runQSLIMFinder: Run a list of QSLIMFinder jobs

In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference

Description

Run a list of QSLIMFinder jobs

Usage

runQSLIMFinder(commands_list, file_list, max_memory = 5000, onLSF = T,
  recursive = F, lsf_keyword = "TERM_MEMLIMIT", rm_log = T,
  memory_step = 100, memory_start = 200, Njobs_limit = 490)

modifyMemoryInBsub(commands, memory)

LSFrunQSLIMFinder(commands, job_name_sig = "batch_", Njobs_limit = 490)

jobsCrashed(commands_list, rm_log = T, lsf_keyword = "TERM_MEMLIMIT")

Arguments

commands_list	list containing: 1. command to set up enviromental variable IUPred_PATH; 2. character vector of bash commands that will lauch QSLIMFinder as a job on LSF cluster; 3, 4, 5 - directories where LSF should write stout and sterr
file_list	data.table containing path to files and directories for QSLIMFinder: fastafile, queryfile, outputdir, outputfile
max_memory	max memory to use for a job
onLSF	use LSF cluster to run QSLIMFinder jobs
recursive	how to create directories
lsf_keyword	character, LSF termination reason keyword (https://www.ibm.com/support/knowledgecenter/en/SSETD4_9.1.3/lsf_admin/termination_reasons_lsf.html). Defaults to "TERM_MEMLIMIT"
rm_log	remove log after checking for termination reason
Njobs_limit	integer, the number of LSF jobs allowed to run simultaneously
commands	character vector of commands generated by QSLIMFinderCommand that will launch QSLIMFinder jobs, commands_list[[2]]
memory	integer, how much memory should the job use
job_name_sig	string common to all job names

Value

list: character vector, commands that have crashed even at max_memory; data.table, corresponding rows of file_list

jobsCrashed(): vector of commands that crashed

Author(s)

Vitalii Kleshchevnikov

See Also

QSLIMFinderCommand

vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.