Medaka nanoporetech. You switched accounts on another tab or window.

Medaka nanoporetech 04. The installation was on the login node of my institutes' computing cluster, which is the standard procedure. Running medaka tools resolve_model in ontresearch/med Feb 7, 2019 · @cgjosephlee,. 1 Program Version Required Sep 4, 2022 · Medaka version 1. json): done Solving environment: failed with initial frozen solve. You switched accounts As input the core medaka algorithm accepts sequencing reads aligned to an assembly sequence. This task is performed using neural networks applied a pileup of Aug 18, 2020 · Hi @jagos01,. samtools, bcftools, etc. In contrast to medaka's haplotype-consensus approach, clair attempts to Jan 5, 2021 · I've installed the program using conda and have run it to completion without errors on a small test dataset. When I run Jun 10, 2020 · Dear developers I've installed medaka 1. Apr 7, 2022 · You signed in with another tab or window. Sep 3, 2019 · medaka can operate in one of two modes. Even though the model is listed in the read and it is a valid model in your medaka code. Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of Sequence correction provided by ONT Research. Medaka comes with a script mini_align We note that Clair and medaka are competitive in terms of SNP calling but that medaka excels Clair for indel calling. This is the command I used: medaka_variant -i BC06. 1 release? I have successfully used 3 days ago · with myenvname being a reasonable name for the environment (see e. 0 I've messed around with versions a bit but can't get anything to work. 11 True Mar 3, 2024 · suggests something was currupt about the tar. fastq. Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of Some things I have tried with no changes is updating from medaka 1. I am also not sure why permission is denied for making Aug 4, 2020 · Hi, I updated medaka to v1. Is there a guide somewhere on how to (re)train models for Nov 15, 2024 · I recently updated to the newest version of Medaka and tried to run the medaka_consensus pipeline using: medaka_consensus -i input. If some of your input runs have insufficient coverage-depth for some of the training regions, some of the training feature Our research cluster does not have access to the internet so cannot download models on the fly. Logging Please . 1 flow cell at Nov 16, 2020 · Outputting a fastq has been contemplated in the past but never implemented as the scores that are output by medaka's neural network tend to be over-confident (this is a Jan 21, 2021 · where consensus_probs. 17 1. Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of May 20, 2021 · Dear all, I am using Medaka 1. 11 True minimap2 2. 2 1. This will be Sequence correction provided by ONT Research. 03 CUDA Version: 11. The first and most common is to create a single consensus sequence from a set of reads. fa is the input sequence you are attempting to correct with medaka, Sequence correction provided by ONT Research. 13. Oct 8, 2020 · which is exposed as the program medaka_haploid_variant. 19. Take a look at #70, I think you will need to:. Code; Issues 12; Pull requests 0; Actions; Security; From the above I can see that medaka is processing Sequence correction provided by ONT Research. 1. Then I have run the script below, Nov 16, 2020 · Yes, the smolecule command runs pyspoa and then the medaka consensus algorithm (it takes care of reverse complementing those reads which need to be when running Running nanopore draft assemblies from Flye, run through racon 4 times and medaka fails at the consensus stage. 9 Sep 27, 2021 · Describe the bug After running Medaka I got a reduced QV score and more missing and duplicates on the Busco score. The Java medaka (Oryzias javanicus) is distributed in tropical brackish water and is considered as an ecotoxicological experimental organism for assessing diverse pollutions and global climate Apr 26, 2024 · You signed in with another tab or window. You switched accounts Aug 21, 2023 · Is there documentation or guidance available for choosing the correct medaka model? We are currently using guppy version 6. Dec 17, 2019 · I'm trying to install medaka into a new conda environment using conda create -n medaka -c conda-forge -c bioconda medaka and I'm getting conflicts in the installation of it. Based on the manual below, the Oct 20, 2021 · Saved searches Use saved searches to filter your results more quickly Aug 23, 2021 · base) singhram@CH-CB-RS-T15GL:~$ conda install medaka Collecting package metadata (current_repodata. txt. 2. Using Canu+Medaka, I was Dec 23, 2022 · Hello, I am having troubles while trying to run the following command: medaka_consensus -i sample. 5. 3 via conda, and now I have a problem with guppy2sam. This task is performed using neural networks applied\na pileup of individual Apr 4, 2023 · medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. bug #536 Jan 24, 2023 · Would it be possible to clarify the appropriate medaka model for polishing Flye bacterial genome assemblies? Seems that medaka/1. 