user: What is the c source code of the assembly code below?

```asm
<main>:
  endbr64
  push   %rbp
  mov    %rsp,%rbp
  push   %r15
  push   %r14
  push   %r13
  push   %r12
  push   %rbx
  mov    %rsi,%rbx
  sub    $0x88,%rsp
  mov    %fs:0x28,%rax
  mov    %rax,-0x38(%rbp)
  mov    %rsp,%rax
  cmp    %rax,%rsp
  je     L243
L421:
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  cmp    %rax,%rsp
  jne    L421
L243:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    0x8(%rbx),%rsi
  mov    %rsp,%rdi
  mov    %rsp,-0x98(%rbp)
  call   <strcpy@plt>
L45:
  cmp    -0x98(%rbp),%rsp
  je     L402
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L45
L402:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    0x10(%rbx),%rsi
  mov    %rsp,%rdi
  mov    %rsp,%r14
  call   <strcpy@plt>
L499:
  cmp    %r14,%rsp
  je     L381
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L499
L381:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    0x18(%rbx),%rsi
  mov    %rsp,%rdi
  mov    %rsp,-0x58(%rbp)
  call   <strcpy@plt>
L282:
  cmp    -0x58(%rbp),%rsp
  je     L225
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L282
L225:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    0x20(%rbx),%rsi
  mov    %rsp,%rdi
  mov    %rsp,-0xa0(%rbp)
  call   <strcpy@plt>
L162:
  cmp    -0xa0(%rbp),%rsp
  je     L210
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L162
L210:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    -0x58(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  lea    D112(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D233(%rip),%rsi
  mov    %rsp,%rdi
  call   <fopen@plt>
  mov    %rax,-0xa8(%rbp)
  mov    %rsp,%rax
L247:
  cmp    %rax,%rsp
  je     L639
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L247
L639:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  lea    D122(%rip),%r15
  mov    -0x58(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  lea    D158(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r15,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    -0x98(%rbp),%rbx
  mov    %rsp,%rdi
  mov    %rbx,%rsi
  call   <strcat@plt>
  lea    D207(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r15,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %rbx,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D68(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    -0xa0(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D131(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D26(%rip),%rsi
  mov    %rsp,%rdi
  call   <fopen@plt>
  mov    $0x2a,%edx
  mov    $0x1,%esi
  lea    D50(%rip),%rdi
  mov    %rax,%rcx
  mov    %rax,-0x88(%rbp)
  call   <fwrite@plt>
  mov    %rsp,%rax
L91:
  cmp    %rax,%rsp
  je     L357
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L91
L357:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    -0x58(%rbp),%rsi
  mov    %rsp,%rdi
  mov    %rsp,-0x50(%rbp)
  call   <strcpy@plt>
  lea    D45(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    -0x98(%rbp),%rbx
  mov    %rsp,%rdi
  mov    %rbx,%rsi
  call   <strcat@plt>
  lea    D128(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %rbx,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D64(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
L240:
  cmp    -0x50(%rbp),%rsp
  je     L89
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L240
L89:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  lea    D22(%rip),%rsi
  xor    %ebx,%ebx
  mov    -0x50(%rbp),%rdi
  call   <fopen@plt>
  mov    %rsp,%r12
  mov    %rax,%r13
  test   %rax,%rax
  jne    L575
  jmp    L376
  xchg   %ax,%ax
L321:
  add    $0x1,%ebx
L575:
  mov    %r13,%rdx
  mov    $0x3e8,%esi
  mov    %r12,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L321
  mov    %r13,%rdi
  call   <fclose@plt>
L474:
  movslq %ebx,%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     L238
L610:
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  cmp    %rcx,%rsp
  jne    L610
L238:
  and    $0xfff,%edx
  sub    %rdx,%rsp
  test   %rdx,%rdx
  je     L378
  orq    $0x0,-0x8(%rsp,%rdx,1)
L378:
  mov    %rsp,-0x90(%rbp)
  mov    %rax,%rdx
  mov    %rsp,%rcx
  and    $0xfffffffffffff000,%rax
  and    $0xfffffffffffffff0,%rdx
  sub    %rax,%rcx
L390:
  cmp    %rcx,%rsp
  je     L394
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L390
L376:
  mov    -0x50(%rbp),%rdi
  call   <perror@plt>
  jmp    L474
L394:
  mov    %rdx,%rax
  and    $0xfff,%eax
  sub    %rax,%rsp
  test   %rax,%rax
  je     L94
  orq    $0x0,-0x8(%rsp,%rax,1)
L94:
  mov    -0x50(%rbp),%rdi
  lea    D22(%rip),%rsi
  call   <fopen@plt>
  mov    %rax,-0x48(%rbp)
  test   %rax,%rax
  je     L348
  mov    %rsp,-0x70(%rbp)
  mov    -0x90(%rbp),%r13
  mov    %rsp,%rbx
  movl   $0x0,-0x50(%rbp)
  jmp    L487
  nop
L74:
  mov    %r12,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  cltq
  cmpb   $0xa,(%r12,%rax,1)
  jne    L414
  movb   $0x0,(%r12,%rax,1)
L414:
  mov    %r13,%rdi
  mov    %r12,%rsi
  add    $0x3e8,%r13
  call   <strcpy@plt>
  mov    -0x58(%rbp),%rsi
  mov    %rbx,%rdi
  call   <strcpy@plt>
  mov    %rbx,%rdi
  lea    D158(%rip),%rsi
  call   <strcat@plt>
  mov    %rbx,%rdi
  mov    %r14,%rsi
  call   <strcat@plt>
  mov    %rbx,%rdi
  mov    %r15,%rsi
  call   <strcat@plt>
  mov    -0x98(%rbp),%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    %rbx,%rdi
