nanopolish: Tutorial on README seems wrong

I keep getting the error: variants: too many arguments when I follow the tutorial in the README.md about using parallel.

For example:

        python {params.makerangescript} {input.fasta} | \
        parallel --results {params.results} -P 1 \
            nanopolish variants --consensus \
             -o {params.vcfs}.{{1}}.vcf \
             -w {{1}} \
             -r {input.reads} \
             -b {input.bam} \
             -g {input.fasta} \
             -t {threads} \
             --min-candidate-frequency 0.1

follows the README.md, but the help prompt now says this about --consensus: --consensus=FILE run in consensus calling mode and write polished sequence to FILE.

It seems like the command line usage has changed a little bit, and I was wondering if you could clarify the correct usage of nanopolish with parallel? Thank you!

About this issue

Original URL
State: closed
Created 6 years ago
Comments: 15 (8 by maintainers)

Most upvoted comments

Hi,

The command should be:

python3 $nanopolish_dir/scripts/nanopolish_makerange.py $prefix.assembly.raw.fa | $parallel_dir/parallel --results nanopolish.results -P 8 $nanopolish_dir/nanopolish variants --consensus -o $prefix.polished.{1}.vcf -w {1} --ploidy $ploidy -r $long_reads -b $prefix.minimap2.bam -g $prefix.assembly.raw.fa -t $threads

(note the -o after --consensus)

For your other questions:

Yes, that should be fine
-P 8 means to polish 8 segments of the genome at once (the total number of threads used will be 8 x $threads)
This value does not have a big effect on the results. I suggest 0.2.

Jared

jts on Aug 20, 2018