# Metaboigniter
## Open GitHub codespace
Use the following link to open a GitHub codespace with most of the required software installed:
> ⚠️
> If you do it manually, make sure to select the bigger machine with 4 cores and 16GB RAM
[](https://github.com/codespaces/new?hide_repo_select=true&repo=1177012938&skip_quickstart=true&ref=updt_dockerfile&machine=standardLinux32gb&devcontainer_path=.devcontainer%2Fdevcontainer.json&geo=EuropeWest)
## Getting the data
```bash
bash data/MTBLS8735/download.sh
python bin/reindex_mzml.py -i data/MTBLS8735/
```
## Inspect the general config
The config file `nextflow.config` in the root directory contains the general configuration
for the run, including the input data, output directory and resource limits. You can edit
this file to change these settings, or you can override them on the command line when you
run the pipeline.
## Inspect Metaboigniter arguments
Help message for nf-core/metaboigniter v2.0.1
```
>>> nextflow run nf-core/metaboigniter --help
N E X T F L O W ~ version 25.10.4
Launching `https://github.com/nf-core/metaboigniter` [reverent_joliot] DSL2 - revision: 55d8254760 [2.0.1]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/metaboigniter v2.0.1-g55d8254
------------------------------------------------------
Typical pipeline command:
nextflow run nf-core/metaboigniter -profile --input samplesheet.csv --outdir
Generic controls
--requantification [boolean] If set to true, requantification will be
performed
--identification [boolean] If set to true, identification will be
performed. Remember to set identification
specific parameters
--polarity [string] Polarity of the data (accepted: positive,
negative) [default: positive]
--parallel_linking [boolean] If set, the linking will be performed in
parallel, see nr_partitions in linking
--ms2_collection_model [string] Set wether the MS2 collections have been done
on all the MS1 data. If there is a separate MS2
file, set to separate (accepted: separate,
paired) [default: paired]
Mapping and Identification
--mz_tolerance_pyopenms [number] mz tolerance (ppm) for finding C13
[default: 20]
--rt_tolerance_pyopenms [number] rt tolerance for finding C13 [default:
5]
--ms2_use_feature_ionization [boolean] If set, detected adduct will be used in
identification
--sirius_sirius_ppm_max [number] Maximum allowed mass deviation in ppm for
decomposing masses (ppm) [default: 10]
--sirius_sirius_ppm_max_ms2 [number] Maximum allowed mass deviation in ppm for
decomposing masses in MS2 (ppm).If not
specified, the same value as for the MS1 is
used. [default: 10]
--sirius_sirius_no_recalibration [boolean] Disable recalibration of input spectra
--sirius_sirius_profile [string] Name of the configuration profile
(accepted: default, qtof, orbitrap, fticr)
[default: default]
--sirius_sirius_candidates [integer] The number of formula candidates in the SIRIUS
output [default: 10]
--sirius_sirius_candidates_per_ion [integer] Minimum number of candidates in the output for
each ionization. Set to force output of results
for each possible ionization, even if not part
of highest ranked results. [default: 1]
--sirius_sirius_ions_considered [string] the iontype/adduct of the MS/MS data. Example:
[M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can
also provide a comma separated list of
adducts. [default:
[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-]
--sirius_sirius_db [string] Search formulas in the Union of the given
databases db-name1,db-name2,db-name3. If no
database is given all possible molecular
formulas will be respected (no database is
used). Example: possible DBs:
ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE
--sirius_runpassatutto [boolean] If set, passatutto will be run
--sirius_fingerid_db [string] Search structures in the Union of the given
databases db-name1,db-name2,db-name3. If no
database is given all possible molecular
formulas will be respected (no database is
used). Example: possible DBs:
ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE
--sirius_email [string] E-mail for your SIRIUS account.
--sirius_password [string] Password for your SIRIUS account.
