I am dealing with Illumina paired-end, 150 bp read-length datasets.

Here's what my fastq files looklike:

@SRR3405394.1 1 length=151
NCGACTGAGGTAATTACAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGGTACAGATCGGAA
+SRR3405394.1 1 length=151
#<GGGGAGGIGGGIGGIIIIIGIIIIIIIIIIGIIIIIIIGGIIGIGGIIIIIGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIGGIGGIIGGIIIIIGGGIIIIIGGIIIIGIIIGIGII<GGGGAGIGGAGG

I use this command to align with bwa:

bwa aln -t8 index 1.fastq > 1.sai
bwa aln -t8 index 2.fastq > 2.sai
bwa sampe index 1.sai 2.sai 1.fastq 2.fastq > aln_bwa.sam

When I look at my SAM file, I see this:

@SQ SN:selected LN:4641665
@PG ID:bwa  PN:bwa  VN:0.7.13-r1126 CL:bwa sampe index 1.sai 2.sai 1.fastq 2.fastq
SRR3405394.1    77  *   0   0   *   *   0   0   NCGACTGAGGTAATTACAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGGTACAGATCGGAA #<GGGGAGGIGGGIGGIIIIIGIIIIIIIIIIGIIIIIIIGGIIGIGGIIIIIGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIGGIGGIIGGIIIIIGGGIIIIIGGIIIIGIIIGIGII<GGGGAGIGGAGG
SRR3405394.1    141 *   0   0   *   *   0   0   GTACCCTGCACGTTCACGGGTCAGACCGCCTGGGCCGAGTGCGGAGATACGACGTTTGTGCGTAATCTCAGACAGCGGGTTGTTCTGGTCCATAAACTGAGACAGCTGGCTGGAACCGAAGAACTGTAATTACCTCAGTCGTAGATCGGAA GGAAGIIGIIIGIGIIGGGIIGGGGIGGIIAGGGIIGGGGGIGIGGGGIIGGGIGGGGGIIIIIGGIIIIIIIIIIIIGIIIGIIIIGIIIGGIIIGIIIIAGGIIIGGAGIGGGGGGI<GGGGIIIIIGGGIGIIIGIIIIIAGGIIIIG

All my reads are flagged 77 / 141, i.e. they're not aligned. What's the problem? I have a feeling that the quality scores are not recognized, but that's just a wild guess based on some quick reading.

Thank you in advance, TP