Generate PBS scripts for submission to the OSC to run the QIIME parallel blast pick OTUs script on multiple input sequence data sets.

usage: [-h] -i INPUT_FNA [INPUT_FNA ...] [-t WALLTIME] [-n JOB_NAME] [-v]

Required arguments

-i INPUT_FNA [INPUT_FNA ...], --input_fna INPUT_FNA [INPUT_FNA ...]

The names of the sequence files that will be have PBS scripts generated to process them. The expected input is from the script (e.g. 0.fna, 1.fna, …, n.fna).

-t WALLTIME, --walltime WALLTIME

The maximum running time to specify to the OSC queuing system for each script.

-n JOB_NAME, --job_name JOB_NAME

A descriptive name for the job script that will appear when checking the job status. Max length is 15 characters, but ‘_#’ will be appended to the name you provide to differentiate among all the jobs, so this parameter will be truncated if necessary to accommodate for the number of input files.

-h, --help

Show the help message and exit

-v, --verbose

This will cause the program to print the full path for each output file to the command line. This can be used for informational purposes or to pipe (|) to the PBS multi-submission script to automate job submission as soon as the scripts are created.