--sirius_split [boolean] If set, SIRIUS will be run in parallel. See
mgf_splitmgf_pyopenms parameter for
segmentation
--split_consensus_parts [integer] For running MS2 mapping in parallel set this
higher than 1 [default: 20]
--run_ms2query [boolean] If set, MS2Query will be run
--sirius_runfid [boolean] If set, FingerID will be run. This has to be
run together with run_sirius
--run_sirius [boolean] If set SIRIUS will run
Annotation
--algorithm_metabolitefeaturedeconvolution_charge_min_metaboliteadductdecharger_openms [integer] Minimal possible charge [default: 1]
--algorithm_metabolitefeaturedeconvolution_charge_max_metaboliteadductdecharger_openms [integer] Maximal possible charge [default: 1]
--algorithm_metabolitefeaturedeconvolution_charge_span_max_metaboliteadductdecharger_openms [integer] Maximal range of charges for a single analyte,
i.e. observing q1=[5,6,7] implies span=3.
Setting this to 1 will only find adduct
variants of the same charge [default:
1]
--algorithm_metabolitefeaturedeconvolution_q_try_metaboliteadductdecharger_openms [string] Try different values of charge for each feature
according to the above settings ('heuristic'
[does not test all charges, just the likely
ones] or 'all' ), or leave feature charge
untouched ('feature'). (accepted: feature,
heuristic, all) [default: feature]
--algorithm_metabolitefeaturedeconvolution_retention_max_diff_metaboliteadductdecharger_openms [number] Maximum allowed RT difference between any two
features if their relation shall be
determined [default: 1]
--algorithm_metabolitefeaturedeconvolution_retention_max_diff_local_metaboliteadductdecharger_openms [number] Maximum allowed RT difference between between
two co-features, after adduct shifts have been
accounted for (if you do not have any adduct
shifts, this value should be equal to
'retention_max_diff', otherwise it should be
smaller!) [default: 1]
--algorithm_metabolitefeaturedeconvolution_mass_max_diff_metaboliteadductdecharger_openms [number] Maximum allowed mass tolerance per feature.
Defines a symmetric tolerance window around the
feature. When looking at possible feature
pairs, the allowed feature-wise errors are
combined for consideration of possible adduct
shifts. For ppm tolerances, each window is
based on the respective observed feature mz
(instead of putative experimental mzs causing
the observed one)! [default: 5]
--algorithm_metabolitefeaturedeconvolution_unit_metaboliteadductdecharger_openms [string] Unit of the 'max_difference' parameter
(accepted: Da, ppm) [default: ppm]
--algorithm_metabolitefeaturedeconvolution_max_neutrals_metaboliteadductdecharger_openms [integer] Maximal number of neutral adducts(q=0) allowed.
Add them in the 'potential_adducts'
section! [default: 1]
--algorithm_metabolitefeaturedeconvolution_use_minority_bound_metaboliteadductdecharger_openms [boolean] Prune the considered adduct transitions by
transition probabilities. [default:
true]
--algorithm_metabolitefeaturedeconvolution_max_minority_bound_metaboliteadductdecharger_openms [integer] Limits allowed adduct compositions and changes
between compositions in the underlying graph
optimization problem by introducing a
probability-based threshold: the minority bound
sets the maximum count of the least probable
adduct (according to 'potential_adducts' param)
within a charge variant with maximum charge
only containing the most likely adduct
otherwise. E.g., for 'charge_max' 4 and
'max_minority_bound' 2 with most probable
adduct being H+ and least probable adduct being
Na+, this will allow adduct compositions of
'2(H+),2(Na+)' but not of '1(H+),3(Na+)'.
Further, adduct compositions/changes less
likely than '2(H+),2(Na+)' will be discarded as
well. [default: 1]
--algorithm_metabolitefeaturedeconvolution_min_rt_overlap_metaboliteadductdecharger_openms [number] Minimum overlap of the convex hull' RT
intersection measured against the union from
two features (if CHs are given) [default:
0.66]
--algorithm_metabolitefeaturedeconvolution_intensity_filter_metaboliteadductdecharger_openms [boolean] Enable the intensity filter, which will only
allow edges between two equally charged
features if the intensity of the feature with
less likely adducts is smaller than that of the
other feature. It is not used for features of
different charge.
