Nanopolish help please

#1

Hi there,

Does anyone know the paths to call the nanopolish_makerange.py and nanopolish_merge.py scripts that should be part of the nanopolish linuxbrew package?

Thanks,

Tim.

#2

Their exact location will depend on the version on nanopolish that you have installed, but you should be able to locate the scripts with find:

find /home/linuxbrew -name "nanopolish_merge.py"
find /home/linuxbrew -name "nanopolish_makerange.py"

then run them as suggested in the readme with:

python /home/linuxbrew/.linuxbrew/Cellar/nanopolish/VERSION/scripts/nanopolish_makerange.py draft.fa | \
parallel --results nanopolish.results -P 8 nanopolish variants --consensus polished.{1}.fa -w {1} -r reads.fa -b reads.sorted.bam -g draft.fa -t 4 --min-candidate-frequency 0.1

#3

Hi therem,

Thanks for your help.

BTW, I think there is a problem with the latest (0.9.0) linuxbrew package.

Cheers,

Tim.

#4

Could you elaborate on the problems you’re having with nanopolish?

#5

Yes of course - sorry that wasn’t helpful.

When I tried to run it I’d get “error in nanopolish (fast stop)****” pop up constantly.

#6

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