# Command Line Pipeline Execution And Runtime Benchmarking

> Use when when you have peak-abundance .csv files and assigned molecular formula data from FT-ICR MS preprocessing, and you need to verify that a published pipeline's runtime claims (e.g., '<1 min for 40 samples', '~2 min for 120 samples') hold true on your own datasets or reference datasets.

- Skill: `holobiomicslab/command-line-pipeline-execution-and-runtime-benchmarking` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/command-line-pipeline-execution-and-runtime-benchmarking`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/command-line-pipeline-execution-and-runtime-benchmarking/raw
- Safety review: PASS (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- License: CC-BY-4.0
- Author: HolobiomicsLab (https://skillmd.com/u/holobiomicslab)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/holobiomicslab/command-line-pipeline-execution-and-runtime-benchmarking

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# command-line-pipeline-execution-and-runtime-benchmarking

## Summary

Execute a fully automated command-line pipeline on FT-ICR MS data and measure wall-clock runtime across sample-size conditions to validate that observed performance matches published benchmarks. This skill verifies reproducibility of computational efficiency claims by comparing empirical runtimes against reference thresholds.

## When to use

When you have peak-abundance .csv files and assigned molecular formula data from FT-ICR MS preprocessing, and you need to verify that a published pipeline's runtime claims (e.g., '<1 min for 40 samples', '~2 min for 120 samples') hold true on your own datasets or reference datasets. Use this skill when computational efficiency is a selection criterion or a reproducibility target.

## When NOT to use

- If raw FT-ICR MS spectra preprocessing is required; MetaboDirect does not provide raw spectra data preprocessing.
- If your datasets lack pre-assigned molecular formulas; the pipeline accepts only peak abundance and assigned molecular formula data.
- If you need to benchmark individual filter steps or sub-tasks in isolation; this skill measures end-to-end main pipeline runtime only.

## Inputs

- Peak-abundance .csv files (average ~1025 peaks per sample)
- Assigned molecular formula data (.csv format with elemental composition)
- MetaboDirect v0.3.4 or later (cloned from GitHub)
- Python 3.8+ and R 4.0+ environments

## Outputs

- Wall-clock runtime in seconds for pipeline execution
- Output .csv files (data matrices, transformed features, analysis results)
- Visualization files (Van Krevelen diagrams, elemental/molecular class composition plots)
- Runtime comparison report against reference benchmarks

## How to apply

Clone the pipeline repository and install Python dependencies (NumPy, pandas, seaborn, py4cytoscape, matplotlib) and R libraries (vegan, SYNCSA, tidyverse, RColorBrewer, etc.). Obtain or download peak-abundance .csv files with assigned molecular formulas from public repositories (e.g., OSF). Execute the main pipeline via command-line interface with default parameters, excluding optional steps (e.g., KEGG database queries or transformation network calculation) unless benchmarking the full pipeline. Record wall-clock runtime in seconds using system timing utilities (e.g., Unix `time` command). Verify that all expected output .csv files and visualization files are generated without errors. Compare observed runtime against reference benchmarks; for the bacterium-phage dataset (36 samples, ~495 assigned molecular formulas per sample), expect ~36 seconds for main pipeline steps.

## Related tools

- **MetaboDirect** (Command-line pipeline for automated analysis and visualization of FT-ICR MS data; executed to measure runtime performance) — https://github.com/Coayala/MetaboDirect
- **Python 3.8** (Runtime environment and dependency management for MetaboDirect execution)
- **R 4.0.2** (Statistical and visualization environment required by MetaboDirect R modules (vegan, SYNCSA, tidyverse))
- **NumPy, pandas** (Python dependencies for data manipulation and matrix operations in MetaboDirect pipeline)
- **vegan, SYNCSA** (R packages for chemodiversity analysis and multivariate statistics within MetaboDirect)

## Examples

```
time metabodirect -i peak_abundance.csv -f molecular_formulas.csv -o output_dir
```

## Evaluation signals

- Wall-clock runtime for bacterium-phage dataset (36 samples, ~495 assigned formulas per sample) is approximately 36 seconds (or <1 min as published).
- All expected output .csv files are generated without errors during pipeline execution.
- All visualization files (Van Krevelen diagrams, elemental composition plots) are successfully created.
- Observed runtime falls within or below published reference benchmarks for the same sample size and peak/formula count.
- No runtime warnings, missing file errors, or incomplete data matrix outputs are reported in standard output or logs.

## Limitations

- MetaboDirect does not provide raw spectra data preprocessing; input data must already be peak-detected and molecular formulas must be pre-assigned (typically via separate MS processing software).
- Benchmark times may vary depending on hardware specifications (CPU, RAM), which should be documented alongside runtime measurements.
- KEGG database queries and transformation network calculation are optional steps that significantly increase runtime; published benchmarks exclude these, so runtime cannot be fairly compared if they are included.
- Pipeline runtime is sensitive to the number of detected peaks and formula assignments per sample; datasets with very high peak counts may not match published benchmarks for smaller datasets.

## Evidence

- [other] Execute the main MetaboDirect pipeline using the command-line interface with default parameters for data pre-processing, data diagnostics, data exploration, and chemodiversity analysis, excluding KEGG database queries and transformation network calculation.: "Execute the main MetaboDirect pipeline using the command-line interface with default parameters for data pre-processing, data diagnostics, data exploration, and chemodiversity analysis, excluding"
- [other] Record wall-clock runtime (seconds) for the phage dataset execution and the S. fallax leachate dataset execution using system timing utilities.: "Record wall-clock runtime (seconds) for the phage dataset execution and the S. fallax leachate dataset execution using system timing utilities."
- [other] For the bacterium-phage dataset (36 samples with average 495 assigned molecular formulas per sample), the main MetaboDirect pipeline steps without KEGG mapping or transformation network calculation completed in less than 1 min (~36 s).: "For the bacterium-phage dataset (36 samples with average 495 assigned molecular formulas per sample), the main MetaboDirect pipeline steps without KEGG mapping or transformation network calculation"
- [results] 40 samples were processed in less than 1 min whereas 120 samples took as little as 2 min to generate all the figures, plots, and outputs.: "40 samples were processed in less than 1 min whereas 120 samples took as little as 2 min to generate all the figures, plots, and outputs"
- [methods] MetaboDirect does not provide raw spectra data preprocessing.: "MetaboDirect does not provide raw spectra data preprocessing"
- [readme] MetaboDirect requires Python (3.5 and above), R (4 and above) and Cytoscape (3.8 and above) with the following libraries/modules.: "MetaboDirect requires Python (3.5 and above), R (4 and above) and Cytoscape (3.8 and above) with the following libraries/modules"