jts
commented
3 years ago In the error logs you should see messages printed that say "post-run summary" or similar. Could you paste some examples of those?
Closed madelaam closed 3 years ago
jts
commented
3 years ago In the error logs you should see messages printed that say "post-run summary" or similar. Could you paste some examples of those?
madelaam
commented
3 years ago Hello,
I cannot find the posr-run summary, I have just attached the folder where all the output is.
Thank you.
From: Jared Simpson notifications@github.com Sent: 22 February 2021 10:24 PM To: jts/nanopolish nanopolish@noreply.github.com Cc: MEDINA, Adela (VIAPATH LLP) adela.medina@nhs.net; Author author@noreply.github.com Subject: Re: [jts/nanopolish] Empty vcf (#885)
In the error logs you should see messages printed that say "post-run summary" or similar. Could you paste some examples of those?
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madelaam
commented
3 years ago madelaam
commented
3 years ago I done it, Thank you!
Hello,
I am trying to get a polished sequence after canu: python3 '/home/grid/nanopolish/scripts/nanopolish_makerange.py' '/data/Varicovorax/Varicovorax/20210204_1720_X2_FAP14911_6902f034/Analysis/Canu/Varicovorax.canu.unitigs.fasta' | parallel --results '/data/Varicovorax/Varicovorax/20210204_1720_X2_FAP14911_6902f034/Analysis/Nanopolish/voricovorazx.results' -P 2 \ '/home/grid/nanopolish/nanopolish' variants --consensus -o '/data/Varicovorax/Varicovorax/20210204_1720_X2_FAP14911_6902f034/Analysis/Nanopolish/voricovorax.polished.{1}.vcf' -w {1} -r '/data/Varicovorax/Varicovorax/20210204_1720_X2_FAP14911_6902f034/Analysis/varicovorax.fasta' -b '/data/Varicovorax/Varicovorax/20210204_1720_X2_FAP14911_6902f034/Analysis/Minimap/voricovorax.sorted.bam' -g '/data/Varicovorax/Varicovorax/20210204_1720_X2_FAP14911_6902f034/Analysis/Canu/Varicovorax.canu.unitigs.fasta' -t 2 --min-candidate-frequency 0.1
And I getting empty vcf files:
fileformat=VCFv4.2
nanopolish_window=tig00000001:0-43935
INFO=
INFO=
INFO=
INFO=
INFO=
INFO=
INFO=
INFO=
INFO=
INFO=
FORMAT=
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
Thank you.