RepEnrich2_setup error - Githubissues

nerettilab / RepEnrich2

RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.

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RepEnrich2_setup error #21

Closed xiaoyonf closed 3 years ago

xiaoyonf commented 3 years ago

Hi, I tried the command: python RepEnrich2_setup.py ./hg38_repeatmasker.txt ./hg38.fa ./setup_folder_hg38 But encountered the error: File "RepEnrich2_setup.py", line 40 print "Error: Bowtie2 or BEDTools not loaded" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(int "Error: Bowtie2 or BEDTools not loaded")? I checked my .bash_profile and there are path set up for both tools. Can you help me to find anything wrong here? Thanks Xiaoyong Fu

nskvir commented 3 years ago

Hi Xiaoyong, Repenrich was built with Python2.7 but it looks like you might be using Python 3 instead based on the syntax error. Also, be sure you have all the dependencies (like Bowtie2 and Bedtools) installed and loaded prior to the setup.

Let me know if this helps!

xiaoyonf commented 3 years ago

Thank you, nskvir. I have now run it successfully in cluster by using python2.7 and other annotated dependences. Very best, Xiaoyong