Common confusing errors

Error in ``phenoDataFromPaths(files)``: Directory tree must be level

This error means that there is probably a mismatch between the files specified in your sequence file and those present in your data folder. The pick_peaks code goes through all files it finds in the sequence file’s File Name column and tries to pick peaks for them.

A value is trying to be set on a copy of a slice from a DataFrame

This is a non-fatal error. Don’t worry about it.

A subdirectory or file already exists, or other copying files errors

Errors related to making directories and copying files should also be non-fatal. As long as the processing continues after them, you can ignore them.

IOError: [Errno 13] Permission denied: file_name

This error means that one of the files that the code is trying to edit, like the processing_tracker or summary_file are open in another program. Close them and try again.

Rscript, pickpeaks.R, or alignpeaks.R not found

Make sure that the paths to the respective files are correct. These are in the preprocessingmtab.py module, in either (or both, in the case of the call to Rscript) pickpeaks() or alignpeaks(). If there are spaces in the file path and you are using a DOS command prompt, enclose the string that has spaces in quotation marks (“).