--adducts_pos [string] possible positive adducts for adduct detection
in the format of adduct:charge:probablity
[default: H:+:0.6 Na:+:0.1 NH4:+:0.1
H-1O-1:+:0.1 H-3O-2:+:0.1]
--adducts_neg [string] possible negative adducts for adduct detection
in the format of adduct:charge:probablity
[default: H-1:-:0.8 H-3O-1:-:0.2]
Alignment and Linking
--algorithm_max_num_peaks_considered_mapalignerposeclustering_openms [integer] The maximal number of peaks/features to be
considered per map. To use all, set to
'-1'. [default: 1000]
--algorithm_superimposer_mz_pair_max_distance_mapalignerposeclustering_openms [number] Maximum of m/z deviation of corresponding
elements in different maps. This condition
applies to the pairs considered in hashing.
[default: 0.5]
--algorithm_superimposer_num_used_points_mapalignerposeclustering_openms [integer] Maximum number of elements considered in each
map (selected by intensity). Use this to
reduce the running time and to disregard weak
signals during alignment. For using all
points, set this to -1. [default: 2000]
--algorithm_pairfinder_ignore_charge_mapalignerposeclustering_openms [boolean] false [default]: pairing requires equal charge
state (or at least one unknown charge '0');
true: Pairing irrespective of charge
state
--algorithm_pairfinder_distance_rt_max_difference_mapalignerposeclustering_openms [number] Never pair features with a larger RT distance
(in seconds). [default: 100.0]
--algorithm_pairfinder_distance_mz_max_difference_mapalignerposeclustering_openms [number] Never pair features with larger m/z distance
(unit defined by 'unit') [default: 0.3]
--algorithm_pairfinder_distance_mz_unit_mapalignerposeclustering_openms [string] Unit of the 'max_difference' parameter
(accepted: Da, ppm) [default: Da]
--algorithm_mz_unit_featurelinkerunlabeledkd_openms [string] Unit of m/z tolerance (accepted: ppm, Da)
[default: ppm]
--algorithm_nr_partitions_featurelinkerunlabeledkd_openms [integer] Number of partitions in m/z space [default:
100]
--algorithm_warp_enabled_featurelinkerunlabeledkd_openms [boolean] Whether or not to internally warp feature RTs
using LOWESS transformation before linking
(reported RTs in results will always be the
original RTs) [default: true]
--algorithm_warp_rt_tol_featurelinkerunlabeledkd_openms [number] Width of RT tolerance window (sec)
[default: 100.0]
--algorithm_warp_mz_tol_featurelinkerunlabeledkd_openms [number] m/z tolerance (in ppm or Da) [default:
5.0]
--algorithm_link_rt_tol_featurelinkerunlabeledkd_openms [number] Width of RT tolerance window (sec)
[default: 30]
--algorithm_link_mz_tol_featurelinkerunlabeledkd_openms [number] m/z tolerance (in ppm or Da) [default:
10]
--algorithm_link_charge_merging_featurelinkerunlabeledkd_openms [string] whether to disallow charge mismatches
(Identical), allow to link charge zero (i.e.,
unknown charge state) with every charge state,
or disregard charges (Any). (accepted:
Identical, With_charge_zero, Any) [default:
With_charge_zero]
--algorithm_link_adduct_merging_featurelinkerunlabeledkd_openms [string] whether to only allow the same adduct for
linking (Identical), also allow linking
features with adduct-free ones, or disregard
adducts (Any). (accepted: Identical,
With_unknown_adducts, Any) [default: Any]
Re-Quantification
--extract_mz_window_featurefindermetaboident_openms [number] m/z window size for chromatogram extraction
(unit: ppm if 1 or greater, else Da/Th)
--extract_n_isotopes_featurefindermetaboident_openms [integer] Number of isotopes to include in each peptide
assay.
--detect_peak_width_featurefindermetaboident_openms [number] Expected elution peak width in seconds, for
smoothing (Gauss filter). Also determines the
RT extration window, unless set explicitly via
'extract:rt_window'.
--model_type_featurefindermetaboident_openms [string] Type of elution model to fit to features
(accepted: symmetric, asymmetric, none)
[default: symmetric]
--emgscoring_max_iteration_featurefindermetaboident_openms [integer] Maximum number of iterations for EMG
fitting.
