medaka

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Python 3.12 compatibility for pip

1

It would be useful to be able to install using pip for python3.12

mesti90

Duplicate entries in annotated VCF file

1

**Describe the bug** Hi! I performed bacterial variant calling using \` medaka_haploid_variant \`: \`\`\` medaka_haploid_variant -t 10 -m r1041_e82_400bps_sup_v4.3.0 -i -r -o \`\`\` The resulting medaka.annotated.vcf file contains duplicate variant...

tfwulff

Hi there, I am trying to run medaka using a nextflow script but I keep running into the below issue. Could I please get some assistance on this. Thank you...

setshabaTaukobong

Polishing a GFA

2

**Is your feature request related to a problem? Please describe.** - When I polish a Flye assembly with Medaka I lose assembly information since `medaka_consensus` accepts `fasta` files instead of...

mmcguffi

Medaka consensus error when stitching consensus chunks together

2

Hi, I am encountering a bug when using Medaka, but I can't figure out how I could solve it. Would you happen to have an idea as to what I...

mgils4

Failed to run medaka consensus

1

Hello, i tried running medaka_consensus and i am resulting in the following error. I installed medaka through conda package manager. The command i used to run medaka is the following...

Sabarish2001

Medaka v1.11.3 ImportError - undefined symbol: libdeflate_free_compressor

2

Hi, I tried installing the latest medaka version (1.11.3) from the source, everything went smoothly during the installation. However, I got the error below when I tried to use it....

nbel15

Need help with 'AVX instructions not available' error

2

Hi there, I used pip to install medaka on a Virtualbox VM Ubuntu 22.04. The host machine runs on Windows 11 and has access to AVX instructions. However, when I...

benn888

Hi I'm running medaka consensus for a metagenome assembly from nanopore reads. but it giving the error of "-d must be specified". I have tried to run the command from...

ramnageena11

"Incomplete aux field" when running medaka_consensus for certain fastq files

1

**Describe the bug** Running medaka_consensus on certain fastq-files seem to generate a ""Incomplete aux field" error (see provided data). [data.zip](https://github.com/user-attachments/files/16083224/data.zip) **Environment** - No GPU - medaka 1.12.0 through pip -...

OscarAspelin