  lea    D207(%rip),%rsi
  call   <strcat@plt>
  mov    %rbx,%rdi
  mov    %r14,%rsi
  call   <strcat@plt>
  mov    %rbx,%rdi
  lea    D182(%rip),%rsi
  call   <strcat@plt>
  mov    -0xa0(%rbp),%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    %rbx,%rdi
  mov    %r15,%rsi
  call   <strcat@plt>
  mov    %rbx,%rdi
  mov    %r12,%rsi
  call   <strcat@plt>
  mov    %rbx,%rdi
  lea    D146(%rip),%rsi
  add    $0x3e8,%rbx
  call   <strcat@plt>
  addl   $0x1,-0x50(%rbp)
L487:
  mov    -0x48(%rbp),%rdx
  mov    $0x3e8,%esi
  mov    %r12,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L74
  mov    -0x48(%rbp),%rdi
  call   <fclose@plt>
  lea    -0xf4000(%rsp),%rax
L156:
  cmp    %rax,%rsp
  je     L103
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L156
L103:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,-0x78(%rbp)
  lea    -0xf4000(%rsp),%rax
L636:
  cmp    %rax,%rsp
  je     L609
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L636
L348:
  mov    -0x50(%rbp),%rdi
  call   <perror@plt>
L241:
  mov    -0xa0(%rbp),%r14
  mov    -0x98(%rbp),%rbx
  lea    D164(%rip),%r12
  mov    %r12,%rdi
  mov    %r14,%rdx
  mov    %rbx,%rsi
  call   <printf@plt>
  xor    %eax,%eax
  mov    %r14,%rcx
  mov    %rbx,%rdx
  mov    -0xa8(%rbp),%rdi
  mov    %r12,%rsi
  call   <fprintf@plt>
  mov    -0x38(%rbp),%rax
  sub    %fs:0x28,%rax
  jne    L586
  lea    -0x28(%rbp),%rsp
  xor    %eax,%eax
  pop    %rbx
  pop    %r12
  pop    %r13
  pop    %r14
  pop    %r15
  pop    %rbp
  ret
L609:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  cmpl   $0x0,-0x50(%rbp)
  mov    %rsp,-0x80(%rbp)
  movq   $0x0,-0x58(%rbp)
  movl   $0x0,-0x48(%rbp)
  je     L241
  nopl   0x0(%rax)
L220:
  mov    -0x70(%rbp),%r12
  add    -0x58(%rbp),%r12
  lea    D22(%rip),%rsi
  mov    %r12,%rdi
  call   <fopen@plt>
  mov    %rax,%rbx
  test   %rax,%rax
  je     L650
  lea    -0xf4000(%rsp),%rax
  mov    %rsp,%r12
  cmp    %rax,%rsp
  je     L187
L233:
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  cmp    %rax,%rsp
  jne    L233
L187:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,%r13
  jmp    L244
  nopl   (%rax)
L466:
  cmpb   $0x3e,0x0(%r13)
  jne    L618
L244:
  mov    %rbx,%rdx
  mov    $0xf4240,%esi
  mov    %r13,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L466
  mov    %r12,%rsp
L446:
  mov    -0x90(%rbp),%r14
  mov    -0x58(%rbp),%rax
  xor    %ebx,%ebx
  mov    -0x70(%rbp),%r13
  add    %r14,%rax
  mov    %rax,-0x68(%rbp)
  jmp    L621
  nopl   (%rax)
L547:
  add    $0x1,%ebx
  add    $0x3e8,%r14
  add    $0x3e8,%r13
  cmp    %ebx,-0x50(%rbp)
  je     L628
L621:
  cmp    %ebx,-0x48(%rbp)
  jle    L547
  lea    D22(%rip),%rsi
  mov    %r13,%rdi
  call   <fopen@plt>
  mov    %rax,%r12
  test   %rax,%rax
  je     L422
  lea    -0xf4000(%rsp),%rax
  mov    %rsp,-0x60(%rbp)
  cmp    %rax,%rsp
  je     L73
L504:
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  cmp    %rax,%rsp
  jne    L504
L73:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,%r15
  jmp    L214
  nopl   (%rax)
L55:
  cmpb   $0x3e,(%r15)
  jne    L256
L214:
  mov    %r12,%rdx
  mov    $0xf4240,%esi
  mov    %r15,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L55
  mov    -0x60(%rbp),%rsp
L245:
  mov    -0x78(%rbp),%r15
  mov    %r15,%rdi
  call   <strlen@plt>
  mov    %eax,%r9d
  test   %eax,%eax
  jle    L443
  movslq %eax,%rdi
  mov    -0x80(%rbp),%r10
  xor    %eax,%eax
  xor    %esi,%esi
  xor    %r12d,%r12d
  mov    %r15,%r8
  jmp    L25
  nopl   (%rax)
L570:
  movzbl (%r10,%rax,1),%ecx
  cmp    $0x4e,%cl
  je     L484
  cmp    %cl,%dl
  setne  %dl
  add    $0x1,%rax
  movzbl %dl,%edx
  add    %edx,%r12d
  cmp    %rax,%rdi
  je     L149
L25:
  movzbl (%r8,%rax,1),%edx
  cmp    $0x4e,%dl
  jne    L570
L484:
  add    $0x1,%rax
  add    $0x1,%esi
  cmp    %rax,%rdi
  jne    L25
L149:
  pxor   %xmm0,%xmm0
  sub    %esi,%r9d
  cvtsi2ss %r12d,%xmm0
L481:
  pxor   %xmm1,%xmm1
  mov    %r9d,-0x60(%rbp)
  cvtsi2ss %r9d,%xmm1
  divss  %xmm1,%xmm0
  movss  D116(%rip),%xmm1
  mulss  D41(%rip),%xmm0
  subss  %xmm0,%xmm1
  cvttss2si %xmm1,%edi
  call   <log@plt>
  mov    -0x60(%rbp),%r9d
  mov    -0x68(%rbp),%rdx
  mov    %r12d,%r8d
  mulss  D187(%rip),%xmm0
  mov    %r14,%rcx
  mov    -0x88(%rbp),%rdi
  lea    D221(%rip),%rsi
  mov    $0x1,%eax
  cvtss2sd %xmm0,%xmm0
  call   <fprintf@plt>
  jmp    L547
  nopl   (%rax)
L628:
  addl   $0x1,-0x48(%rbp)
  mov    -0x48(%rbp),%eax
  addq   $0x3e8,-0x58(%rbp)
  cmp    %eax,-0x50(%rbp)
  jne    L220
  jmp    L241
  nopl   (%rax)
L256:
  mov    %r15,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  cltq
  cmpb   $0xa,(%r15,%rax,1)
  jne    L191
  movb   $0x0,(%r15,%rax,1)
L191:
  mov    -0x80(%rbp),%rdi
  mov    %r15,%rsi
  call   <strcpy@plt>
  mov    %r12,%rdi
  call   <fclose@plt>
  jmp    L214
  nopw   0x0(%rax,%rax,1)
L618:
  mov    %r13,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  cltq
  cmpb   $0xa,0x0(%r13,%rax,1)
  jne    L563
  movb   $0x0,0x0(%r13,%rax,1)
L563:
  mov    -0x78(%rbp),%rdi
  mov    %r13,%rsi
  call   <strcpy@plt>
  mov    %rbx,%rdi
  call   <fclose@plt>
  jmp    L244
  nopl   0x0(%rax)
L422:
  mov    %r13,%rdi
  call   <perror@plt>
  jmp    L245
  nopl   (%rax)
L650:
  mov    %r12,%rdi
  call   <perror@plt>
  jmp    L446
L443:
  pxor   %xmm0,%xmm0
  xor    %r12d,%r12d
  jmp    L481
L586:
  call   <__stack_chk_fail@plt>
```

