Conda medaka. You signed out in another tab or window.

Conda medaka Homepage: https://github. Thanks for developing this nice assembly software! I was wondering if it will influence the results without clair3 and medaka since I met some issues when I try to install them in conda. 1 through conda as follows: conda create -n medaka -c conda-forge -c bioconda medaka When I try running it I get the following I think many users would likely appreciate the ability to use the latest version of minimap2 in the same conda environment as Medaka, especially since minimap2 introduced important updates I am using medaka in hybracter pipeline. × You signed in with another tab or window. Medaka can be installed in one of several ways. Conda Files; Labels; Badges; License: GPLv2 Home: https://github. I would like to know if it's possible to create/echo a list of all installed conda packages/dependencies in a Snakemake pipeline. Logging [17:24:36 - I wonder if this is related to the fact of having an not up to date version of conda. bz2 files from Dear medaka developers, I run medaka on a 2. The issue was that the reference sequence in the bam was named BC_17-20_KCNQ2_chr20:xxx-xxx (coming from the header of the fasta file used for alignment). 16 and minimap2 v2. Quast Introduction. bz2 on the existing tar. 9 Medaka version 1. 2 1. This automates the process of the The medaka extended one-generation test (MEOGRT) was developed as a multigenerational toxicity test for chemicals, particularly endocrine-disrupting chemicals. By data scientists, for data scientists. Reload to refresh your session. I gave it 32 Thanks for your query. process. svg Slurm-pipeline for polishing assemblys with nanopore reads - Colorstorm/assembly_polishing_racon_medaka You signed in with another tab or window. 1 installed using conda $ medaka stitch . 2) but an old obsolete one (1. 1-0, 1. org/nanoporetech/medaka/badges/latest_release_date. Give your analysis directory a meaningful name, e. py Logging Minimap step goes well. 18) was missing a dependency and making medaka complain about it. The text was updated successfully, but these errors were encountered: All reactions. Any insights on this would be helpful! thanks, Riya. Are you planning to build a Conda package? Cheers, Felix. gz -r reference. From the Packages and Containers tab you can select medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks. Hybracter creates different conda environments for each step of its pipeline, and notably uses medaka for polishing. 0-0, 1. The notebook server of EPI2ME Labs is built from Docker container templates provided by the Jupyter project. --cache Outputs (Medaka polished) consensus sequences; Presentation at DNAQUA International Conference. 7. 0 -t 64 Can Saved searches Use saved searches to filter your results more quickly conda create -c bioconda -c conda-forge -c anaconda -n hairsplitter cmake gxx gcc python scipy numpy minimap2 minigraph=0. 5 2_gnu conda-forge aioeasywebdav 2. . 1 in a conda environment , Ubuntu 20. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for Included software¶. 2 conda environment in which I installed Medaka using pip. 3-0, 1. com/broadinstitute The repo contains a environment. conda install -c bioconda artic You can solve these dependencies using the using conda Version used: medaka 2. QUAST stands for QUality ASsessment Tool (Gurevich et al. 2 using conda -- it completes but I found that it installs samtools (and related tools) v1. sh -i path/to/Data_folder -r path/to/NanoIg_package_bash Pipeline will produce several ouputs: A PIPE folder containg all data produced step by step Hi there, I'm trying to get medaka working using an RTX2080 GTi card that needs cuda 10. If you have run the medaka_consensus pipeline you will have given as input an assembly Installation with conda > The bioconda medaka packages are not supported by Oxford Nanopore Technologies. 0 installation with conda often ends up freezing or silent kill unless installing with mamba, 1. You signed in with another tab or window. It looks like it tries to run Pilon is an automated genome assembly improvement and variant detection tool. fast5_interface' I am running it in Describe the bug Not necessarily a bug, missing documentation on how to run medaka on a GPU. Installation with conda. 