Bug in run_L1EM.sh: Fails in step5: because ../L1EM/ directory already exists

[Ali-mhm]

BUG:
While running the L1EM package, I found that in the run_L1EM.sh script, the command mkdir ../L1EM/ is used to create the L1EM folder. However, this folder already exists in the core tools setup, so running the script causes an error when trying to create it again.

# RUN EM
echo 'STEP 5: Expectation maximization'
mkdir ../L1EM/
cd ../L1EM/
ls ../G_of_R/*pk2 > G_of_R_list.txt
cp $(ls ../G_of_R/*TE_list.txt | head -1) TE_list.txt
python ${L1EM_code_dir}L1EM.py -g G_of_R_list.txt -l TE_list.txt -t $threads -s $EM_threshold

Suggested fix:
Change the line mkdir ../L1EM/ to mkdir -p ../L1EM/ so that it doesn’t throw an error if the directory already exists and the script can continue running normally.
Thank you @wmckerrow @DanielFaulkner for developing and maintaining this great tool! I appreciate your efforts.

[bszeitz]

Thank you very much for the suggestion! I believe this was deliberately set up this way to make sure that previous results are not overwritten. We are working on an updated version of the code and will definitely take this issue into account.