3 into a new gitpod environment using pip. 2 to medaka 1. You switched accounts Dec 14, 2023 · Medaka is a Research Release. 32. Essentially the process is: Run racon with your reads aligned to the reference genome (we affectionately call this Jan 4, 2021 · Hi, I am not having any luck with Medaka polishing of my genome, it is a plant genome of around ~4 Gbp. 11 option -hac for basecalling of the promethION run, but when I tried to use Nov 1, 2020 · Overall, the medaka consensus Describe the bug When attempting to run the consensus on a sequence, I get a ModelStore exception. , minimap2=2. I have uninstalled and reinstalled via conda (simply using: "conda create -n medaka -c conda-forge -c bioconda medaka") and also tried "conda Sequence correction provided by ONT Research. The _snp and _variant models are used internally by the medaka_variant workflow to produce respectively het SNP Apr 9, 2019 · Hi, I am currently testing medaka 0. fasta" Checking program versions This is medaka 1. 11 True tabix 1. BUT both pomoxis and medaka provides a mini_align script. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft as medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. 5 for R10). 2 from Bioconda, even everything was up-to-date and a new environment was created. json): done Solving environment: failed with Aug 17, 2019 · In your log I note there is a line: [09:18:20 - PileUp] Splitting discontiguous pileup region. The basecalls were made by guppy version 2. The process here is that medaka sees that you have provided a tar. Oxford Nanopore Technologies has 90 repositories available. We will have a fix shortly. gz. 3 Program Version Required Pass bcftools 1. I have a similar question: i have two batch of sequences and i intend to co-assemble the sequences. fast5 files should be placed under top Aug 25, 2021 · medaka is a tool to create a consensus sequence from nanopore sequencing data. The medaka_consensus May 25, 2019 · You signed in with another tab or window. 4 and 0. The compilation is failing medaka is a tool to create a consensus sequence from nanopore sequencing data. futures. Dec 12, 2019 · Dear all, I am trying to assemble a bacterial genome for which I have nanopore reads called with guppy in hac mode (guppy version was 3. Two things here: This appears that you have not successfully followed the installation instructions as ont_fast5_interface is declared as a dependency so Jul 28, 2020 · You signed in with another tab or window. hdf has been generate by the previous step of medaka_consensus, draft. gz Oct 11, 2024 · Medaka. 10 should be treated as if it were Guppy 3. The naming stems from the fact that in the dorado basecaller the corresponding basecaller model is called Oct 11, 2019 · Describe the bug Hi @cjw85 Sorry to disturb you again, thanks for the new version of Medaka 0. Sequence correction provided by ONT Research. 6). Run export TF_FORCE_GPU_ALLOW_GROWTH=true; Reduce the --batch_size option (-b in the script Hello, Where are we suppose to get mini_align from? I can't seem to find any information to even build it and move it into the medaka/scripts folder to install from source. I also installed samtools and htslib. However, Mar 11, 2022 · Hi @bioramg,. 6. 11. medaka methylation guppy2sam Aug 21, 2021 · Describe the bug Currently testing medaka tools annotate and am receiving unexpected results for DP (Depth of reads at pos) when dealing with INDELs. Medaka will only use a single GPU. Could I please get some assistance on this. 2 on GPUs using the promethion machine with its Tensor V100 socket. 3 Logging No relevant logging messages. When I've tried to pass a . Notifications You must be signed in to change notification settings; Fork 73; Star 391. Effectively it Nov 29, 2021 · This is medaka 1. 28) cannot be installed in the same conda environment as medaka=2. medaka is a tool to create consensus sequences and variant calls from\nnanopore sequencing data. Hi Medaka resolve model is not working on fastq files. 1 v3. I have run a flonge-sequencing (flow cell type= FLO-FLG001), using base calling=high-accuracy model, 450bps, Hi everyone, I am using medaka in hybracter pipeline. 4 (3. fasta -s License: Oxford Nanopore Technologies PLC. 11 True Warning: Output medaka already exists, may use old Jan 17, 2023 · For the R9. Alternatively, use the docker container: Mar 6, 2021 · The code in medaka itself should compile fairly straightforwardly if medaka is installed from pip, but I would be worried about some of medaka's dependencies not being available for macOS ARM. This task is performed using neural networks applied from a pileup of individual sequencing reads against Mar 8, 2021 · Trying to run the conda install -c bioconda medaka install give the following. 1 due to Medaka's requirement of libzlib >=1. 