi
  call   <log@plt>
  mov    -0x48(%rbp),%r9d
  mov    -0x4c(%rbp),%r8d
  mov    %r13,%rcx
  mov    -0x58(%rbp),%rdx
  mov    -0x60(%rbp),%rdi
  lea    D176(%rip),%rsi
  mov    $0x1,%eax
  mulss  D228(%rip),%xmm0
  add    $0x3e8,%r13
  cvtss2sd %xmm0,%xmm0
  call   <fprintf@plt>
  cmp    -0x50(%rbp),%r12d
  jl     L331
L383:
  addl   $0x1,-0x64(%rbp)
  mov    -0x64(%rbp),%eax
  addq   $0x3e8,-0x70(%rbp)
  cmp    %eax,-0x68(%rbp)
  jne    L184
  jmp    L605
  nopl   0x0(%rax,%rax,1)
L72:
  mov    %r15,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  cltq
  cmpb   $0xa,(%r15,%rax,1)
  jne    L471
  movb   $0x0,(%r15,%rax,1)
L471:
  mov    -0x88(%rbp),%rdi
  mov    %r15,%rsi
  call   <strcpy@plt>
  mov    %r14,%rdi
  call   <fclose@plt>
  jmp    L82
  nopl   (%rax)
L46:
  mov    %r13,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  cltq
  cmpb   $0xa,0x0(%r13,%rax,1)
  jne    L218
  movb   $0x0,0x0(%r13,%rax,1)
L218:
  mov    -0x80(%rbp),%rdi
  mov    %r13,%rsi
  call   <strcpy@plt>
  mov    %rbx,%rdi
  call   <fclose@plt>
  jmp    L73
  nopl   0x0(%rax)
L105:
  mov    %rbx,%rdi
  call   <perror@plt>
  jmp    L14
  nopl   (%rax)
L144:
  mov    %r12,%rdi
  call   <perror@plt>
  jmp    L87
L372:
  pxor   %xmm0,%xmm0
  xor    %r8d,%r8d
  jmp    L507
L388:
  call   <__stack_chk_fail@plt>
```

tool_calls: name: retrieve_data
arguments: tag: D87
data_type: string
name: retrieve_data
arguments: tag: D257
data_type: string
name: retrieve_data
arguments: tag: D182
data_type: string
name: retrieve_data
arguments: tag: D226
data_type: string
name: retrieve_data
arguments: tag: D231
data_type: string
name: retrieve_data
arguments: tag: D107
data_type: string
name: retrieve_data
arguments: tag: D64
data_type: string
name: retrieve_data
arguments: tag: D85
data_type: string
name: retrieve_data
arguments: tag: D139
data_type: string
name: retrieve_data
arguments: tag: D199
data_type: string
name: retrieve_data
arguments: tag: D68
data_type: string
name: retrieve_data
arguments: tag: D188
data_type: string
name: retrieve_data
arguments: tag: D206
data_type: string
name: retrieve_data
arguments: tag: D106
data_type: byte[4]
name: retrieve_data
arguments: tag: D271
data_type: byte[4]
name: retrieve_data
arguments: tag: D176
data_type: string
name: retrieve_data
arguments: tag: D228
data_type: byte[4]

tool: D87: /Analysis/log.txt

tool: D257: a

tool: D182: /Analysis/

tool: D226: /

tool: D231: _

tool: D107: _di_simulated.csv

tool: D64: w

tool: D85: Isolate_1,Isolate_2,SNPs,Sites,Divergence


tool: D139: Isolates.txt

tool: D199: r

tool: D68: /Intergenic_files/

tool: D188: .fasta

tool: D206: %s di calculated.