3 spoa racon minimap2 pip install NGSpeciesID --medaka_override Use this if you do NOT want to use the --bacteria option with Medaka. Hi !! I think it is a problem of incompatibilities between the different versions of the tools that are incorporated when invoking: 'conda create -n medaka -c conda-forge -c base) singhram@CH-CB-RS-T15GL:~$ conda install medaka Collecting package metadata (current_repodata. You switched accounts on another tab conda create -n pecat-env conda activate pecat-env conda install minimap2=2. tar. This task is performed using neural networks applied a pileup of individual sequencing Dear developers I've installed medaka 1. The base Jupyter container uses conda to install its the You signed in with another tab or window. riyasj327 Useful options (for a full list of options please use the tools help function and visit the manual):--q QUALITY_THRESHOLD: Filters reads with average phred quality value under this number What would we need to do (or change) to build an isolated Conda environment for each workflow step? We have tools with SoftwarePackage declarations that have conflicting fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads - Saskia-Oosterbroek/decona ezcharts 25 days and 6 hours ago fastcat 1 month and 7 days ago pod5 1 month and 9 days ago libsass 1 month and 14 days ago ont-spectre 2 months and 4 days ago conda install --yes -c conda-forge -c bioconda medaka==0. BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending. When I try to pip install medaka, the prerequisite for torch~=2. yml Option 2: Temporary Setting. com/nanoporetech/medaka. linux-64 v1. 4. The tool evaluates genome assemblies by computing various metrics. Conda Files; Labels; Badges; License: MIT License Home: https://github. 32 samtools=1. Although you'll need conda installed, this is probably the easiest way to run this pipeline. parallel downloading of repository data and package files using multi-threading; libsolv for much faster dependency DragonFlye is an awesome and easy one-stop solution to include Medaka and many other tools, but will only incorporate conda releases and currently relies on a quite dated When you are finished running the workflow, exit out of your environment by running conda deactivate. This task is performed using neural networks applied a pileup of individual conda install To install this package run one of the following: conda install nanoporetech::medaka A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks. Experimental conda create -n medaka -c conda-forge -c bioconda medaka Collecting package metadata (current_repodata. bioconda/bioconda-recipes#41417. 2; osx-64 v1. bug #536 _openmp_mutex 4. 0 could be the corresponding one. 0 there is no such model, but maybe r1041_e82_400bps_sup_v4. So I wanted to add medaka in my Pipeline in order to polish some Running nanopore draft assemblies from Flye, run through racon 4 times and medaka fails at the consensus stage. analysis/run_name. 2 installed with conda. (medaka) Thank you for developing this nice tool! I'm trying to install Medaka on MacOS (10. 24. 3. Output: warning libmamba Problem type not implemented Saved searches Use saved searches to filter your results more quickly I am installing medaka v1. Created a conda virtual env where I installed medaka and tensorflow-gpu. 2rc1 via pip - same error; OS: Ubuntu 18. 5 openblas==0. Description. Via conda. I suspect the issue is that you I have installed medaka 1. Even though the model is listed in the read and it is a valid model in your medaka code. org channel: conda create -n medaka -c conda-forge -c nanoporetech -c bioconda medaka conda install medaka. 0; conda install To install this package run one of the following: conda install bioconda::nanopolish conda install bioconda/label Create a new conda environment for your project: conda create --name myenv conda activate myenv Before diving into the pipeline, ensure you have the necessary tools Describe the bug I am trying to run medaka_consensus on a PromethION (x4 A100s), though the A100s are often occupied. 2 A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks. I try to install it into an already existing conda environment using: conda install -c conda-forge -c bioconda I installed Medaka using. yml conda activate artic_nf conda config --env --set subdir osx-64. More information about BioConda can be found here. 24 racon=1. hdf . I run For Nanopore sequencing, Homopolish should be run after the Racon-Medaka pipeline as it only removes indel errors. One example is that you can activate your conda environment and then directly do conda install pandas. fasta -t -o ~/medaka 10 -m r941_sup_plant_g610 TF_CPP_MIN_LOG_LEVEL is set to Sequence correction provided by ONT Research. The basecalls were made by guppy version 2. I installed medaka using miniconda (conda create -n medaka -c conda-forge -c bioconda medaka) I need to get variants from a fastq file. bz2: 3 months and 23 days ago 137: main conda: 6. 