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rlebbink
05-05-2017, 05:44 PM
Hi,

I am in the field of molecular biology, and I am currently aligning a huge file with DNA sequences to another file using terminal. There are all kinds of programs for this, I use a program called bowtie. The file to align is 10GB. I used to do this on my macbook pro using an terminal account quite easily, where it would run a few hours to do this. However, for some reason the same analysis now takes 2-3 days to run, I don't know why. What I can see, is that the activity in terminal seems to be intermittent. It analyses for a couple minutes, then it stops for a long time, where it occasionally 'reactivates' and starts aligning again. I have the same when analyzing on an external drive, or on the hard-drive.

Does anyone know how this can happen? And more importantly, how to fix it and keep the analysis going till complete? This would be much appreciated!
Cheers
RJ

Raz0rEdge
05-05-2017, 05:50 PM
Welcome to Mac-Forums..

With the application running, open up another terminal window or tab and run the 'top' command and find the 'Bowtie' app and see what its state is. It's possible that with a large file you are spending a lot of it waiting to load chunks of data and then processing it. Is it normal to have to process files of that size? Can that large file be broken down into smaller files and then the output put back together?

rlebbink
05-05-2017, 06:04 PM
Hi, I am not sure how to check the status. Any hints?
Regarding the size, this cannot be changed easily, some files are even much bigger, up to 100GB. This is sequencing data to sequence 600 million DNA molecules at the same time.... the output files are huge

Raz0rEdge
05-05-2017, 06:24 PM
Running the 'top' command in a Terminal window/tab will show you the status for all the applications. They will be things like sleeping, running, etc. In the case of Bowtie, it should likely be running all the time to ensure that its constantly processing the data..

MacInWin
05-06-2017, 06:21 PM
What you might do is to open Activity Monitor in the Utilities folder, let it be parked and running on the screen. Now go to terminal and start the process working. Watch Activity Monitor on the CPU tab to see what processes are using the CPU. You can sort the column to put the heavy user at the top by clicking on the column header. Follow the column labeled "% CPU" to see if terminal shows up and stays high. From that you can at least see if Terminal is, in fact, intermittent.

ron4mac
05-08-2017, 08:58 PM
Look into running Bowtie by invoking it with nice. It runs the process with an altered priority.
For example: nice -20 Bowtie -f dnadata

[edit: that may need to be nice --20 Bowtie -f dnadata (double hyphen to enter a negative value) ]