Categories
Tag: conda
Plugin error from deblur: Deblur cannot operate on sample IDs that contain underscores – Technical Support
I read that I might need to rename the files and reinstall with manifest or perform deblur outside qiime2. I would happy to get a detailed step on how to rectify this error as I am new to qiime. QIIME 2 Version: qiime2-2023.7 in conda environment Command ran:qiime deblur denoise-16S…
installation issue with qiime2-shotgun-2023.9 – Technical Support
I have experienced installation issue with qiime2-shotgun-2023.9please help me to resolve this issue.Collecting package metadata (repodata.json): doneSolving environment: failed ResolvePackageNotFound: gxx_impl_linux-64=13.2.0 libgomp=13.2.0 bracken=2.9 xcb-util-image=0.4.0 keyutils=1.6.1 xkeyboard-config=2.38 jack=1.9.22 libcups=2.3.3 alsa-lib=1.2.8 libsanitizer=13.2.0 libgcc-devel_linux-64=13.2.0 gfortran_impl_linux-64=13.2.0 attr=2.5.1 libstdcxx-ng=13.2.0 xcb-util=0.4.0 gcc_impl_linux-64=13.2.0 libnsl=2.0.0 libstdcxx-devel_linux-64=13.2.0 xcb-util-wm=0.4.1 libcap=2.66 xcb-util-keysyms=0.4.0 pulseaudio=16.1 libsystemd0=252 xcb-util-renderutil=0.3.9 libxkbcommon=1.5.0 _openmp_mutex=4.5 libgfortran-ng=13.2.0 libgcc-ng=13.2.0 libudev1=253 gridss=2.13.2…
conda – How to install Bioconda packages
The Bioconda channel builds packages with the Conda Forge channel prioritized. This requires users to likewise prioritize the Conda Forge channel when installing Bioconda packages (see Bioconda documentation). That is, the correct formulation for specifying channels at install time is: conda install -c conda-forge -c bioconda foo Global configuration and…
Installing sagemath on tljh – The Littlest JupyterHub
mig39 October 13, 2023, 3:49am 1 So I’ve installed TLJH on a ubuntu22.04 vm. It’s working great, I have it exposed to the internet, installed letsencrypt, and some users. So far so good I want to install sagemath for some students to use as well, inside this Jupyter environment. I’ve…
MACS3 installation
MACS3 installation 1 I am trying to install MACS2/MACS3 in the Ubuntu 20.04 environment. I am having issues I have no idea how to solve (fairly new to this environment and this is my first post!). Using the commands: sudo apt install MACS3 or pip install MACS3 (and for MACS2…
Windows 10: rstudio reticulate keras tensorflow :: anaconda vs. miniconda vs. python
The number of issues I’m having with a STABLE python environment operating beneath R/Rstudio is overwhelming… and the permutations of installation steps is far too flexible to inspire confidence with any approach. First, I used reticulate to uninstall_miniconda. I wiped the computer of any trace of python. I have updated…
Docker image to use Rscript
Hi! I am having some issues combining docker with snakemake workflows. I have some rules that involve running an R script on the input(s) and producing some output(s). Until now, I’ve also been able to solve the environments for these R scripts with conda environments , however, I’m now at…
How to Install PyTorch on Windows
This tutorial explains the steps to install PyTorch on Windows. PyTorch is a free and open source machine learning library developed by Facebook’s AI Research lab. It is built on the Torch library and is mainly used for tasks like computer vision and natural language processing (NLP). Prerequisites Make sure…
Failure to Verify when reinstalling updated version of QIIME2 – Technical Support
I am trying to install an updated version of QIIME2 on a departmental computer. I first ran into some problems with permissions, but once an override code was identified I am now getting an unfamiliar error response during the final stage of installation. Wget is working find from what I…
Z2jh 500 : Internal Server Error – Zero to JupyterHub on Kubernetes
I have installed z2jh on a local k8s cluster. Sometimes I get 500 error, other times it works fine.I’m using jupyterhub Version 3.0.0, helm chart 2.0.0 500 : Internal Server ErrorThe error was:Failed to connect to Hub API at ‘hub:8081/hub/api’. Is the Hub accessible at this URL (from host: jupyter-hammad-20ali-20baig)?…
Encountering unknown error in ancom – Technical Support
Hello fellow qiime2 users,I’ve been trying to figure out differentially abundant microbial population in diabetic patients but facing so many obstacles that I can’t figure out alone as a novice metagenomic analyst, so I need your help and I’m attaching all the files I used and errors I got below….
feature-classifier not producing an output – Technical Support
Hello, I have a problem with the feature classifier.So I tried this on multiple computers (with intel and AMD chips) and with multiple versions of QIIME2 (QIIME2 2023.5 and 2023.7)So I have a dual boot on my computer with Windows and Linux Ubuntu, newest release. It has 16 GB of…
Cannot install Pytorch 1.0.1 – PyTorch Forums
I am working on project that requires pytorch 1.0.1 and python 3.6.5 . So I have downloaded the wheel file but when I install using pip install torch-1.0.1-cp36-cp36m-linux_x86_64.whl but i am getting the following error: ERROR: torch-1.0.1-cp36-cp36m-linux_x86_64.whl is not supported wheel on this platform .I have created conda environment that…
pytorch – torch.cuda.is_available() is False, when correct CUDA is installed. What could be wrong?