--emgscoring_init_mom_featurefindermetaboident_openms [boolean] Alternative initial parameters for fitting
through method of moments.
Quantification
--algorithm_signal_to_noise_peakpickerhires_openms [number] Minimal signal-to-noise ratio for a peak to be
picked (0.0 disables SNT estimation!)
--algorithm_common_noise_threshold_int_featurefindermetabo_openms [number] Intensity threshold below which peaks are
regarded as noise. [default: 10]
--algorithm_common_chrom_peak_snr_featurefindermetabo_openms [number] Minimum signal-to-noise a mass trace should
have. [default: 3]
--algorithm_common_chrom_fwhm_featurefindermetabo_openms [number] Expected chromatographic peak width (in
seconds). [default: 5]
--algorithm_mtd_mass_error_ppm_featurefindermetabo_openms [number] Allowed mass deviation (in ppm). [default:
20]
--algorithm_mtd_reestimate_mt_sd_featurefindermetabo_openms [boolean] Enables dynamic re-estimation of m/z variance
during mass trace collection stage.
[default: true]
--algorithm_mtd_quant_method_featurefindermetabo_openms [string] Method of quantification for mass traces. For
LC data 'area' is recommended, 'median' for
direct injection data. 'max_height' simply uses
the most intense peak in the trace.
(accepted: area, median, max_height) [default:
area]
--algorithm_epd_enabled_featurefindermetabo_openms [boolean] Enable splitting of isobaric mass traces by
chromatographic peak detection. Disable for
direct injection. [default: true]
--algorithm_epd_width_filtering_featurefindermetabo_openms [string] Enable filtering of unlikely peak widths. The
fixed setting filters out mass traces outside
the [min_fwhm, max_fwhm] interval (set
parameters accordingly!). The auto setting
filters with the 5 and 95% quantiles of the
peak width distribution. (accepted: off,
fixed, auto) [default: fixed]
--algorithm_ffm_enable_rt_filtering_featurefindermetabo_openms [boolean] Require sufficient overlap in RT while
assembling mass traces. Disable for direct
injection data.. [default: true]
--algorithm_ffm_isotope_filtering_model_featurefindermetabo_openms [string] Remove/score candidate assemblies based on
isotope intensities. SVM isotope models for
metabolites were trained with either 2% or 5%
RMS error. For peptides, an averagine cosine
scoring is used. Select the appropriate noise
model according to the quality of measurement
or MS device. (accepted: metabolites (2%
RMS), ...) [default: metabolites (5% RMS)]
--algorithm_ffm_mz_scoring_13c_featurefindermetabo_openms [boolean] Use the 13C isotope peak position (~1.003355
Da) as the expected shift in m/z for isotope
mass traces (highly recommended for
lipidomics!). Disable for general metabolites
(as described in Kenar et al. 2014,
MCP.).
Input/output options
--input [string] Path to comma-separated file containing
information about the samples in the
experiment.
--outdir [string] The output directory where the results will be
saved. You have to use absolute paths to
storage on Cloud infrastructure.
--email [string] Email address for completion summary.
--multiqc_title [string] MultiQC report title. Printed as page header,
used for filename if not otherwise
specified.
Generic options
--multiqc_methods_description [string] Custom MultiQC yaml file containing HTML
including a methods description.
!! Hiding 150 params, use --validationShowHiddenParams to show them !!
------------------------------------------------------
If you use nf-core/metaboigniter for your analysis please cite:
* The pipeline
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/metaboigniter/blob/master/CITATIONS.md
------------------------------------------------------
```
## Run Metaboigniter
We will run the latest version `2.0.1` using an example dataset.
- uses `nextflow.config` and the following parameters:
```bash
nextflow run nf-core/metaboigniter -profile docker,arm -r 2.0.1
```
more verbosely running also the MS2 identification step:
```bash
nextflow run nf-core/metaboigniter -profile docker,arm -r 2.0.1 -resume \
--input data/MTBLS8735/samplesheet.csv \
--outdir results \
--identification --run_ms2query
```
## Troubleshooting
### Ensure mzML files are correctly indexed
Metaboigniter does not reindex mzML files itself, but relies on using an indexed
version of the mzML files. If you encounter index access errors us `pyopenms`
to reindex the mzML files, see the script at
[`bin/reindex_mzml.py`](../bin/reindex_mzml.py)
for an example of how to do this.
