[?]This page[?] says:

Some functions of FASTX-Toolkit do not work with FASTA-formatted sequences on multiple lines, thus it is sometimes necessary to transform the file so that fasta_formatter each sequence is on a single line.

Pierre is probably right. You need to reformat your fastq so it's in 4 lines.

Try using this script to reformat you fastq into 4 lines:

import sys

inFile = open(sys.argv[1],'r')

header = ''
seq = ''
qual = ''

seqs = False
quals = False
for line in inFile:
    if line[0] == "@":
        if header != '':
            print "@" + header
            print seq.upper()
            print "+" + header
            print qual

        header = line[1:].strip()
        seqs = True
        quals = False
        qual = ''
        seq = ''
    elif line[0] == "+":
        seqs = False
        quals = True
    else:
        if quals:
            qual += line.strip()
        if seqs:
            seq += line.strip()

print "@" + header
print seq
print "+" + header
print qual

Save as yourName.py. Use by:

python yourName.py yourFastaq.fastq > reformatted.fastq

does fastq_quality_filter accepts the fastq files having more than 4 lines per records (name,seq,name2,qualitie)?