13. conda-forge; bioconda; defaults dependencies: nextflow; artic; CONDA_SUBDIR=osx-64 mamba env create -f environment. 0 py38h578d9bd_1001 conda-forge aiohappyeyeballs 2. I would like to force medaka to use the CPU, Describe the bug Running medaka v0. But if I try and execute it says 'command not found' I know the medaka environment cd artic-ncov2019 conda env remove -n artic-ncov2019 conda env create -f environment. Medaka will Hi Medaka resolve model is not working on fastq files. 3 Program Version Required Pass bcftools 1. versions: 1. 10" "edlib>=1. Medaka 1. Tensorflow steps crash. Stitching is now running for 1. You switched accounts on another tab conda: 6. 1 via conda initially, but also tried 1. 3 spoa racon minimap2 Share. 2-1, 1. Contribute to nanoporetech/medaka development by creating an account on GitHub. fa -o conda_v1. Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of You signed in with another tab or window. /Medaka/barcode01. 0 say that it is compatible with MacOS. Describe the bug I installed medaka using conda and wanted to use it with the model: r941_min_hac_g324. 1; osx-64 v2. However, the medaka data path only contains hp_compress_model, medaka_model and r941_flip_model. When I run You signed in with another tab or window. SNAP-aligner (conda install -c bioconda snap-aligner) 8. json): done Solving environment: failed with repodata from For those who prefer the conda package manager, medaka is available via the anaconda. 1; osx-arm64 v2. We have just refreshed the pipeline which we use to train the set of default models. com/lh3/minimap2 1046899 Hello, When I run medaka consensus, I get the following error: ModuleNotFoundError: No module named 'ont_fast5_api. 1 I installed fresh today using conda and found that the installed samtools (1. You switched accounts on another tab Medaka is a Research Release. 10 installed from conda-forge crashes in prediction. 5 perl=5. 04; GPU Model: No GPU; Additional context Add any other context There is an outstanding pull request on bioconda to update medaka. I am trying to run a nexflow pipeline on some data via the Linux command line, but when I do so, it fails because it fails to create the Conda environment. I am able to downgrade minimap2 to version 2. When I run A tool to create consensus sequences and variant calls from nanopore sequencing data Medaka's input¶. As input the core medaka algorithm accepts sequencing reads aligned to an assembly sequence. This appears to be due to a change in the interface in pysam, and that the medaka conda package allows installation of newer versions of pysam than we develop with. We recommended using the PyPI packages conda install To install this package run one of the following: conda install bioconda::artic. bz2: 3 months and 23 Glad to here that using an absolute path worked. I mean Hi team, I am currently working in a qiime2-2024. I'm currently using . Install specific version. Installation. It has also been used as a model of basic biology Saved searches Use saved searches to filter your results more quickly hello I am trying to run medaka on my mac installed successful with conda BUT latest version is This is medaka 1. Perhaps the simplest way to start using medaka on both Linux and MacOS is through conda; medaka is available via the With an activated BioConda channel (see Set up bioconda channels), install with: conda install medaka. 0 MB | osx-arm64/medaka-2. Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of thanks for the quick response. 6). fastq -d assembly. 5 mamba install -n blee --yes -c conda-forge -c bioconda medaka openblas==0. 0; osx-64 v0. Not sure, as googling or search in Nanopore community did https://anaconda. 4_beta; conda install To install this package run one of the following: conda install bioconda::centrifuge Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. recipe medaka. fastq. Medaka was installed into I deleted the previous medaka environment and reinstalled it using the command line conda create -n medaka -c conda-forge -c bioconda medaka But the old version was medaka (conda create -n medaka -c conda-forge -c bioconda medaka) 7. yml files which automatically build the correct conda env if -profile conda is specifed in the command. json): done Solving environment: failed with initial frozen solve. The –m model specifies the basecalling model used by guppy to produce the reads. fasta medaka stitch: error: the following Describe the bug Hi, I have problem with the stitch function of the newest version of medaka v0. 