How to store bowtie log?

[vixensjlin]

Hello there:

Under windows 7, I am trying to align reads by Bowtie like this
bowtie -t hg19 -S -p4 -m 1 -q XXXXXX.fastq > XXXXXX.sam

And after the alignment, the screen showed:

Time loading forward index: 00:00:15
Time loading mirror index: 00:00:14
Seeded quality full-index search: 01:26:49
# reads processed: 37763608
# reads with at least one reported alignment: 26849716 (71.10%)
# reads that failed to align: 3594644 (9.52%)
# reads with alignments suppressed due to -m: 7319248 (19.38%)
Reported 26849716 alignments to 1 output stream(s)
Time searching: 01:27:18
Overall time: 01:27:18

Is there a way to store the above log? I saw tophat got logs, but I cannot find any log file after the alignment.

Thanks!

[Apexy]

Hello vixensjlin,

At least this works for me in unix
bowtie -t hg19 -S -p4 -m 1 -q XXXXXX.fastq > XXXXXX.sam 2>&1 | tee hg19.XXX.log
Kindly check if there is a 'tee' unix command in windows.

HTH

MBandi

[CraigJ]

Similar to what Apexy said, you can use 2> to redirect stdout to a file (bowtie writes the summary log files to stdout). But it isn't necessary to pipe into tee for this.

So your command would just be:
bowtie -t hg19 -S -p4 -m 1 -q XXXXXX.fastq > XXXXXX.sam 2> XXXXXX.log

This is how I store the bowtie logs on my unix machine - I believe stdout redirection works the same on windows, so should work there too.