tool_calls: name: extract_symbolic_data
arguments: label: D112
datatype: string
name: extract_symbolic_data
arguments: label: D233
datatype: string
name: extract_symbolic_data
arguments: label: D122
datatype: string
name: extract_symbolic_data
arguments: label: D158
datatype: string
name: extract_symbolic_data
arguments: label: D207
datatype: string
name: extract_symbolic_data
arguments: label: D68
datatype: string
name: extract_symbolic_data
arguments: label: D131
datatype: string
name: extract_symbolic_data
arguments: label: D26
datatype: string
name: extract_symbolic_data
arguments: label: D50
datatype: string
name: extract_symbolic_data
arguments: label: D45
datatype: string
name: extract_symbolic_data
arguments: label: D128
datatype: string
name: extract_symbolic_data
arguments: label: D64
datatype: string
name: extract_symbolic_data
arguments: label: D22
datatype: string
name: extract_symbolic_data
arguments: label: D182
datatype: string
name: extract_symbolic_data
arguments: label: D146
datatype: string
name: extract_symbolic_data
arguments: label: D164
datatype: string
name: extract_symbolic_data
arguments: label: D116
datatype: byte[4]
name: extract_symbolic_data
arguments: label: D41
datatype: byte[4]
name: extract_symbolic_data
arguments: label: D187
datatype: byte[4]
name: extract_symbolic_data
arguments: label: D221
datatype: string

