Error during creating a hisat2 index

Question

[XBria]

Hi, when running the following command

extract_splice_sites.py chrX_data/genes/chrX.gtf > chrX.ss

error comes up :

bash: /home/XBria/bin/extract_splice_sites.py: /opt/anaconda1anaconda2anaconda3/bin/python: bad interpreter: No such file or directory

anyone has experienced the same ? Please help !

• which python /home/XBria/anaconda2/bin/python

Answer 1

[WouterDeCoster]

Can you show me the top lines of /home/XBria/bin/extract_splice_sites.py? Looks like you have an odd shebang which should be changed to /home/XBria/anaconda2/bin/python

[XBria]

#!/opt/anaconda1anaconda2anaconda3/bin/python

This is the first line of the script.

[XBria]

You are right, I forgot to change that :)

Thanks

[XBria]

Dear Wouter,

The problem solved, although I still cannot run the program, since there is a syntax error :

extract_splice_sites.py chrX_data/genes/chrX.gtf > chrX.ss
  File "/home/XBria/bin/extract_splice_sites.py", line 105
    file=stderr)
        ^
SyntaxError: invalid syntax

I checked the code in github too. the same codes. How may I solve this one ?

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

I guess your error is caused by using python2, while the script is written for python3. Or maybe it will work with Python2.7 but you are using an older one.

Anyway: unless you have good reasons to use something older, use Python3.

[XBria]

It worked. someone wrote on the internet so I add that here for someone who has the same problem and needs help. As you said, it is because of the different version of the written script and running python. I just fix the problem by removing file= it worked.

Thanks Wouter for the comment.