This program uses the Work Queue system to distributed tasks among processors. After starting sand_filter_master, you must start a number of work_queue_worker(1) processes on remote machines. The workers will then connect back to the master process and begin executing tasks. The actual filtering is performed by sand_filter_kernel(1) on each machine.
-p <port> | |
Port number for queue master to listen on. (default: 9123) | |
-s <size> | |
Number of sequences in each filtering task. (default: 1000) | |
-r <file> | |
A meryl file of repeat mers to be filtered out. | |
-R <n> | |
Automatically retry failed jobs up to n times. (default: 100) | |
-k <size> | |
The k-mer size to use in candidate selection (default is 22). | |
-w <size> | |
The minimizer window size. (default is 22). | |
-u | If set, do not unlink temporary binary output files. |
-c <file> | |
Checkpoint filename; will be created if necessary. | |
-d <flag> | |
Enable debugging for this subsystem. (Try -d all to start.) | |
-F <number> | |
Work Queue fast abort multiplier. (default is 10.) | |
-Z <file> | |
Select port at random and write it out to this file. | |
-o <file> | |
Send debugging to this file. | |
-v | Show version string |
-h | Show this help screen |
% sand_compress_reads mydata.fasta mydata.cfa % work_queue_worker localhost 9123 & % sand_filter_master mydata.cfa mydata.candTo speed up the process, run more work_queue_worker(1) processes on other machines, or use condor_submit_workers(1) or sge_submit_workers(1) to start hundreds of workers in your local batch system.