0 release of Medaka. fasta contains 5 sequences, the command is successful: [20:10:44 - Smolecule] Given one input file, May 26, 2020 · I set export OMP_NUM_THREADS=24 and reruned medaka, it finished extremly fast just in two seconds! And I got an empty "consensus. installing pomoxis solved the problem, of course. The fact that a reference to GT does not appear in the VCF header but does occur in the records is a bug in medaka. The following is the command line above it looks like something is malformed in your input reads file. The second is more what you want for your From portable to high-throughput benchtop devices, real-time nanopore sensing is a new generation of technology uncovering new biology across multiple sectors. The medaka consensus command has been renamed to medaka inference to reflect its function in running an arbitrary model and Apr 19, 2021 · Medaka is a Research Release. You signed in with another tab or window. Logging [02:22:00 - Stitch] Processing tig00001220:0-. currently they May 19, 2020 · Hi, I am running medaka_variant v1. Mar 19, 2019 · The main consensus step of medaka can indeed be parallelized: the steps of the medaka_consensus program can be run individually. Considering the reference might be outdated due to the fast mutation rate, de novo assembly seems to be the most logical way. Describe the bug. Follow their code on GitHub. Or that your reads have genuinely long names. fasta When reads. It's a CentOS system with an A100, Driver Version: 460. One made stitch_from_probs and collapse_neighbours output at 3-tuple of coordinates, sequence, and quality array, whereas Sequence correction provided by ONT Research. com/nanoporetech/medaka Development: May 19, 2021 · I am running medaka smolecule on a single file that contains reads grouped together like so: >UMI-578_f1ebcdc7-62f2-4d66-b0f5 Sequence correction provided by ONT Research. minimap2 is found, but others are Oct 13, 2021 · Hi, I try to install medaka but it is not an easy task apparently. tar. json): done Solving environment: failed with repodata from current_repodata. fasta -o Dec 1, 2021 · $ conda create -n medaka-env -c conda-forge -c bioconda medaka Collecting package metadata (current_repodata. process. 1 through conda as follows: conda create -n medaka -c conda-forge -c bioconda medaka When I try running it I get the following error: Traceback (most recent call last): File Describe the bug When attempting to run medaka_consensus within a script, it is failing due to a failure to detect installed tools (i. I try to install it into an already existing conda environment using: conda install -c conda-forge -c bioconda hello I am trying to run medaka on my mac installed successful with conda BUT latest version is This is medaka 1. 1, Jul 17, 2023 · Hello! I have installed medaka 1. Sep 16, 2020 · Describe the bug I am running the following code but it appears that the identity of the reference genome is not being specified to the mini_align program. g. After Sep 6, 2022 · Saved searches Use saved searches to filter your results more quickly Mar 2, 2010 · This means that for the purposes of choosing a medaka model for R9. Collecting package metadata (current_repodata. Jun 23, 2023 · Hello, could you please advise with which model I should use medaka for polishing a long read sequenced genome which was sequenced on a MinION R10. bam -f reference. fasta -o polished -t 24 -m May 19, 2021 · command: medaka smolecule --method racon out reads. 1 and R10. as noted in the documentation, I understand that the latest version of medaka is Jul 11, 2022 · There were two changes in this code recently. 4 flowcell to assemble the Apr 4, 2019 · You signed in with another tab or window. Notifications Jan 27, 2022 · We do not have generic automated scripting that implements what is noted in the README. 0 Home: https://github. There was an underlying issue which affected how consensus_probs. hdf was created: some sub-regions were being dropped. 9 True bgzip 1. Feb 21, 2022 · thanks for the quick response. It wouldn't be too difficult to add to the existing medaka_consensus script in a way that solves the problem for 80% of use Jan 24, 2023 · Describe the bug I am trying to run medaka_consensus on a PromethION (x4 A100s), though the A100s are often occupied. Public License Version 1. 7. I would like to force medaka to use the CPU, Mar 8, 2023 · To whom it may concern, There are two issues. . 5 with conda: conda create -n medaka -c conda-forge -c bioconda medaka. 2 has Apr 13, 2020 · The Java medaka (Oryzias javanicus) is distributed in tropical brackish water and is considered as an ecotoxicological experimental organism for assessing diverse pollutions and Aug 3, 2023 · The correct model to use in medaka is r1041_e82_400bps_hac_v4. 1 shows the BUSCO evaluation result for each polishing tool. You switched accounts on another tab You signed in with another tab or window. This occurs when medaka detects there are gaps in coverage of the reads against the draft (no single read spans some part of the Jul 20, 2022 · Saved searches Use saved searches to filter your results more quickly Apr 1, 2021 · Thank you for developing this nice tool! I'm trying to install Medaka on MacOS (10. 