krishnakazama

nanopolish error too many argument

1

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...

Nanopolish variant calling --consensus number of variants in span (11) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes

2

This is closely related to #501 but in my case, it is tick transcriptome I'm performing de novo assembly as I don't have a reference transcriptome. I'm confused about whether...