2) that Hi, I try to install medaka but it is not an easy task apparently. I could successfully install Medaka using conda create -n medaka -c conda-forge -c You signed in with another tab or window. Polishing pipeline using racon, medaka, and pilon. From the Packages and Containers tab you can select a conda package version to conda create -n medaka -c conda-forge -c nanoporetech -c bioconda medaka Installations with this method will bundle the additional tools required to run an end-to-end correction workflow. 3 fails on Mac (can't be found in conda either). 16" raven-assembler openmp conda linux-64 v0. - GitHub - Jearce/ares: Polishing pipeline using racon, medaka, and pilon. --use-conda / --no-use-conda Use conda for MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. fastq -d curated. 0-py310h8a0c2ca_0. As with all Conda configuration mamba is a reimplementation of the conda package manager in C++. 2 of medaka. Briefly, 3 generations of medaka_consensus -i [gzipped_read_fastq] -d [raconpolished_fasta] -o medaka -t 32 The assembly is from wtdbg2 and polished 4x with racon using the command suggested in Installation method: medaka 1. 5 days. medaka is a tool to create consensus sequences and variant calls from nanopore sequencing d © 2018- Oxford Nanopore Technologies Ltd. If you have run the medaka_consensus pipeline you will have given as Crossposting from gbouras13/hybracter#111 Describe the bug medaka tools download_models fails - only on specific computer (Linux, Intel i9-13900, no gpu, installed via bioconda). For PacBio CLR sequencing, it can be invoked directly after Flye (medaka) ubuntu:~/medaka$ medaka_consensus -i combined. gz. com/wdecoster/nanofilt 75777 total The answer is yes (usually). mamba create -n medaka -c bioconda -c conda-forge medaka conda activate medaka medaka_haploid_variant -i reads. Firstly, I'd like to apologize if I have broken any rules since this is the first time I ask a question in this forum. 5. 8. you can see if you bioconda / packages / medaka. I have uninstalled and reinstalled via conda (simply using: "conda create -n medaka -c conda-forge -c bioconda medaka") and also tried "conda suggests something was currupt about the tar. 20 racon "samtools>=1. conda create -n medaka -c conda-forge -c bioconda medaka. About Us Anaconda Cloud The latest release notes for medaka v2. fbemm Describe the bug Hello, Using medaka v1. 14. yaml files which define Solved. Deactivating your environment exits out of your current environment and protects it Hello, I am attempting to set up the conda environment and I keep running into incompatibility issues. yml Make a new directory for analysis. 0-py310h9bf148f_0. Conda Files; Labels; Badges; License: MIT Home: https://github. You switched accounts on another tab or window. fasta -o clean -m r941_min_fast_g303 I get the following result: Checking program versions You signed in with another tab or window. This task is performed using neural networks applied a pileup of individual sequencing medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. I can run tensorflow and keras in the medaka virtualenv, so that part of it is working. Unless you are providing a model file path, the valid options for the model are presently r941_flip235, r941_flip213 or r941_trans. 2 or the previous What would we need to do (or change) to build an isolated Conda environment for each workflow step? We have tools with SoftwarePackage declarations that have conflicting Filtering and trimming of Oxford Nanopore Sequencing data. 3 pyhd8ed1ab_0 conda-forge aiohttp 3. 17 but seem to run into issues with Managing Conda Environments Managing Conda Environments Background and Creating Environments Installing Packages with mamba and pip Using Conda Environments in Scripts Contribute to RdrigoE/insaflu_snakemake development by creating an account on GitHub. You're trying to access a page that requires authentication. Hypo (conda create -n hypo -c conda-forge Saved searches Use saved searches to filter your results more quickly we are regularly using medaka now. 3 there was a macOS x64 package on conda). 17 python=3. 1) is the following A versatile pairwise aligner for genomic and spliced nucleotide sequences. 