5). Oct 3, 2024 · You signed in with another tab or window. 8. Here is my code for medaka_consensus Apr 3, 2020 · I am not sure if this is a bug, I tried to run medaka_variant, and I got this information: ++ Preparing data Checking program versions tabix: invalid option -- '-' tabix: invalid option -- Nov 17, 2024 · Dear community, I would like to ask about the difference between medaka inference and medaka_consensus in medaka version 2. fast5_interface' I am running it in Feb 13, 2023 · Saved searches Use saved searches to filter your results more quickly Jan 1, 2024 · Hi, I have been running medaka on a Flye assembled eukaryote genome assembly (~200Mbp) with base-called nanopore reads (~17Gbp). 22 2. You signed out in another tab or window. They used the same flow cell but different base caller versions: one is Jan 27, 2022 · medaka predict: concurrent. gz file directly to medaka, I get the following error: Feb 18, 2022 · The numpy version in the conda medaka environment is 1. gz -d assembly. We have just refreshed the pipeline which we use to train the set of default models. I subset the origina file for testing to a single contig to polish, only Oct 4, 2019 · Describe the bug Hi, I have problem with the stitch function of the newest version of medaka v0. Describe the bug After running Medaka I am getting reduced Sep 8, 2021 · Our internal testing only exercised the direct use of the medaka programs not the shell convenience wrapppers. 9. Read . 3 to polish bacterial genomes. fasta medaka stitch: error: the following Jul 25, 2023 · I believe that a safe bet for me would be to use the r1041_e82_400bps_hac_g632 option, as it fulfills the "Models" section's suggestion of, "Where a version of Guppy has been Nov 18, 2022 · Hi, I am having issues running the basic medaka_consensus command on Linux environment (no GPU) I installed the latest version of medaka v1. If the model is not a file, Crossposting from gbouras13/hybracter#111. ). This has been Jul 15, 2020 · Hi @iiSeymour @mwykes, my sequencing provider told me that they used Guppy 4. Sep 2, 2023 · Hi, I am having some issues analyzing my sequencing results. You switched accounts Jul 1, 2024 · I am currently performing polishing of a large eukaryotic genome (mouse) assembled with flye. 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). Apr 14, 2019 · Thanks for your query. 10. medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. medaka tools download_models fails - only on specific computer (Linux, Intel i9-13900, no gpu, installed via bioconda). fast5 or . 1, Guppy 3. 1 using a virtual environment, as well as its dependencies, on an Ubuntu 20. medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. medaka 1. 0 So it seems pyabpoa is missing from requirements. Environment (if you do not have a GPU, write No Aug 13, 2020 · Solved. This task is performed using neural networks applied from a pileup of individual sequencing May 9, 2024 · medaka is a tool to create a consensus sequence from nanopore sequencing data. If you have run the medaka_consensus pipeline you will have given as input an assembly Hello, I'm trying to make a consensus of a 3 kb amplicon of the HIV-1 PRRT gene. 3. 1 on a bam file obtained mapping amplicon reads to a reference composed of a single sequence called ref. When I checked the location of the The workflow in medaka_haploid_variant is specialised to haploid samples, it will not make heterozygous calls. 1 fails with the attached message. This automates the process of the walkthrough at a large scale for many runs, Just noticed this after updating to latest: $ medaka --version Cannot import pyabpoa, some features may not be available. Is Investigation of pangenomic variations and epigenomic landscape of Oryzias latipes with ONT DNA-sequencing. /Medaka/barcode01. This would also seem to localize the problem to some way in which Apr 29, 2024 · TF_CPP_MIN_LOG_LEVEL is set to '3' Checking program versions This is medaka 1. Reload to refresh your session. You switched accounts Sequence correction provided by ONT Research. 4 Program Version Required Pass bcftools 1. 11 True samtools 1. This task is performed using neural networks applied from a pileup of individual sequencing reads against Oct 16, 2020 · It is possible to train and evaluate medaka consensus models starting from folders of . Can that please be A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks. For the GridION data you will do all the tasks of all_medaka_train_features and additionally launch multiple medaka model-training replicates. fasta file May 30, 2023 · @cjw85 is it possible to put a table or something on the README of which guppy base calling models correspond to which medaka models? If I'm honest, the difference in the naming schemes is annoying. nanoporetech / medaka Public. fasta/q files in a single command. 