Is there a more elegant solution to the bwa-mem: paired reads have different names error? I'm currently trying to run bwa-mem on Influenza substrains using the following command: 

~/bwa mem h5n1_1_cons.fa h5n1_1_read1.fq h5n1_1_read2.fq


h5n1_1_cons.fa is the consensus sequence for substrain h5n1_1, and the fq files are paired end reads 1 and 2. Running the program gives me this error: 

[mem_sam_pe] paired reads have different names: "JQ714243-920-1", "JQ714243-920-2"


Visual inspection shows that the read names are identical until the last character. I have found a package (bbmap) with a utility, bbrename.sh, that renames the sequences, producing:

./bbrename.sh in=h5n1_1_read1.fq out=fixed prefix=h5n1_1


which yields the following output

-bash-4.2$ head fixh5n1_1_read1.fq
@h5n1_0
gaaaatgtctcaggagttgatgcatggtgtttaatctttggtttgcgctg
+
@4&gt;C5?7FA?9@@@;1,-4B+E??4E9,DA&gt;6CB)*2.)?7/.'65+75/
@h5n1_1
catcagttggattttgcctaaggatgtccaccatccttatcccaccaatt
+
7(9?)=C3AEF+@@F=C-E&gt;EE57CD:;'?.*?7;&gt;:3&gt;2.;29..)=2'
@h5n1_2
catgcatttgttggaataatgttctcacaaatcaactgtattgaccgctg


This fixes the problem and allows BWA-MEM to work. However, header information is discarded. Is there another way to ensure the header names are the same while retaining all header information?
Assuming the read name lines only contain things like @JQ714243-920-1 and nothing else, then sed -i '1~4 s/-[12]$//' file.fastq (N.B., example updated a bit for safety, thanks to @terdon) will remove the -1 and -2 suffixes.

However, you should try to figure out why the read names were munged into that form to begin with (at least Illumina machines won't produce that, I don't know about others).