newbie BWA alignment question

[Opusone]

another newbie question - I am trying to use BWA to align paired end reads to human ref genome.

here is the sequence of what i did -
1) alignment
bwa align ref fq1 > 1.sai

2) make sam
bwi sampe ref 1.sai 2.sai fq1 fq2 > .sam

3) convert to bam
samtools view -S -b .sam -o .bam

4) sort bam
samtools sort .bam .sorted

5) index bam
samtools index .sorted

6) check stats
samtools flagstat .bam > .stat

everything finished running without any error, but when i check the .stat file, this is what i see

0 + 0 duplicates
0 + 0 mapped (0.00%:nan%)
61091524 + 0 paired in sequencing
30545762 + 0 read1
30545762 + 0 read2
0 + 0 properly paired (0.00%:nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (0.00%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

in every sample, there is very few to no aligned reads. can anyone comment on what could possibly be the issue here and if there is a way to check the output after each stage in this process. thanks.

[swbarnes2]

.sams are human readable. So start by looking at those.

You did index the genome too, right?

[MBekritsky]

Did you align the second set of fastq sequences? All I see is
bwa align ref fq1 > 1.sai
but not
bwa align ref fq2 > 2.sai