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jts / nanopolish

Signal-level algorithms for MinION data
MIT License
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nanopolish error too many argument #1027

Closed krishnakazama closed 1 year ago

krishnakazama commented 1 year ago

python3 /home/niabguest/krishna/apps/nanopolish/scripts/nanopolish_makerange.py /home/niabguest/krishna/hyl2_basecalling/canu_assembly/trim_assembly/assembly_small/assembly.contigs.fasta | parallel --results /home/niabguest/krishna/apps/nanopolish/scripts/nanopolish.results -P 7 /home/niabguest/krishna/apps/nanopolish/nanopolish variants --consensus -o /home/niabguest/krishna/hyl2_basecalling/polishing/nanopolishing/polish.{1}.vcf -w {1} -r /home/niabguest/krishna/hyl2_basecalling/polishing/nanopolishing/1D_mapping/basecall.fastq.gz -b /home/niabguest/krishna/hyl2_basecalling/polishing/nanopolishing/mapping/samindex_mapping.sorted.bam.bai -g /home/niabguest/krishna/hyl2_basecalling/canu_assembly/trim_assembly/assembly_small/assembly.contigs.fasta t-14

I'm using the above command for polishing this is the error I'm getting-### variants: too many arguments

jts commented 1 year ago

Hi,

Were you able to solve this? I don't see an obvious error, but you've provided the .bai file instead of the .bam file for the -b argument.

Jared