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 (“).