RADIS
Analysis of RAD-seq data for InterSpecific phylogeny


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# ERROR 1
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DESCRIPTION OF THE ERROR

Step 1 (data cleaning) ended with and error. 
Files are created in the 03_FIL directory but nothing is created in the 04_PUR directory
So far, the error was reported by users who worked with either Windows of MAC to prepare their barcodes_lib_names.txt files.

ERROR MESSAGE (in the stderr file)

ls: cannot access /home/cruaud/rad_actias/outdir_datacleaning_lib1/*/04_PUR/*.fq_1: No such file or directory
Illegal division by zero at /home/cruaud/programs/radis/bin/../lib/General.pm line 980.

CAUSE 

Different end of line characters are produced by Windows or Mac as compared to Linux and Linux does not understand them.

SOLUTION

use a DOS/MAC to UNIX text file format converter 

If needed, install the program on your computer (https://sourceforge.net/projects/dos2unix/)
then use the following commands :

mac2unix barcodes_lib_names.txt          #this will change format from Mac native to full UNIX
dos2unix barcodes_lib_names.txt          #this will change format from Windows to UNIX 
sed -i '/^$/d' barcodes_lib_names.txt    #this will remove extra spaces introduced by Mac 

and rerun radis.

Nota : for more experienced users To avoid reruning radis from the begining you can move manually the files from the 03_FIL directory to the 04_PUR directory and rename them after you sample codes.