Lisanne,

I don't normally see blank lines in a FASTQ file, I'd expect it to look like this:

@D5N3XBQ1:149:C0TCLACXX:2:1101:1342:2245 1:N:0:
TTAATAAAAGCTATTGAT
+
BB**?BHGG9?0?8888B
@D5N3XBQ1:149:C0TCLACXX:2:1101:1583:2228 1:N:0:
ATCGGGCGCAGGGACAGA
+
E99)?0?@6;'5>(;BE@
@D5N3XBQ1:149:C0TCLACXX:2:1101:1688:2238 1:N:0:
GCTGCCCTCCACCATATC

It also looks like the 3rd read is truncated, as the quality scores are missing.

However, a quick test with bowtie suggests that the blank lines aren't a problem. Is your fastq file compressed? (e.g. with gzip) That would give the error you're describing:

bowtie index.ebwt test.fastq.gz 
Error: reads file does not look like a FASTQ file
Command: bowtie index.ebwt test.fastq.gz

Piping uncompressed fastq into bowtie works

zcat test.fastq.gz | bowtie index.ebwt -
D5N3XBQ1:149:C0TCLACXX:2:1101:1342:2245 1:N:0:    +    XIV    548234    TTAATAAAAGCTATTGAT    BB**?BHGG9?0 8888B    0    5:G>A,14:G>T
D5N3XBQ1:149:C0TCLACXX:2:1101:1583:2228 1:N:0:    -    XI    611698    TCTGTCCCTGCGCCCGAT    @EB;(>5';6@?0?)99E    0    8:T>G,13:C>T
# reads processed: 2
# reads with at least one reported alignment: 2 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 2 alignments to 1 output stream(s)