Where are my results saved?

Every finished analysis is saved on your own computer, in a folder called CacaoIQ Results. You choose its location the first time you open CacaoIQ. The suggested location is Documents\CacaoIQ Results on Windows and ~/Documents/CacaoIQ Results on a Mac.

Opening the folder

Any of these takes you there:

• The folder icon in the top bar.
• Results folder on an analysis in the Analyses list.
• About (the ⓘ icon in the top bar) → Results folder, which also shows the path.

Changing the folder

Change it in About → Results folder, or with Change next to “Results will be saved to …” just above Start Run in any run panel. If you change it, keep the old folder until you have checked which runs it holds.

If the folder is synced to a cloud service (OneDrive, Dropbox, Google Drive, iCloud Drive), CacaoIQ says so next to the path. Results saved there are uploaded to that service, so choose a local folder if your data must stay on your computer.

How the folder is organized

The folder is organized by workflow, then run, then trait:

CacaoIQ Results\
  Gene Discovery\
    2026-10-02_trial2024_pheno_eb6e5992\   one folder per run: date, data file, run code
      README.txt            what was run, settings, CacaoIQ version, key results
      run_settings.json     the exact settings, for reproducing the run
      genotype_QC\          marker and sample QC, relationship matrix, QC plots
      linkage_map\          the genetic map (Full analysis only)
      pod_count (log)\      one folder per trait
        phenotype_model\    BLUPs or adjusted values, the transform used, model checks
        heritability\
        GWAS\               marker table, Manhattan and QQ plots, summary
        QTL\                interval-mapping scan, permutation threshold (Full analysis only)
        candidate_genes\    gene tables per region, gene summary
  Phenotypic Modeling\
  GCA-SCA\
  Diversity Panel\

• A run is one upload analyzed with one set of settings. Traits selected together share one run folder, with one genotype QC, relationship matrix and linkage map.
• A trait analyzed on both a transformed and the raw scale gets two trait folders, for example pod_count (log) and pod_count (raw).
• Files are copied to the folder as each trait finishes.
• A Trait correlations study is saved only when you click Save to Results Folder, under Phenotypic Modeling\. Saved studies don’t appear in the list of analyses; delete their folder by hand if you no longer need it.

CacaoIQ’s working folder

Large intermediate files stay in CacaoIQ’s own working folder, not in your results folder. They include converted and cleaned copies of your genotype data and the phenotype rows each model used. They are needed to rerun an analysis.

• Windows: %APPDATA%\cacaoiq-app (usually C:\Users\<your name>\AppData\Roaming\cacaoiq-app). To open it, type %APPDATA% in the File Explorer address bar. It also holds the run history and the run logs, and uninstalling CacaoIQ keeps it.
• Mac: ~/Library/Application Support/cacaoiq-app/.

What CacaoIQ never changes

Your uploaded phenotype and genotype files are only read, never modified.

Deleting results

The trash icon on an analysis deletes it after a confirmation. This removes that trait’s folder from your results folder (or the whole run folder when it was the last trait), together with CacaoIQ’s working files for it. Small candidate-gene files, which can be shared between runs, stay in the working folder. Hide all above the list only hides analyses from view; Show hidden brings them back.

The “Licensed to” line

Each README.txt, each run_settings.json and each chart image saved by CacaoIQ records who the copy is licensed to: the organization, the number of seats (when the license states one) and the license ID. No person’s name is ever included, even for older license files. CSV tables are left unchanged, so they open in other software as usual.

Related articles

• My license expired: what happens to my results?
• Does my data leave my computer?
• Quick or Full analysis: which one do I need?