Error While running Hisat2: extract_splice

Error While running Hisat2: extract_splice_sites.py

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6.9 years ago

Bioinfonext ▴ 470

Hi,

I am getting error while running extract_splice_sites.py from Hisat2:

/NGS_TOOLS/hisat2-2.1.0/extract_splice_sites.py transcript.gtf >transcript.ss
Traceback (most recent call last):
  /NGS_TOOLS/hisat2-2.1.0/extract_splice_sites.py", line 25, in <module>
    from collections import defaultdict as dd, Counter
ImportError: cannot import name Counter

Can anyone suggest how I can resolve it?

Thanks

rna-seq • 3.1k views

ADD COMMENT • link updated 6.9 years ago by Ram 44k • written 6.9 years ago by Bioinfonext ▴ 470

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What version of python are you using?

ADD REPLY • link 6.9 years ago by badribio ▴ 290

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Hi, Actually I am running hisat2 on HPC cluster where we have all python version installed, I add particular python version in my path by using module add python3

So I tried with python3 also but it did not work>

ADD REPLY • link 6.9 years ago by Bioinfonext ▴ 470

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Thanks Badribio,

I loaded pyhton 2.7.8 ,

module load apps/python/2.7.8/

And now script is working.

ADD REPLY • link 6.9 years ago by Bioinfonext ▴ 470

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