FAQs General

  • How can I check the status of a pipeline module?

    • You can check the corresponding *_info log files (preimp_dir_info, pcaer_info, impute_dir_info, postimp_navi_info) in your home directory. The 4th (second to last) column (tab delimited) of this file bares the name for each performed step (for an detailed explanation of these please refer to this document).

    • "finished" or "fini" indicates a successful run of this pipeline module.

    • If your job queue is empty and this step is not present, please follow this troubleshoot document.

  • Ricopili (any) module pipeline stops (either by accident or an error that was then fixed). Do I need to start a new run in a new directory?

    • No need. Rerun the pipeline as usual (using your previous command) and it will pick it from where it was left.

    • It might be necessary to add the flag "--force".

  • Are there any general analysis tips to use the pipeline somewhere?

    • Yes, Please find here.

  • I have problem with pdflatex/latex or Pipeline cannot find pdflatex?

    • For Broad Users:

      • Please add PATH=/psych/ripke/share/latex_2019/bin/x86_64-linux:$PATH to your ~/.my.bashrc i(n your home directory) and restart the terminal.

    • Please report output of these commands:

      • which pdflatex

      • which latex

  • Is there a Docker version of Ricopili?

  • Is there a publication ready methodology available for the RICOPILI?

  • Is their template for QC based on Ricopili output?

    • Yes, you can find the Template QC report for cohorts based on Ricopili results. This report is useful in sharing with collaborators and recording a short analysis description for studies involving many cohorts.