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Java JCA - Input length must be multiple of 8 for padded decypher

I'm currently doing an assignment for a college course using Java's JCA.
The application takes in a file and encrypts it (or decrypts it) using DES-ECB. I am fully aware that it's not a secure encryption algorithm.
It encrypts fine, I believe, however when decrypting it blows up with a "Input length must be multiple of 8" even though the original message is being padded with PKCS5.
I have read all literature and quetions regarding this problem here on StackOverflow, but none of the answers seem to resolve this issue, which leads me to believe I am somehow corrupting the message/file...
For the encryption:
Cipher cipher = Cipher.getInstance("DES/ECB/PKCS5Padding");
cipher.init(Cipher.ENCRYPT_MODE, symmetricKey);
File file = new File(filePath);
FileOutputStream outputStream = new FileOutputStream("encrypted_"+file.getName());
CipherInputStream cipherStream = new CipherInputStream( new FileInputStream(file), cipher);
byte[] buffer = new byte[MAX_BUFFER]; //buffer para leitura
int bytes; //bytes a ler
//Encoder base64 - Apache Commons Codec
Base64 encoder = new Base64();
while ( (bytes = cipherStream.read(buffer)) != -1 ) {
byte[] encodedBuffer = encoder.encode(buffer);
outputStream.write(encodedBuffer, 0, bytes);
}
cipherStream.close();
outputStream.flush();
return outputStream;
For the decryption:
Cipher cipher = Cipher.getInstance("DES/ECB/PKCS5Padding");
cipher.init(Cipher.DECRYPT_MODE, symmetricKey);
File file = new File(filePath);
FileInputStream cipheredStream = new FileInputStream(file);
FileOutputStream outputStream = new FileOutputStream("decrypted_"+file.getName());
CipherOutputStream cipherOutStream = new CipherOutputStream(outputStream, cipher);
byte[] buffer = new byte[MAX_BUFFER];
int bytes;
//Decoder base 64 - Apache Commons Codec
Base64 decoder = new Base64();
cipheredStream.read(buffer);
byte[] decodedBuffer = decoder.decode(buffer);
byte[] output = cipher.doFinal(decodedBuffer);
cipherOutStream.write(output);
//TODO bug here -> use this for big files
/*while ( (bytes = cipheredStream.read(buffer)) != -1 ) {
byte[] decodedBuffer = decoder.decode(buffer);
cipherOutStream.write(decodedBuffer, 0, bytes);
}*/
cipherOutStream.close();
cipheredStream.close();
return outputStream;
I've tried using AES to no avail; I've tried no padding, obviously it didn't work.
I'm just lost and would appreciate knowing what I'm doing wrong.

Thanks to #Topaco, the solution was found using Base64InputStream.
Because the deciphering was being done BEFORE decoding, it was generating that error. It was fixed by doing this encryption side:
Base64OutputStream encoder = new Base64OutputStream(outputStream);
while ( (nBytes = cipherStream.read(buffer, 0, MAX_BUFFER)) != -1 )
encoder.write(buffer, 0, nBytes);
And decryption side the exact opposite:
Base64InputStream decoder = new Base64InputStream(fileInputStream);
while ( (nBytes = decoder.read(buffer, 0, MAX_BUFFER)) != -1 )
cipherOutStream.write(buffer, 0, nBytes);

Issues with reading & decrypting very LARGE files, in bytes, in Java

When reading from a very large encrypted file in Java, I am using the following code:
FileInputStream in = new FileInputStream("file.txt");
ByteArrayOutputStream baos = new ByteArrayOutputStream();
Writer writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(saveLocation), "utf-8"));
int read;
byte buffer[] = new byte[16384];
byte getData[] = new byte[16384];
while((read = in.read(buffer)) != -1)
{
baos.write(buffer, 0, read);
Cipher cipher = Cipher.getInstance(symCipher);
IvParameterSpec ivParameterSpec = new IvParameterSpec(initVecBytes);
cipher.init(Cipher.DECRYPT_MODE, originalKey, ivParameterSpec);
byte[] original = cipher.doFinal(baos.toByteArray());
String s = new String(original);
writer.append(s);
baos.reset();
}
writer.close();
As the file is very large (too large for me to load into memory in one go) I am reading it into a small buffer, then encrypting the small bytes of data and finally, writing them to a file.
However, when I do this, some of the data looks to be corrupted:
</AddressLine><_��SR����_�hEE</AddressLine></AddressLines><Postcode>
When I use a smaller file that isn't 16k it works fine, I only seem to get small amounts of corrupted data at the start of a new array read, then it's fine again until the next array read, and so on.
Anyone got any idea why this isn't working properly?

It's not working because most ciphers are stateful. Specifically, in cipher block chaining mode the plaintext must be XOR-ed with previous cipher text block. But every 16k, you are XORing it with the IV instead. You can't re-initialize the Cipher in the middle of a decryption operation.
Here are the five lines of code to which EJP alluded.
Cipher cipher = Cipher.getInstance(symCipher);
cipher.init(Cipher.DECRYPT_MODE, originalKey, new IvParameterSpec(initVecBytes));
try (InputStream in = Files.newInputStream(Paths.get("file.txt"))) {
Files.copy(new CipherInputStream(in, cipher), Paths.get(saveLocation));
}

Get rid of the ByteArrayOutputStream and the Writer and write the decrypted arrays directly to a FileOutputStream.
Use the same Cipher for the whole file, both when encrypting and decrypting, and initialize it once, not once per read.
You can do all this in about five lines of code with a CipherInputStream.