tool: D112: /Analysis/log.txt

tool: D233: a

tool: D122: /

tool: D158: /Analysis/

tool: D207: _

tool: D68: _di_upstream_

tool: D131: .csv

tool: D26: w

tool: D50: Isolate_1,Isolate_2,SNPs,Sites,Divergence


tool: D45: /Analysis/Core_genome_alignment/

tool: D128: _Core_genome_alignment/

tool: D64: _isolates.txt

tool: D22: r

tool: D182: /Intergenic_files_upstream_

tool: D146: .fasta

tool: D164: %s di upstream %s calculated.


tool: {"D116": [0x00,0x00,0x80,0x3f]}

tool: {"D41": [0xab,0xaa,0xaa,0x3f]}

tool: {"D187": [0x00,0x00,0x40,0xbf]}

tool: D221: %s,%s,%i,%i,%0.6f


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 upstream_len[arg_len];
  strcpy(upstream_len, argv[4]);
  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_upstream_");
  strcat(output_file_name, upstream_len);
  strcat(output_file_name, ".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/Core_genome_alignment/");
  strcat(isolates_file_name, species);
  strcat(isolates_file_name, "_Core_genome_alignment/");
  strcat(isolates_file_name, species);
  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_upstream_");
      strcat(isolate_file_name_array[isolate_count], upstream_len);
      strcat(isolate_file_name_array[isolate_count], "/");
      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 upstream %s calculated.\n", species, upstream_len);
  fprintf(log_file, "%s di upstream %s calculated.\n", species, upstream_len);
  return 0;
}
```