tool: {"D106": [0x00,0x00,0x80,0x3f]}

tool: {"D271": [0xab,0xaa,0xaa,0x3f]}

tool: D176: %s,%s,%i,%i,%0.6f


tool: {"D228": [0x00,0x00,0x40,0xbf]}

assistant: ```c
int main(int argc, char *argv[]) {
  int arg_len = 1000;
  char species[arg_len];
  strcpy(species, argv[1]);
  char analysis[arg_len];
  strcpy(analysis, argv[2]);
  char base_dir[arg_len];
  strcpy(base_dir, argv[3]);
  char log_file_name[arg_len];
  strcpy(log_file_name, base_dir);
  strcat(log_file_name, "/Analysis/log.txt");
  FILE *log_file = fopen(log_file_name, "a");
  char output_file_name[arg_len];
  strcpy(output_file_name, base_dir);
  strcat(output_file_name, "/Analysis/");
  strcat(output_file_name, analysis);
  strcat(output_file_name, "/");
  strcat(output_file_name, species);
  strcat(output_file_name, "_");
  strcat(output_file_name, analysis);
  strcat(output_file_name, "/");
  strcat(output_file_name, species);
  strcat(output_file_name, "_di_simulated.csv");
  FILE *output = fopen(output_file_name, "w");
  fprintf(output, "Isolate_1,Isolate_2,SNPs,Sites,Divergence\n");
  char isolates_file_name[arg_len];
  strcpy(isolates_file_name, base_dir);
  strcat(isolates_file_name, "/Analysis/");
  strcat(isolates_file_name, analysis);
  strcat(isolates_file_name, "/");
  strcat(isolates_file_name, species);
  strcat(isolates_file_name, "_");
  strcat(isolates_file_name, analysis);
  strcat(isolates_file_name, "/");
  strcat(isolates_file_name, "Isolates.txt");
  char isolate_name[arg_len];
  int isolate_count;
  isolate_count = 0;
  FILE *isolates_file = fopen(isolates_file_name, "r");
  if (isolates_file != NULL) {
    while (fgets(isolate_name, sizeof isolate_name, isolates_file) != NULL) {
      isolate_count++;
    }
    fclose(isolates_file);
  } else {
    perror(isolates_file_name);
  }
  char isolate_name_array[isolate_count][arg_len];
  char isolate_file_name_array[isolate_count][arg_len];
  isolate_count = 0;
  FILE *isolates_file_2 = fopen(isolates_file_name, "r");
  if (isolates_file_2 != NULL) {
    while (fgets(isolate_name, sizeof isolate_name, isolates_file_2) != NULL) {
      int isolate_name_len;
      isolate_name_len = strlen(isolate_name);
      if (isolate_name[(isolate_name_len - 1)] == '\n') {
        isolate_name[(isolate_name_len - 1)] = '\0';
      }
      strcpy(isolate_name_array[isolate_count], isolate_name);
      strcpy(isolate_file_name_array[isolate_count], base_dir);
      strcat(isolate_file_name_array[isolate_count], "/Analysis/");
      strcat(isolate_file_name_array[isolate_count], analysis);
      strcat(isolate_file_name_array[isolate_count], "/");
      strcat(isolate_file_name_array[isolate_count], species);
      strcat(isolate_file_name_array[isolate_count], "_");
      strcat(isolate_file_name_array[isolate_count], analysis);
      strcat(isolate_file_name_array[isolate_count], "/Intergenic_files/");
      strcat(isolate_file_name_array[isolate_count], isolate_name);
      strcat(isolate_file_name_array[isolate_count], ".fasta");
      isolate_count++;
    }
    fclose(isolates_file_2);
  } else {
    perror(isolates_file_name);
  }
  int a;
  int b;
  int i;
  int genome_max = 1000000;
  char genome1[genome_max];
  char genome2[genome_max];
  int count;
  count = 0;
  for (a = 0; a < isolate_count; a++) {
    FILE *file1 = fopen(isolate_file_name_array[a], "r");
    if (file1 != NULL) {
      char line1[genome_max];
      while (fgets(line1, sizeof line1, file1) != NULL) {
        if (line1[0] != '>') {
          int line1_len = strlen(line1);
          line1_len = (line1_len - 1);
          if (line1[line1_len] == '\n') {
            line1[line1_len] = '\0';
          }
          strcpy(genome1, line1);
          fclose(file1);
        }
      }
    } else {
      perror(isolate_file_name_array[a]);
    }
    for (b = 0; b < isolate_count; b++) {
      if (a > b) {
        FILE *file2 = fopen(isolate_file_name_array[b], "r");
        if (file2 != NULL) {
          char line2[genome_max];
          while (fgets(line2, sizeof line2, file2) != NULL) {
            if (line2[0] != '>') {
              int line2_len = strlen(line2);
              line2_len = (line2_len - 1);
              if (line2[line2_len] == '\n') {
                line2[line2_len] = '\0';
              }
              strcpy(genome2, line2);
              fclose(file2);
            }
          }
        } else {
          perror(isolate_file_name_array[b]);
        }
        int genome_len;
        genome_len = strlen(genome1);
        int snp;
        snp = 0;
        int n;
        n = 0;
        for (i = 0; i < genome_len; i++) {
          if (genome1[i] == 'N' || genome2[i] == 'N') {
            n++;
          } else {
            if (genome1[i] != genome2[i]) {
              snp++;
            }
          }
        }
        int sites;
        sites = (genome_len - n);
        float div;
        div = ((float)snp / sites);
        float JC_div;
        JC_div = (((float)-3 / 4) * (log(1 - (((float)4 / 3) * div))));
        fprintf(output, "%s,%s,%i,%i,%0.6f\n", isolate_name_array[a], isolate_name_array[b], snp, sites, JC_div);
        count++;
      }
    }
  }
  printf("%s di calculated.\n", species);
  fprintf(log_file, "%s di calculated.\n", species);
  return 0;
}
```