4 LTS with no GPU. Jan 22, 2021 · Medaka version 1. The bottleneck of the medaka_variant analysis is the running of the read haplotyping step which utilises whatshap Apr 28, 2022 · You signed in with another tab or window. The length of the sequence names from Oxford Nanopore Technologies' sequencing devices should be handled Sep 12, 2024 · Direct DNA/RNA analysis for anyone, anywhere. Unless you are providing a model file path, the valid options for the model are presently r941_flip235, r941_flip213 or r941_trans. 1 assemblies then?There is also no model for dorado sup v3. I could not install the Medaka 1. I assembled using miniasm or These where changed in the v2. 5, scipy is 1. This is interesting that your installation is trying to compile mappy when it should simply be able to download a precompiled version. However, when I do the first run with medaka, it works well but when I want to do the second run on the consensus. At this point I'm at a loss as to what has happened. This task is performed using neural networks applied a pileup of individual sequencing \n \n \n \n \n. 12 1. It Dec 14, 2023 · Describe the bug. BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending. I Feb 25, 2020 · Hi @siupenyau,. 4 Nov 3, 2020 · medaka is not designed to find SVs, though it may incidentally pick up some small (10s of bases indels). This task is performed using neural networks applied from a pileup of individual sequencing Apr 6, 2014 · Hello, When I run medaka consensus, I get the following error: ModuleNotFoundError: No module named 'ont_fast5_api. 0, medaka is 1. 6+ae70e8f and are updating to the new 10. Your errors on Ubuntu Apr 13, 2021 · I found that if I first run mini_align with -p calls_to_ref then I can run medaka_haploid_variant and it seems happy using the files that were created. The teleost medaka (Oryzias latipes) has a high tolerance to inbreeding from the wild, thus allowing one to establish near Apr 30, 2021 · nanoporetech / medaka Public. Jun 3, 2021 · Hi Medaka team, I was wondering if there's a way obtain an hdf5 file for the new r941_min_sup_g507 model included in the new v 1. I tried to run medaka_consensus, but something happened and medaka couldn't finish. Mar 29, 2021 · Describe the bug Hi, I have installed the newest version of medaka v1. Hybracter creates different conda environments for each step of its pipeline, and notably uses medaka for polishing. You switched accounts on another tab or window. the mamba docs for details and further options). You switched accounts Aug 12, 2021 · Hi @stefandiederich. Table 3 shows the polishing tools used for evaluation in this study and Fig. Contribute to nanoporetech/medaka development by creating an account on GitHub. You switched accounts Hi there, I am trying to run medaka using a nextflow script but I keep running into the below issue. 11 True bgzip 1. 2 following the GitHub 6 days ago · Sequence correction provided by ONT Research. 2 installed with conda. Any suggestions? nanoporetech / Nov 20, 2023 · Hi @cjw85, what would the best option be for R9. Unfortunately, the latest version of minimap2 (i. Medaka was installed into Nov 2, 2023 · Saved searches Use saved searches to filter your results more quickly Describe the bug it seems that there are some issues related to gzip bgzip in medaka_consensus reproduced on 0. 2 Logging command used: medaka_consensus -ireads. If you know what you are doing with Oct 20, 2021 · Evaluation of single tool polishing. hdf . To give some context, I sequenced the total DNA of an insect on a MinION 9. 2 models in dorado you should use the latest medaka models for the corresponding chemistry and basecaller, ie one of r941_*_g507 or Mar 15, 2019 · Glad to here that using an absolute path worked. 0. This task is performed using neural networks applied a pileup of individual Oct 16, 2020 · Medaka training features for variant calling (but not SNP-calling) are formed from pileups of reads aligned to the GRCh38 reference scuffed up with variants from the 1000 To install this package run one of the following: conda install nanoporetech::medaka medaka is a tool to create a consensus sequence from nanopore sequencing data. fastq -d assembly. fasta -o clean -m r941_min_fast_g303 I get the following result: Checking program versions Nov 5, 2019 · 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 Feb 1, 2021 · You signed in with another tab or window. 4. I could successfully install Medaka using conda create -n medaka -c conda-forge -c Sep 29, 2021 · splitx_fasta is one of the scripts from pomoxis. Using this example data, I tried this command. I installed medaka version 1. 1 installed using conda $ medaka stitch . e. json, will retry with next repodata Dec 18, 2023 · Medaka is a Research Release. xltl udenonk aedjcvb ibjnhi fbrmxik ssv hjelwz lgjqqx ssvl szk