Output & Results

Command Line Output

When running the workflow you should see output similar to:

N E X T F L O W   ~  version 24.04.4
Launching `https://github.com/mriffle/nf-carafe-ai-ms` [berserk_banach] DSL2 - revision: 5f76d10037 [main]
executor >  local (3)
[skipped  ] get_mzmls:MSCONVERT (1)                  | 1 of 1, stored: 1 ✔
[f0/98faae] diann_search:DIANN_SEARCH_LIB_FREE       | 1 of 1 ✔
[ea/71d9ac] carafe:CARAFE                            | 1 of 1 ✔

Completed at: 11-Sep-2024 12:28:28
Duration    : 5m 40s
CPU hours   : 0.7
Succeeded   : 3

The first line shows the version of Nextflow you are running. The second line shows the version of the workflow you are running. The third line shows the executor you are using. An executor in Nextflow describes the actual system the steps of the workflow are running on. The next several lines show the actual steps of the workflow as they are running. If a particular step is run multiple times (e.g., converting many RAW files to mzML using msconvert or unzipping Bruker .d.zip files), the percent complete shows the percentage of the files that have been processed. The final four lines appear when the workflow completes, showing the completion time, how long it took, and the number of steps that succeeded.

Workflow Log

The log file called .nextflow.log will appear in the directory in which the workflow was run. It can be helpful for determining the cause of any problems. A log file will also be generated for each task executed by the workflow, which will be described below.

Output Files

The results will be placed in a subdirectory called results/nf-carafe-ai-ms.

citations.txt

This file lists the programs that were used during the workflow run and the citation that should be referenced in any manuscripts prepared using data generated by this workflow. Only programs that were actually executed are included. For example, if msconvert was not needed (because the input was already mzML), its citation will not appear.

versions.txt

This file lists the programs that were actually run during the workflow, along with the version of each program and the container image used. This is useful for reproducibility and for documenting the exact software versions used in an analysis. Only programs that were actually executed are included.

Subdirectories are created for each program that runs as part of the workflow:

panorama Subdirectory

This directory contains logs for file transfers from PanoramaWeb. There will be a *.stderr and *.stdout for each file that was transferred. Any errors encountered transferring that file will be present in the stderr file. And the command line output of the transfer program can be found in the stdout file.

diann Subdirectory

This directory contains files output by running DIA-NN.

  • diann.stdout - The command line output of DIA-NN.

  • diann.stderr - Any error output generated by DIA-NN.

  • diann_version.json - Contains the version and container image of DIA-NN used (JSON format).

  • report.tsv or report.parquet - Matrix of all precursor ions identified, along with different kinds of quantities, quality metrics and annotations. The format depends on the DIA-NN version (TSV for 1.x, Parquet for 2.x).

carafe Subdirectory

This directory contains files output by running Carafe

  • carafe.stdout - The command line output of Carafe.

  • carafe.stderr - Any error output generated by Carafe.

  • carafe_version.json - Contains the version and container image of Carafe used (JSON format).

  • carafe_spectral_library.tsv - The spectral library created by Carafe in DIA-NN format.

  • parameter.txt - The Carafe parameters used for this run.

  • carafe_spectral_library.dlib - The spectral library created by Carafe in EncyclopeDIA format. Only present if output_format is set to 'encyclopedia'.

  • encyclopedia-convert-tsv.stdout - If EncyclopeDIA is the requested output format, this is the console output of the conversion to a DLIB file.

  • encyclopedia-convert-tsv.stderr - If EncyclopeDIA is the requested output format, this is the error output (if any) of the conversion to a DLIB file.