```bash
pip install pyopenms
# python -m pip install pyopenms
python bin/reindex_mzml.py -h
python bin/reindex_mzml.py --input_dir data/
```
### Corrupt files
When downloading the files, it is possible that error occur. Try to redownload any file that
fails to be processed.
### MS2Query downloads
```bash
# downloaded into your work folder by a process
# e.g. ls -lh work/5f/c28db2c487c595610fa3108e5bd8cb/downloads
-rw-rw-rw- 1 root root 483M Jun 9 11:27 library_GNPS_15_12_2021_ms2ds_embeddings.pickle
-rw-rw-rw- 1 root root 722M Jun 9 11:27 library_GNPS_15_12_2021_s2v_embeddings.pickle
-rw-rw-rw- 1 root root 62M Jun 9 11:27 ms2ds_model_GNPS_15_12_2021.hdf5
-rw-rw-rw- 1 root root 327M Jun 9 11:27 ms2query_library.sqlite
-rw-rw-rw- 1 root root 574K Jun 9 11:27 ms2query_random_forest_model.onnx
-rw-rw-rw- 1 root root 3.9M Jun 9 11:27 spec2vec_model_GNPS_15_12_2021.model
-rw-rw-rw- 1 root root 133M Jun 9 11:28 spec2vec_model_GNPS_15_12_2021.model.syn1neg.npy
-rw-rw-rw- 1 root root 133M Jun 9 11:28 spec2vec_model_GNPS_15_12_2021.model.wv.vectors.npy
```
## Example output of a local run
stdin
N E X T F L O W ~ version 25.10.4
Launching `https://github.com/nf-core/metaboigniter` [fervent_spence] DSL2 - revision: 55d8254760 [2.0.1]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
nf-core/metaboigniter v2.0.1-g55d8254
Core Nextflow options
revision : 2.0.1
runName : fervent_spence
containerEngine : docker
launchDir : /Users/heweb/Documents/repos/dsp_course_metabolomics_intro
workDir : /Users/heweb/Documents/repos/dsp_course_metabolomics_intro/work
projectDir : /Users/heweb/.nextflow/assets/nf-core/metaboigniter
userName : heweb
profile : docker,arm
configFiles :
Generic controls
identification : true
Mapping and Identification
mz_tolerance_pyopenms : 20.0
rt_tolerance_pyopenms : 5.0
sirius_sirius_ppm_max : 10.0
sirius_sirius_ppm_max_ms2 : 10.0
run_ms2query : true
run_sirius : true
Annotation
algorithm_metabolitefeaturedeconvolution_retention_max_diff_metaboliteadductdecharger_openms : 1.0
algorithm_metabolitefeaturedeconvolution_retention_max_diff_local_metaboliteadductdecharger_openms: 1.0
Alignment and Linking
algorithm_superimposer_scaling_bucket_size_mapalignerposeclustering_openms : 0.0050
algorithm_superimposer_shift_bucket_size_mapalignerposeclustering_openms : 3.0
algorithm_superimposer_max_shift_mapalignerposeclustering_openms : 1000.0
algorithm_superimposer_max_scaling_mapalignerposeclustering_openms : 2.0
algorithm_pairfinder_second_nearest_gap_mapalignerposeclustering_openms : 2.0
algorithm_pairfinder_distance_rt_exponent_mapalignerposeclustering_openms : 1.0
algorithm_pairfinder_distance_rt_weight_mapalignerposeclustering_openms : 1.0
algorithm_pairfinder_distance_mz_exponent_mapalignerposeclustering_openms : 2.0
algorithm_pairfinder_distance_mz_weight_mapalignerposeclustering_openms : 1.0
algorithm_pairfinder_distance_intensity_exponent_mapalignerposeclustering_openms : 1.0
algorithm_pairfinder_distance_intensity_weight_mapalignerposeclustering_openms : 0.0
algorithm_link_rt_tol_featurelinkerunlabeledkd_openms : 30.0
algorithm_link_mz_tol_featurelinkerunlabeledkd_openms : 10.0
algorithm_distance_rt_exponent_featurelinkerunlabeledkd_openms : 1.0
algorithm_distance_rt_weight_featurelinkerunlabeledkd_openms : 1.0
