Hi Satyajeet

I am trying to get this log to work for batch processing multiple files - would something like this work?

#!/bin/bash
#Alignment using bowtie2
for file in *.fq ; do

    (bowtie2 -p60 --met-file "path/to/metrics/$file_metrics.txt"  -x path/to/refgenome -U "$file" -S "path/to/output/$file.sam") 2>$file.log

done

Thanks!

Almost all bioinformatic tools write to stderr for some reason.
I guess the logic is that if they output data on stdout it can be piped to something else, whilst info messages go to stderr - but I agree this is totally un-POSIX, and would never fly outside of bioinformatics. But hey - its not a big deal at the end of the day.