trouble repeating a BWA alignment command

[efoss]

I aligned a fastq file to a refseq data base successfully as follows:

create an index:

bwa index -p RefSeqbwaidx -a bwtsw /mnt/fred/home/efoss/gene_databases/refGene.txt.07Jun2010.fa

(
The refGene.txt.07June2010.fa file has a format like this:

>NM_002697
CGGAGGAGCAGCGAGTCAAGATGAGAGTTCAGCCGCGGCGGCAGCAGCAGCAGACTGGAAAAGTAAGAAGAGCTTTCCTGCCTTTTTAATTACCAAACTA
CTCTCAGTTTTCAATGAATCAGTTCAAAGAAAGAATGCAGTCTTTCTATACCTGACTCAAGAATGAACAATCCGTCAGAAACCAGTAAACCATCTATGGA
GAGTGGAGATGGCAACACAGGCACACAAACCAATGGTCTGGACTTTCAGAA
)


I align my reads:

bwa aln -t 6 RefSeqbwaidx /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r1.fq > sequence_r1.fq.bwa

and I convert the output to SAM format:

bwa samse RefSeqbwaidx sequence_r1.fq.bwa /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r1.fq > sequence_r1.fq.sam

I look into the SAM file and everything looks good. Now I go to align the corresponding "r2" file from the same experiment:

bwa aln -t 6 RefSeqbwaidx /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r2.fq > sequence_r2.fq.bwa

The alignment takes a similar amount of time, the messages reported back as the computer is working look the same, but then in the end my sequence_r2.fq.bwa file is empty. Does anyone have an idea about what is going on?

Thank you.

Eric