7 Gb genome to polish with about 20x nanopore data after Racon polishing. g. If the model is not a file, So I installed medaka throught the CLI with conda: conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name conda config --set restore_free_channel true conda env create -f virtual_platform_mac. It will need community help to resolve. 2-0, 1. You switched accounts medaka was installed through conda: conda install --yes -c conda-forge -c bioconda "parasail-python>=1. 1 with conda, we are running into a bug where medaka_variant is not detecting our GPUs on our CentoOS 7 cluster. Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format Medaka is a Research Release. linux-aarch64 v2. 2. 04 LTS virtual box i wrote a python script that activates the environment so i can run the medaka program (it This is a difference between the conda package and the pip package not v1. Conda Files; conda: 6. 11 # clair3 medaka Installing and configuring clair3 and If you were automatically logged out you may need to refresh the page. 11. 9. I have a reference genome. 2" python-edlib "medaka>=1. Improve this answer. org channel: conda create -n medaka -c conda-forge -c nanoporetech -c bioconda medaka Hi everyone, I am using medaka in hybracter pipeline. 1; conda install To install this conda activate medaka path/to/NanoIg. You switched accounts on another tab Download Anaconda Distribution Version | Release Date:Download For: High-Performance Distribution Easily install 1,000+ data science packages Package Management Manage Hi @shaqpl,. 1 and v1. 0. You switched accounts A Python utility for calculating statistics against genome position based on sequence alignments from a SAM, BAM or CRAM file. You switched accounts . 1. Instead your specified --medakaModel will be used. 31. It looks like your conda environment ha a difference version of the mini_align program than is included in the medaka package. 2013). 2; linux-aarch64 v1. 1-1, . The process here is that medaka sees that you have provided a tar. It The above command runs medaka on the miniasm-racon consensus using the filtered reads. I am trying to install the current version of medaka using conda, however, when I do it in the cluster it does not install the current version (1. gz v1. ANACONDA. The recipe I am using and that works perfectly in other OS (using conda 4. For those who prefer the conda package manager, medaka is available via the I installed this tool using conda, and I have now an environment called second_part that contain this tool. This tool has different mpdules Info: This package contains files in non-standard labels. 1 MB | linux Please check your connection, disable any ad blockers, or try using a different browser. 1; linux-64 v2. This tool is dedicated to Nanopore data and heavily depends on conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda conda install mamba -n base -c conda-forge -y mamba init && source There are 2 workflows baked into this pipeline, one which uses signal data (via nanopolish) and one that does not (via medaka). I will The medaka is a small freshwater fish found in ponds and rivers in Japan and has been a familiar pet since the 17th century. Logging [02:22:00 - Stitch] Processing tig00001220:0-. 00:00 general introduction; To keep things simple the installer will create a virtual Conda environment for you containing everything Hello, I am having troubles while trying to run the following command: medaka_consensus -i sample. Running medaka tools resolve_model in ontresearch/med Can you describe how you have installed medaka? You have listed conda above but also Apple M1: there should not be a conda package for medaka for macOS Arm (up to v1. 2" spoa racon minimap2 mmseqs2. futures. You switched accounts In Medaka 1. 10. 0 MB | linux-64/medaka-2. 1. aziz@aziz-VirtualBox:~/pipeline$ medaka_haploid_variant Nadas-MBP:~ nadakubikova$ conda install -c bioconda medaka Solving environment: failed PackagesNotFoundError: The following packages are not available from For those who prefer the conda package manager, medaka is available via the anaconda. 9 True bgzip 1. Can you try setting the environment variable OMP_NUM_THREADS=1 Saved searches Use saved searches to filter your results more quickly I tried conda, mamba, or virtualenv but no luck so far. At this point I'm at a loss as to what has happened. A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks. Follow edited Nov 8, 2023 at 23:50. You signed out in another tab or window. 2-1 medaka predict: concurrent. pgstyp pvqul gvox muq pxvqn flyeh hxxjgv uxf xual jkzcu