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BTW: I've gotten into the habit, especially since most of my commands are run on a batch queuing system, of redirecting all commands to a file so that I can examine them while they are running. E.g.,
my_command_that_is_sent_to_the_queue 2>&1 | tee my_command.stdout.stderr.txt
This probably does not apply to you but I wanted to mention it in case someone could use the idea.
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I believe that the text you want is put out on stderr not stdout. So you should be able to capture it via a redirect to stderr. E.g., in bash:
2>myfile-log.txt
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Redirecting terminal output of Bowtie
A slightly trivial question perhaps, but does anyone know why it isn't possible to redirect the output of Bowtie to a text file? I.e. the text printed to the terminal, rather than the actual alignments?
Here's the command, which always outputs a text file of zero size:
bowtie -p 3 -S mm9 -1 myfile1.fastq -2 myfile2.fastq myfile.sam > myfile-Log.txt
Many thanks,
AdamTags: None
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