algorithm_distance_mz_exponent_featurelinkerunlabeledkd_openms : 2.0
algorithm_distance_mz_weight_featurelinkerunlabeledkd_openms : 1.0
algorithm_distance_intensity_exponent_featurelinkerunlabeledkd_openms : 1.0
algorithm_distance_intensity_weight_featurelinkerunlabeledkd_openms : 1.0
algorithm_lowess_delta_featurelinkerunlabeledkd_openms : -1.0
model_linear_x_datum_min_maprttransformer_openms : 1.0E-15
model_linear_x_datum_max_maprttransformer_openms : 1.0E+15
model_linear_y_datum_min_maprttransformer_openms : 1.0E-15
model_linear_y_datum_max_maprttransformer_openms : 1.0E+15
model_b_spline_wavelength_maprttransformer_openms : 0.0
model_b_spline_num_nodes_maprttransformer_openms : 5
model_b_spline_boundary_condition_maprttransformer_openms : 2
model_lowess_span_maprttransformer_openms : 0.666666666666667
model_lowess_num_iterations_maprttransformer_openms : 3
model_lowess_delta_maprttransformer_openms : -1.0
Re-Quantification
extract_mz_window_featurefindermetaboident_openms : 10.0
extract_rt_window_featurefindermetaboident_openms : 0.0
extract_n_isotopes_featurefindermetaboident_openms : 2
extract_isotope_pmin_featurefindermetaboident_openms : 0.0
detect_peak_width_featurefindermetaboident_openms : 60.0
detect_min_peak_width_featurefindermetaboident_openms : 0.2
detect_signal_to_noise_featurefindermetaboident_openms : 0.8
model_add_zeros_featurefindermetaboident_openms : 0.2
model_check_min_area_featurefindermetaboident_openms : 1.0
model_check_boundaries_featurefindermetaboident_openms : 0.5
model_check_width_featurefindermetaboident_openms : 10.0
model_check_asymmetry_featurefindermetaboident_openms : 10.0
emgscoring_max_iteration_featurefindermetaboident_openms : 100
Quantification
algorithm_signal_to_noise_peakpickerhires_openms : 0.0
algorithm_spacing_difference_gap_peakpickerhires_openms : 4.0
algorithm_spacing_difference_peakpickerhires_openms : 1.5
algorithm_missing_peakpickerhires_openms : 1
algorithm_signaltonoise_max_intensity_peakpickerhires_openms : -1
algorithm_signaltonoise_auto_max_stdev_factor_peakpickerhires_openms : 3.0
algorithm_signaltonoise_auto_max_percentile_peakpickerhires_openms : 95
algorithm_signaltonoise_auto_mode_peakpickerhires_openms : 0
algorithm_signaltonoise_win_len_peakpickerhires_openms : 200.0
algorithm_signaltonoise_bin_count_peakpickerhires_openms : 30
algorithm_signaltonoise_min_required_elements_peakpickerhires_openms : 10
algorithm_signaltonoise_noise_for_empty_window_peakpickerhires_openms : 1.0E+20
algorithm_common_noise_threshold_int_featurefindermetabo_openms : 10.0
algorithm_common_chrom_peak_snr_featurefindermetabo_openms : 3.0
algorithm_common_chrom_fwhm_featurefindermetabo_openms : 5.0
algorithm_mtd_mass_error_ppm_featurefindermetabo_openms : 20.0
algorithm_mtd_min_trace_length_featurefindermetabo_openms : 5.0
algorithm_mtd_max_trace_length_featurefindermetabo_openms : -1.0
algorithm_epd_min_fwhm_featurefindermetabo_openms : 1.0
algorithm_epd_max_fwhm_featurefindermetabo_openms : 60.0
algorithm_ffm_local_rt_range_featurefindermetabo_openms : 10.0
Input/output options
input : data/samplesheet.csv
outdir : results
Institutional config options
config_profile_name : Metabonaut example dataset
config_profile_description : Example data from Metabonaut.
