Sirius CLI Help#

Why this page?#

During my development I found it easier to use a markdown based documentation instead of always using the --help command. I thought it might be useful for someone else.

General command structure.#

sirius [-hV] [--noCite] [--recompute] [--cores=<numOfCores>]
              [--instance-buffer=<initialInstanceBuffer>] [--log=<logLevel>]
              [--maxmz=<maxMz>] [--workspace=<workspace>]
              [[-o=<outputProjectLocation>] [--no-compression]
              [--update-fingerprint-version]
              [--naming-convention=<projectSpaceFilenameFormatter>]]
              [[-i=<inputPath>[,<inputPath>...] [-i=<inputPath>[,
              <inputPath>...]]... [--ignore-formula] [--allow-ms1-only]]
              [-z=<parentMz> [--adduct=<ionType>] [-f=<formula>] -2=<ms2File>[,
              <ms2File>...] [-1=<ms1File>[,<ms1File>...]]]...] [COMMAND]

Options#

Command	Description
-h, –help	Show this help message and exit.
-V, –version	Print version information and exit.
–log, –loglevel=	Set logging level of the Jobs SIRIUS will execute. Valid values: SEVERE, WARNING, INFO, FINER, ALL. Default: WARNING.
–cores, –processors=	Number of CPU cores to use. If not specified, Sirius uses all available cores.
–instance-buffer, –compound-buffer, –initial-compound-buffer=	Number of compounds that will be loaded into the Memory. A larger buffer ensures that there are enough compounds available to use all cores efficiently during computation. A smaller buffer saves Memory. To load all compounds immediately, set it to -1. Default (numeric value 0): 3 x –cores. Note that for <DATASET_TOOLS> the compound buffer may have no effect because these tools may have to load compounds simultaneously into the memory. Default: 0.
–workspace=	Specify Sirius workspace location. This is the directory for storing property files, logs, databases, and caches. This is NOT for the project-space that stores the results! Default is $USER_HOME/.sirius-<MINOR_VERSION>.
–recompute	Recompute results of ALL tools where results are already present. Per default, already present results will be preserved, and the instance will be skipped for the corresponding Task/Tool.
–maxmz=	Only consider compounds with a precursor m/z lower or equal [–maxmz]. All other compounds in the input will be skipped. Default: Infinity.
–noCite, –noCitations, –no-citations	Do not write summary files to the project-space.

Specify OUTPUT Project-Space#

Command	Description
-o, –output, –project=	Specify the project-space to write into. If no [–input] is specified, it is also used as input. For compression use the File ending .zip or .sirius.
–naming-convention=	Specify a naming scheme for the compound directories in the project-space. Default % index_%filename_%compoundname.
–no-compression	Does not use compressed project-space format (not recommended) when creating the project-space. If an existing project-space is opened, this parameter has no effect.
–update-fingerprint-version	Updates Fingerprint versions of the input project to the one used by this SIRIUS version. WARNING: All Fingerprint related results (CSI: FingerID, CANOPUS) will be lost!

Specify multi-compound inputs (.ms, .mgf, .mzML/.mzXml, .sirius)#

Command	Description
-i, –input=[,…]	Specify the input in multi-compound input formats: Preprocessed mass spectra in .ms or .mgf file format, LC/MS runs in .mzML/.mzXml format or already existing SIRIUS project-spaces (uncompressed/compressed) but also any other file type e.g. to provide input for STANDALONE tools.
–ignore-formula	Ignore given molecular formula if present in .ms or .mgf input files.
–allow-ms1-only	Allow MS1 only data to be imported.

Specify generic inputs (CSV) on a per compound level#

Command	Description
-1, –ms1=[,…]	MS1 spectra files.
-2, –ms2=[,…]	MS2 spectra files.
-z, –mz, –precursor, –parentmass=	The mass of the parent ion for the specified ms2 spectra.
–adduct, –ionization=	Specify the adduct for this compound. Default: [M+?]+.
-f, –formula=	Specify the neutralized formula of this compound. This will be used for tree computation. If given, no mass decomposition will be performed.

Commands#

Command	Description
`config`	Override all possible default configurations of this toolbox from the command line.
`project-space, PS`	Modify a given project space: Read project(s) with `--input`, apply modification and write the result via `--output`. If either `--input` or `--output` is given, the modifications will be made in-place.
`custom-db, DB`	Generate a custom searchable structure database. Import multiple files with compounds as SMILES or InChi into this DB.
`similarity`	Computes the similarity between all compounds in the dataset and outputs a matrix of similarities.
`decomp`	Small tool to decompose masses with given deviation, ionization, chemical alphabet, and chemical filter.
`mgf-export, MGF`	Exports the spectra of a given input as MGF.
`ftree-export`	Exports the fragmentation trees of a project into various formats.
`prediction-export, EPR`	Exports predictions from CSI: FingerID and CANOPUS.
`fingerprinter, FP`	Compute SIRIUS compatible fingerprints from PubChem standardized SMILES in TSV format.
`gui, GUI`	Starts the graphical user interface of SIRIUS.
`asService, rest, REST`	Experimental/unstable: Starts SIRIUS as a background (REST) service that can be requested via a REST-API.
`login`	Allows a user to log in for SIRIUS Webservices (e.g., CSI: FingerID or CANOPUS) and securely store a personal access token.
`settings`	Configure persistent (technical) settings of SIRIUS (e.g., ProxySettings or ILP Solver).
`install-autocompletion`	Generates and installs an Autocompletion-Script with all subcommands. Default installation is for the current user.
`write-summaries, W`	Write summary files from a given project space into the given project space or a custom location.
`lcms-align, A`	Preprocessing: Align and merge compounds of multiple LCMS Runs. Use this tool if you want to import from mzML/mzXml.
`canopus, compound-classes`	Compound Tool: Predict compound categories for each compound individually based on its predicted molecular fingerprint (CSI: FingerID) using CANOPUS.
`formula, tree, sirius`	Compound Tool: Identify molecular formulas for each compound individually using fragmentation trees and isotope patterns.
`passatutto`	Compound Tool: Compute a decoy spectra based on the fragmentation trees of the given input spectra. If no molecular formula is provided in the input, the top-scoring computed formula is used.
`fingerprint`	Compound Tool: Predict molecular fingerprints from MS/MS and fragmentation trees for each compound individually using CSI: FingerID fingerprint prediction.
`zodiac, rerank-formulas`	Dataset Tool: Identify Molecular formulas of all compounds in a dataset together using ZODIAC.
`structure, search-structure-db`	Compound Tool: Search in molecular structure db for each compound individually using CSI: FingerID structure database search.