I'm using Bowtie2 to align some simulated E coli reads, on my laptop so it's taking a while, and the only measure of progress is the increasing size of the sam file Bowtie is writing. Unfortunately, I don't know how big that sam file should eventually get -- is there any rough guide to estimating the size of a sam file based on the size of the input fastq files? Is it nice and simple and they should be roughly the same size, or will it vary depending on the quality of the alignment?
Estimation by size is difficult, because reads without mapping will only contribute very little. But you can do something like this:

```
ID=`tail -n1 .sam | cut -f1`  # gives you the latest mapped read id
LINE=`grep -n "^@$ID" .fastq | cut -f1 -d:`  
   # last id line (use > for fasta)
TOTAL=`cat .fastq | wc -l` # total lines
echo "scale=5; $LINE/$TOTAL * 100" | bc  # percentage done
```

[edit] the syntax should work now.

[edit] bc scale.