Max job request options
max_cpus : 8
max_memory : 14.GB
max_time : 6.h
[81/f8c70e] NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_FEATUREFINDERMETABO (MS_D_POS) [100%] 10 of 10 ✔
[31/91ac9e] NFC…E_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPALIGNERPOSECLUSTERING (Multiple files) [100%] 1 of 1 ✔
[04/074ef6] NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPRTTRANSFORMER (MS_B_POS) [100%] 10 of 10 ✔
[2c/12d19b] NFCORE_METABOIGNITER:METABOIGNITER:ANNOTATION:OPENMS_METABOLITEADDUCTDECHARGER (MS_B_POS) [100%] 10 of 10 ✔
[c0/4e586a] NFCORE_METABOIGNITER:METABOIGNITER:ANNOTATION:PYOPENMS_C13DETECTION (MS_QC_POOL_4_POS) [100%] 10 of 10 ✔
[e2/abd21a] NFCORE_METABOIGNITER:METABOIGNITER:LINKER:OPENMS_FEATURELINKERUNLABELEDKD (Linked_data) [100%] 1 of 1 ✔
[82/8de1f5] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:PYOPENMS_MSMAPPING (Linked_data) [100%] 1 of 1 ✔
[e5/29283a] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:OPENMS_FILEFILTER (Linked_data) [100%] 1 of 1 ✔
[e9/d8a5d7] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:PYOPENMS_SPLITCONSENSUS (Linked_data) [100%] 1 of 1 ✔
[b8/913b64] NFC…\_METABOIGNITER:METABOIGNITER:IDENTIFICATION:PYOPENMS_GENERATESEARCHPARAMS (Linked_data_part9) [100%] 20 of 20 ✔
[9d/bf7756] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:PYOPENMS_CONCTSV_UNMAPPED (MSMS_2_A_CE20_POS) [100%] 9 of 9 ✔
[58/a6b59f] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:GENERAL_MERGEMSFILE (Linked_data) [100%] 1 of 1 ✔
[61/30fee6] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:GENERAL_MERGEMGFFILE (Linked_data) [100%] 1 of 1 ✔
[54/2f5ab5] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:SIRIUSMAPPED:SIRIUS_SEARCH (Linked_data) [100%] 1 of 1 ✔
[8e/5be8f1] NFC…IGNITER:METABOIGNITER:IDENTIFICATION:SIRIUSMAPPED:PYOPENMS_CONCTSVSIRIUS (sirius_Linked_data) [100%] 1 of 1 ✔
[- ] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:SIRIUSMAPPED:PYOPENMS_CONCTSVFINGERID -
[85/7f0e9f] NFC…TION:MS2QUERYMAPPED:MS2QUERY_MODELDOWNLOADER:MS2QUERY_DOWNLOADMODEL (Downloading model files) [100%] 1 of 1 ✔
[ea/59bd7e] NFC…IGNITER:METABOIGNITER:IDENTIFICATION:MS2QUERYMAPPED:MS2QUERY_CHECKMODELFILES (checking files) [100%] 1 of 1 ✔
[97/2b1f52] NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:MS2QUERYMAPPED:MS2QUERY_SEARCH (Linked_data) [100%] 1 of 1 ✔
[a1/66c3c6] NFC…R:METABOIGNITER:IDENTIFICATION:MS2QUERYMAPPED:PYOPENMS_CONCTSVMS2QUERY (ms2query_Linked_data) [100%] 1 of 1 ✔
[fe/fec7ef] NFCORE_METABOIGNITER:METABOIGNITER:PYOPENMS_EXPORTIDENTIFICATION (Linked_data) [100%] 1 of 1 ✔
[64/c2f478] NFCORE_METABOIGNITER:METABOIGNITER:MULTIQC [100%] 1 of 1 ✔ -[nf-core/metaboigniter] Pipeline completed successfully-
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
WARN: Input `tuple` must define at least two elements -- Check process `NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:MS2QUERYMAPPED:MS2QUERY_SEARCH`