Decrypt file in parts

So I have these large files (6GB+) that I need to decrypt on a 32 bit computer. The general procedure that I used previously was to read the entire file in memory, then pass it on to the decrypt function and then write it all back to a file. This doesn't really work due to memory limitations. I did try passing the file in parts to the decrypt function but it seems to mess up around the boundaries of where I break up the file before sending it to the decrypt function.
I've tried breaking up the file in parts relative to key size but that doesnt seem to matter. I tried a byte array of size 2048 as well as a byte aray of size 294 thinking that might be the special boundary but, no luck. I can see parts of the file correctly decrypted but parts which are total gibberish.
Is it just NOT POSSIBLE to decrypt the file in chunks? If there is a way, then how?
Here is my decryption function / my attempt to decrypt in parts.
private Path outFile;
private void decryptFile(FileInputStream fis, byte[] initVector, byte[] aesKey, long used) {
//Assume used = 0 for this function.
byte[] chunks = new byte[2048]; //If this number is greater than or equal to the size of the file then we are good.
try {
if (outFile.toFile().exists())
outFile.toFile().delete();
outFile.toFile().createNewFile();
FileOutputStream fos = new FileOutputStream(outFile.toFile());
OutputStreamWriter out = new OutputStreamWriter(fos);
IvParameterSpec spec = new IvParameterSpec(Arrays.copyOfRange(initVector, 0, 16));
SecretKeySpec key = new SecretKeySpec(aesKey, "AES");
Cipher cipher = Cipher.getInstance("AES/CFB/NoPadding");
cipher.init(Cipher.DECRYPT_MODE, key, spec);
int x;
while ((x = fis.read(chunks, 0, chunks.length)) != -1) {
byte[] dec = cipher.doFinal(Arrays.copyOfRange(chunks, 0, x));
out.append(new String(dec));
}
out.close();
fos.close();
} catch (Exception e) {
e.printStackTrace();
LOG.error(ExceptionUtils.getStackTrace(e));
}
}

Consider using Cipher#update(byte[], int, int, byte[], int) instead of doFinal() for multipart operations. This will take care of part boundaries for you.
The last part of the deciphered data can be obtained by calling the doFinal(byte[] output, int outputOffset) method.

Manually implementing RSA in Java using BigInteger

I'm trying to implement RSA encryption and decryption of files in Java using BigInteger.
I have my parameters p, q, e, n, d
I read a file into a byte[]
System.out.println("Opening file: " + infile);
File file = new File(infile);
FileInputStream fis = new FileInputStream(file);
int filelength = (int)file.length();
byte[] filecontent = new byte[filelength];
fis.read(filecontent);
fis.close();
And then make a BigInteger from that byte[]
BigInteger plaintext = new BigInteger(filecontent);
Then encryption is simply
BigInteger ciphertext = plaintext.modPow(e, n);
And I write the ciphertext to a new encrypted file
FileOutputStream fos = new FileOutputStream(outfile);
fos.write(ciphertext.toByteArray());
fos.close();
Decryption is pretty much the same
BigInteger plaintext = ciphertext.modPow(d, n);
This worked perfectly fine when I first tested it with a small text file. It encrypted and decrypted just fine. However as I started to test with some other files like a jpg or zip, everything fell apart. I can't pinpoint the problem debugging but I do notice sometimes the conversion from the file byte[] to BigInteger results in an empty BigInteger object.
Is there something I have to do to the byte[] before encryption?

To solve this , you need to divide the file into chunk, which means for example take every 256 bit as a part and encrypt it ., and so on.

Why CipherOutputStream cannot write to ByteArrayOutputStream?

I am trying to encrypt a string and store the encrypted bytes in primitive array of bytes using CipherOutputStream which is backed by ByteArrayOutputStream but the size of ByteArrayOutputStream object remains zero and it does not conatin any bytes after something is written to CipherOutputStream object. Here is the code.
ByteArrayOutputStream out = new ByteArrayOutputStream();
CipherOutputStream cos = new CipherOutputStream(out, c);
PrintWriter pw = new PrintWriter(cos);
pw.println("Write something");
cos.flush();
out.flush();
System.out.println(out.size());
pw.close();
So I tried to make a comparison by changing the ByteArrayOutputStream to FileOutputStream using the code below. It turned out that the encrypted bytes are written to the target file. Does anyone have any idea why I cannot use ByteArrayOutputStream here? Can you suggest a solution as well?
FileOutputStream out = new FileOutputStream("/path/encrypted.txt");
CipherOutputStream cos = new CipherOutputStream(out, c);
PrintWriter pw = new PrintWriter(cos);
pw.println("Write something");
pw.close();

The only difference between these snippets is that in the first case you check the content before closing the stream, whereas in the second case - after closing. So, I guess you need to close the stream before checking.

The problem is the cipher.
Cipher cipher = Cipher.getInstance("RSA");
Has no padding.
Use
Cipher cipher = Cipher.getInstance("RSA/ECB/PKCS1Padding");
instead