Xenome not outputting FASTQ formatted files?

[Seq^3]

Any users of Xenome run into this? You start with an input file that follows FASTQ format (line 1 begins with @ and line 3 begins with +):

@HISEQ03:124:C3R2RACXX:5:1101:2218:1990 1:N:0:TGACCA
ATGCNAACTACATTGCCTGGTGTCAAGGTGGGAAAATCCTCTTTTATAACATAAAATCCTCTTCTAATCCATGTTGACCCAAGTCCTGGCTGTCTGAGGG
+
<BBF#0BBFFFFFFFFIIBFFFBFFBFF<FFFIFFFFF<FFBFIIFFFFFFIIFFFIIIIIIIIIIBFIFFFFFFBFFBFFFFBBBBBBBB<BBBBBBBB

but the output loses the @ and + and is then not recognized by Tophat and probably other programs:

HISEQ03:124:C3R2RACXX:5:1101:2218:1990 1:N:0:TGACCA
ATGCNAACTACATTGCCTGGTGTCAAGGTGGGAAAATCCTCTTTTATAACATAAAATCCTCTTCTAATCCATGTTGACCCAAGTCCTGGCTGTCTGAGGG

<BBF#0BBFFFFFFFFIIBFFFBFFBFF<FFFIFFFFF<FFBFIIFFFFFFIIFFFIIIIIIIIIIBFIFFFFFFBFFBFFFFBBBBBBBB<BBBBBBBB

Is there some reason here that I don't understand for the output files to lose this?

Thanks!

[Seq^3]

Well I just added an awk script to the end of it that looks like this. Hacky but it works:

awk '{if (NR % 4 == 1) print \"@\"$0; else if (NR % 4 == 3) print \"+\"$0; else print $0 }'