multi_parallel_pick_otus.py¶
Generate PBS scripts for submission to the OSC to run the QIIME parallel blast pick OTUs script on multiple input sequence data sets.
usage: osc_parallel_pick_otus.py [-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 split_sequence_data.py 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.