How to properly invoke FlatAssembler from an external progra

So, I've made a compiler for my own simplified low-level programming language, the source code is available here, and the executable files are available here. Now, the compiler, "aec.exe" or "aec.c" produces assembly code that can be compiled with FlatAssembler, however, it can't invoke FlatAssembler even if it's installed. The compiler itself is written in JavaScript, in the files "compiler.js" and "compiler.js", and "aec.c" mainly initializes Duktape (the JavaScript engine written in C). So, here is the contents of the "aec.c" file (compiled into "aec.exe" executable):

Code:

#include <stdio.h>
#include <string.h>
#include "duktape.h"
#include "tcc-patch.h"


void handle_fatal(void *udata,const char *msg)
{
    fprintf(stderr,"Fatal error in Javascript: %s\n",(msg?msg:"no message"));
    exit(1);
}

void catch(void *ctx)
{
    fprintf(stderr,"JavaScript reports the following error:\n\"%s\"\n",duk_safe_to_string(ctx,-1));
    duk_destroy_heap(ctx);
    exit(1);
}

int main(int argc, char **argv)
{
    if (argc-2 or strlen(argv[1])<5 or (strcmp(argv[1]+strlen(argv[1])-4,".AEC") and strcmp(argv[1]+strlen(argv[1])-4,".aec")))
    {
        fprintf(stderr,"Please invoke this program from command-line and supply an AEC source file as the only argument, for example:\n"
                "Windows: aec.exe euclid.aec\n"
                "Linux and MacOS: ./aec euclid.aec\n");
        return 1;
    }
#include "readCompiler.h"
    input=fopen("control.js","r");
    if (!input)
    {
        fprintf(stderr,"Can't open 'control.js'?!\n");
        fflush(stderr);
        return 1;
    }
    while (!feof(input))
        if (fscanf(input,"%[^\n]\n",line)){
            strcat(line,"\n");
            strcat(compilerString,line);
        }
    fclose(input);
    fprintf(stderr,"Initializing Duktape!\n");
    fflush(stderr);
    duk_context *ctx=duk_create_heap(0,0,0,0,handle_fatal);
    duk_push_c_function(ctx,getIEEE754,1);
    duk_put_global_string(ctx,"getIEEE754");
    duk_eval_string(ctx,compilerString);
    free(compilerString),free(line);
    duk_set_top(ctx,1);
    fprintf(stderr,"Compilation started!\n");
    fflush(stderr);
    input=fopen(argv[1],"r");
    if (!input)
    {
        fprintf(stderr,"Can't read \'%s\'!\n",argv[1]);
        fflush(stderr);
        return 1;
    }
    int lineNumber=0;
    line=calloc(512,1);
    int hasError=0;
    compilerString=calloc(1024,1);
    if (!compilerString or !line)
    {
        fprintf(stderr,"Out of memory!?\n");
        return 1;
    }
    while (!feof(input)) {
        lineNumber++;
        if (fgets(line,512,input))
        {
            if (line[strlen(line)-1]=='\n') line[strlen(line)-1]=0;
            if (line[strlen(line)-1]=='\r') line[strlen(line)-1]=0;
            memset(compilerString,0,512);
            strcat(compilerString,"compileString(\"");
            int i;
                        for (i=0; line[i]; i++)
                if (line[i]=='\\')
                    strcat(compilerString,"\\\\");
                else if (line[i]=='"')
                    strcat(compilerString,"\\\"");
                else
                    strncat(compilerString,line+i,1);
            strcat(compilerString,"\")");
            duk_push_string(ctx,compilerString);
            if (duk_peval(ctx))
            {
                const char *message=duk_safe_to_string(ctx,-1);
                if (strstr(message,"error")) hasError=1;
                fprintf(stderr,"Message on line %d:\n\"%s\"\n",lineNumber,message);
            }
            duk_pop(ctx);
        }
    }
    free(line);
    free(compilerString);
    fclose(input);
    if (!hasError) {
        duk_eval_string(ctx,"stack.length");
        if (duk_get_int(ctx,-1))
        {
            fprintf(stderr,"Control structures ('If', 'Else', 'While', 'EndIf' and 'EndWhile') appear not to be properly nested, compilation aborted!\n");
            fflush(stderr);
            return 1;
        }
        char *outputFileName=calloc(265,1);
        strncat(outputFileName,argv[1],strlen(argv[1])-4);
        strcat(outputFileName,".asm");
        FILE *output=fopen(outputFileName,"w");
        free(outputFileName);
        if (!output)
        {
            fprintf(stderr,"Can't open output file!\n");
            fflush(stderr);
            return 1;
        }
        duk_eval_string(ctx,"assembler");
        fprintf(output,";Generated by Arithmetic Expression Compiler (https://flatassembler.github.io/compiler.html) run in Duktape.\n"
                "%s",duk_get_string(ctx,-1));
        fclose(output);
        fprintf(stderr,"Compilation finished without errors!\n");
    }
    else
        fprintf(stderr,"Compilation aborted due to the errors reported by JavaScript!\n");
    duk_destroy_heap(ctx);
    return 0;
}

So, how would you modify it to invoke FlatAssembler? And checking whether FlatAssembler is in %PATH% and doing system("fasm assembly_language_file.asm") doesn't work, because then FlatAssembler reports it can't find "win32ax.inc" and other include files.