cfm_predict_batch: Batch CFM prediction using a Linux cluster with a SLURM...

In gjgetzinger/cfmR: R Wrapper for calling the Competitive Fragmentation Modeling for Metabolite Identifiction (CFM-ID) algorithm

Description

Batch CFM prediction using a Linux cluster with a SLURM scheduler

Usage

cfm_predict_batch(
  id,
  out_dir,
  input_smiles_or_inchi,
  prob_thresh_for_prune = 0.001,
  include_annotations = 1,
  apply_post_processing = 1,
  param_filename,
  config_filename,
  slurm_options,
  cpus_per_node,
  nodes
)

Arguments

id	A molecule identifier. Used for the filename of the cfm-predict output file.
out_dir	A directory to write the cfm-predict results.
input_smiles_or_inchi	The smiles or inchi string of the structure whose spectra you want to predict.
prob_thresh_for_prune	The probability below which to prune unlikely fragmentations (default 0.001)
include_annotations	Whether to include fragment information in the output spectra (0 = NO (default), 1 = YES ). Note: ignored for msp/mgf output.
apply_post_processing	Whether or not to post-process predicted spectra to take the top 80 (whichever comes first) (0 = OFF, 1 = ON (default) ).
param_filename	The filename where the parameters of a trained cfm model can be found (if not given, assumes param_output.log in current directory)
config_filename	The filename where the configuration parameters of the cfm model can be found (if not given, assumes param_config.txt in current directory)
slurm_options	A named list of options recognized by sbatch; see Details below for more information.
cpus_per_node	The number of CPUs per node on the cluster; determines how many processes are run in parallel per node.
nodes	The (maximum) number of cluster nodes to spread the calculation over. slurm_apply automatically divides params in chunks of approximately equal size to send to each node. Less nodes are allocated if the parameter set is too small to use all CPUs on the requested nodes.

Value

A slurm_job object containing the jobname and the number of nodes effectively used.

gjgetzinger/cfmR documentation built on May 11, 2020, 1 p.m.