I’m having some trouble getting pytorch to access the GPU. I know that there is an agreement of the CUDA version (11.8). I leave some additional information below, does anyone know what is going on? In case it is relevant, I am working on an HPC. When connecting to the…
pytorch – torch cuda not able to identify gpu on aws g4dn.xlarge
I have created an EC2 instance with GPU g4dn.xlarge and launched it. I want to run some code from command line and this code is pytorch based. While pycuda is able to identify the GPUs the pytorch is not able to identify it. import pycuda.driver as cuda import torch cuda.init()…
gmx_MMPBSA compatibility with Gromacs 2023
I solved the issue. The problem was old version of conda. Accidentally I installed too old version of conda and installation of gmx_mmpbsa failed. I reinstalled conda, which is 22.9.0 (I tried the newest one, but I found this is not a latest one, conda installation mentioned more newest one,…
Job Application for Software Engineer – open source
Who we are Quansight has its roots in the Python data science community. Our founders have had significant involvement in creating and maintaining NumPy, SciPy, Jupyter, Spyder, Dask, Conda, Numba, and other projects, as well as PyData NumFOCUS, and Anaconda. Our mission is to connect companies to open-source communities to…
anaconda – AssertionError: Torch not compiled with CUDA enabled despite installing pytorch w/cuda and all libraries showing up in conda env list
I recently updated my OS (ubuntu). This seemed to break the pytorch installation in all my conda environments. Trying to run pytorch code with cuda in any of these environments , or newly created environments with torch installed ` yields: AssertionError: Torch not compiled with CUDA enabled I tried to…
Support for later Pytorch (1.11 and later) for JetPack4.x – Jetson Xavier NX
For various reasons we are still on RT 32.5 (JetPack 4.x). We are planning to upgrade to JetPack 5.x however it may be a while. In the meanwhile we would like to use later version of Pytorch, 1.11 and later. I am trying to understand our options here. Here is…
rna-seq analysis with Salmon – how to Import and summarize using tximport
Hi! I’m trying to do RNA-seq analysis using salmon and would like to have a matrix of read counts of 10 RNA fastq files. I installed salmon with bioconda, however, I can only find version : 0.8.1 even after ‘conda update salmon’. So I have been doing with version 0.8.1…
CUDA error: CUBLAS_STATUS_EXECUTION_FAILED when using roberta – nlp
Hi everyone, I’m training a model that uses roberta to encoder sentence. I got an error that is:RuntimeError: CUDA error: CUBLAS_STATUS_EXECUTION_FAILED when calling cublasGemmStridedBatchedExFix( handle, opa, opb, m, n, k, (void*)(&falpha), a, CUDA_R_16F, lda, stridea, b, CUDA_R_16F, ldb, strideb, (void*)(&fbeta), c, CUDA_R_16F, ldc, stridec, num_batches, CUDA_R_32F, CUBLAS_GEMM_DEFAULT_TENSOR_OP) My problem is…
Error when running HUMAnN – HUMAnN
Hi, I am keep getting an error when running humann v3.7 humann v3.7 was installed with conda conda install humann -c biobakery –solver=libmambaBefore installing the environment was created and channels were configured as per instructions I downloaded the databases as follow humann_databases –download chocophlan full /home/swijegun/humann/databases/ –update-config yes humann_databases –download…
Getting Started with PyTorch in 5 Steps
PyTorch is a popular open-source machine learning framework based on Python and optimized for GPU-accelerated computing. Originally developed by developed by Meta AI in 2016 and now part of the Linux Foundation, PyTorch has quickly become one of the most widely used frameworks for deep learning research…
Snakemake alignment script
I have been trying to write a simple alignment pipeline with Snakemake. Unfortunately, I have a hard time understanding the error messages. In the example below, the message ” ‘str’ object has no attribute ‘name’ ” is a bit cryptic. Does it means that the expression {input.r1} is incorrect? import…
Conda environments: The pytorch and nvidia channels aren’t playing nicely together and the nvidia channel is out of date – cuDNN
If I set up a conda pytorch environment like this: conda activate pytorch-cuda conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia That works; at least insofar as being able to import torch in python. If, however, I add cuDNN: conda install cudnn -c nvidia Things are no longer…
How to Upgrade PyTorch
The tech giant Meta released the current version of PyTorch in May 2023. It built on the years of progress in the popular development framework ever since its inception in 2016. Data Scientists and programmers both are always looking to upgrade to the latest release to avail all the new…
DESeq2, results(dds, name = ) interpretation results
