Reference-based alignment using MUSKET

Question

[melissachua90]

I'm running MUSKET on my dataset trimmed_data.tar.gz using 1000 threads, 2000 threads, and 4000 threads on a HPC. I've been unable to obtain any results because the software seems to be running for a long time.

./../musket-1.1/musket -k 90 600000000 -p 1000 -zlib 9 -ino
rder trimmed_data.tar.gz -o dataset.fq

When I reduce the threads to 100, I get segmentation fault error.

Answer 1

[Mensur Dlakic]

This is the expected form of the command:

 musket [options] file

That means you can't have the -o switch after file name. Or, if you will, trimmed_data.tar.gz must come last. Also not sure why you are saving the file with .fa extension - presumably this is a fastq file?

Separately, it makes absolutely no sense to run this with 1000 threads (and about 4 times less sense to run it with 4000). There is absolutely no way that your read/write operations can catch up with what thousands of threads can do. I suggest you run this with 10-20 threads, a k-mer size of 21-25. In fact, it says on the program's web page that MAX_KMER_SIZE is 28, so you are way out of the ballpark with 90.

http://musket.sourceforge.net/homepage.htm

[melissachua90]

Thanks for the tip! Should I loop over all the samples individually or can I run Musket on the entire dataset trimmed_data.tar.gz?

[Mensur Dlakic]

There is no need to loop over samples if everything is in one file. You can go with the command you already used but with adjusted k-mer and threads options.

[melissachua90]

Would this command make sense for paired-end reads?

./../musket-1.1/musket -k 21 536870912 -p 20 -zlib 9 –omulti corrected trimmed_data.tar.gz –inorder

[Mensur Dlakic]

File name must come at the end, which means -inorder must move inside. Also, -omulti is for multiple outputs when you have multiple inputs, but you have a single input file which means that -o is more appropriate. Something like:

musket -k 21 536870912 -p 20 -zlib 9 -inorder -o corrected.gz trimmed_data.tar.gz

This is not that difficult to figure out if you read the explanations on musket's web site I referenced above.