medaka

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RuntimeWarning: divide by zero encountered in log10

3

**Describe the bug** There are always runtime warnings of "divide by zero encountered in log10" in each run. **Logging** ``` (medaka1.6) ywan@ICL:~/assembly/medaka$ medaka_consensus -i nanopore.fastq.gz -d /home/ywan/assembly/raw/raven_assembly.fasta -o tmp -m...

wanyuac

Installation on ARMv8 Processor Ubuntu 18

2

**Describe the bug** I'm trying to install medaka on ARMv8 Processor Ubuntu 18, but have been uncessesful. I've tried several ways and changed alot, so my errors keep changing. Here...

SemiQuant

Improving parallelism for medaka_consensus

6

**Is your feature request related to a problem? Please describe.** We are working on some large datasets 20.000 > 100.000 + contigs and realised that one of the bottlenecks in...

jjkoehorst

Reduced QV score and completeness after Medaka

9

Hi, I am not having any luck with Medaka polishing of my genome, it is a plant genome of around ~4 Gbp. **Describe the bug** After running Medaka I am...

EinarBaldvin

Reduced QV score and more missing and duplicates on the busco score

1

**Describe the bug** After running Medaka I got a reduced QV score and more missing and duplicates on the Busco score. Here is my code for medaka_consensus medaka_consensus -i Ae_RdUgA3_F1_male1_VBI_pass_haplotype-RemaAD.fasta.gz...

cjchen5

indexing large genome bam file

4

I'm working on a very large genome (4.5 G), when we run medaka, we gets the following error which seems to be related to bam indexing process because of the...

aoladzad-soundag

Polishing of metagenomes

2

Dear all, I am using Medaka 1.2.3 to polish bacterial genomes. To give some context, I sequenced the total DNA of an insect on a MinION 9.4 flowcell to assemble...

jessydit

1.3.2 read group - can use only 1?

1

**Is your feature request related to a problem? Please describe.** I have samples that are sequenced deeply and the data span multiple nanopore flowcells. When I merge those bams there...

RichardCorbett

Parallelization across regions

1

Thank you. Would you consider adding that as a feature to have it detect a set number of regions or chromosomes and parallelize itself? Also it does not seem like...

cjw85

Add option to write median depth to polished sequence

1

**Is your feature request related to a problem? Please describe.** No problem, just an improvement **Describe the solution you'd like** Write the median depth to the description of each FASTA...

edgardomortiz