medaka

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medaka smolecule concurrent.futures.process.BrokenProcessPool

4

**Describe the bug** When I run medaka smolecule I often get this error, a few data sets work but usually its this error. 2 of the 20 samples I have...

rob234king

Choosing the right model

3

Hi, thank you for developing this tool! I would like to use medaka for polishing a dataset where I only have information about the device. Would it still make sense...

pbelmann

Fixes missing symbols for libdeflate.

4

Version 1.4.4 and 1.5 are affected. Building `htslib.a` on a system that provide libdeflate ends up with an import error: ``` ImportError: virtual_envs/medaka_v1.4.4/lib/python3.8/site-packages/libmedaka.abi3.so: undefined symbol: libdeflate_crc32 ``` A quick solution...

ccoulombe

Why does my attempt at retrofitting medaka smolecule to accept BAM input lead to failure in medaka stitch collapse_neighbors

17

I am working on implementing smolecule into my analysis pipeline that uses medaka to generate amplicon UMI consensus sequences. Until now I have been using a very hacky method of...

gordonrix

parameters for minimap2

1

Hello, I am running medaka_consensus -i toMount/alsoGoodDataDiv16.fastq -d toMount/small.fa -o experimentFolder -m r1041_e82_400bps_sup_g615 The first step in the pipeline I notice is minimap2 -I 16G -x map-ont -d /toMount/small.fa.map-ont.mmi /toMount/small.fa...

inemp

possibility to call mixed bases ?

1

Hello, I am trying medaka implemented in wf-artic to do CoV WGS. Just wondering whether medaka could call mixed bases when a minor variant exceed a certain frequency threshold? For...

alantsangmb

Medaka variant error: "IndexError: index 0 is out of bounds for axis 0 with size 0"

2

**Describe the bug** A clear and concise description of what the bug is including the command that you have run. `medaka variant` crashes with exit status 20 when the command...

BioWilko

medaka versions Mac vs Linux

1

hello I am trying to run medaka on my mac installed successful with conda BUT latest version is ``` This is medaka 1.0.3 Program Version Required Pass bcftools 1.10.2 1.9...

antoine4ucsd

test suite generates untracked files

1

**Describe the bug** Running `make test` creates untracked files in the repository root, which is unexpected. ``` .coverage data.pickle test_hap1.vcf test_hap2.vcf test_ref.fasta ``` **Logging** NA **Environment (if you do not...

tkonopka

> Medaka is a Research Release. > > Research releases are provided as technology demonstrators to provide early > access to features or stimulate Community development of tools. Support for...

BCArg