Hello together, hello Michael, I have an understanding problem using results(dds, …) I have RNAseq data and a grouping of two conditions with interaction of time with the defined reference levels, see code below. And run the code as below. coldata$Cond <- factor(coldata$Cond, levels = c(“A”,”B”)) coldata$Time <- factor(coldata$Time, levels…
DEICODE throwing ‘numpy’ has no attribute ‘int’ error – Community Plugin Support
Hello, I am attempting to use the DEICODE plugin, but I am getting what appears to be an incompatibility error. I am running the qiime2-2023.7 version that was installed in a conda environment for the new (M2) mac. I haven’t had any issues running this version of QIIME2 for other…
Image Classification with PyTorch | by Varrel Tantio | Sep, 2023
Image classification is a fundamental task in computer vision that involves categorizing images into predefined classes or categories. This task has numerous real-world applications, including facial recognition, autonomous vehicles, medical image analysis, and more. In recent years, deep learning frameworks like PyTorch have gained immense popularity for their effectiveness in…
python – Training with PyTorch fails when using 2 GPUs
I’m using a model named Feature-Tokenizer Transformer that was written in PyTorch. I’m running several experiments on a tabular dataset, and until now everything was working fine. But while doing an ablation study (removing some features to check the performance of the model), my jobs were suddenly crashing when I…
Should I Learn Docker to Run Command Line Bioinformatics Tool?
I work in a genomics team where we sometimes teach people from other labs how to run bioinfo command line tools in Linux. Almost all of them are Windows users and never experienced using Linux. We usually help them set up Linux in dual boot so that they can run…
Can’t install CUDA tools 4090 laptop – CUDA Setup and Installation
I can’t use my 4090 laptop for pytorch. I followed the instructions for installing CUDA and even contacted Nvidia customer support but when I run: import torchprint(torch.cuda.is_available()) I get a false statement, showing that torch can’t find my gpu with cuda. Here is what the installer looked like: For reference,…
Current advice for generic SageMath install advice
On Tue, Mar 28, 2023 at 1:34 AM Nils Bruin <nbr…@sfu.ca> wrote: > > What would the current (Spring 2023) easiest instructions be for people to install sage? I’m asking in support of an install-fest for students, so the objective is to have easy solutions for giving students access on whatever…
cancel local run in azureml sdk2
This code is creating a local run with sdk2, and I want to cancel this job, how can I do this? #import required libraries from azure.ai.ml import MLClient, command from azure.ai.ml.entities import Environment from azure.identity import DefaultAzureCredential #connect to the workspace ml_client = MLClient.from_config(DefaultAzureCredential()) # set up pytorch environment env…
scanpy problem for empty cells
Hello everyone, I encountered a problem when I use scanpy analysis my data. When I tried to remove scrublet, and then I encountered following error: filtered out 42144305 cells that have less than 200 genes expressed Running Scrublet normalizing counts per cell /rsrch4/home/canbio/conda/envs/scvi-env/lib/python3.11/site-packages/scanpy/preprocessing/_normalization.py:197: UserWarning: Some cells have zero counts warn(UserWarning(‘Some…
Troubleshooting BWA-MEM2 resources under Docker Galaxy – mapping
Hi Jenna,I ran into this same error.With fastp cleaned data, I can use bwa-mem2 to run a dataset to 1 or 2 genes of the reference hg38. I then tried running the 48 pairs in the collection against the single gene. That works. but when I scaled to the complete…
Can Pytorch Run Without Gpu?
discuss.pytorch.org So, I installed pytorch using the following command: conda install pytorch-cpu==1.0.0 torchvision-cpu==0.2.1 cpuonly -c pytorch The following works: import torch x = torch.rand(5, 3) print(x) But import torchvisio… discuss.pytorch.org Hi as the question suggest, is it possible to use Pytorch without GPU support. I was using Pytorch without GPU…
Stuck at Conda version 23.1.0
Stuck at Conda version 23.1.0 0 Hi all, Despite trying many command lines to update Conda on Ubuntu, I am still stuck at version 23.1.0 of Conda (conda update version is currently 23.7.4). Indeed, here are some examples of command lines I’ve tried: conda update conda conda install conda=23.7.4 conda…
Cannot import name ‘ResultCollection’ from ‘qiime2.sdk’ – Technical Support
I was originally running qiime2-2023.2 but had to install qiime2-2023.5 to go along with the 2023.5 version of q2-fmt-alpha. I tried to generate a raincloud plot and it gave me an error qiime stats plot-rainclouds \ –i-data timepoint-dists.qza \ –i-stats stats_baseline0.qza \ –o-visualization raincloud-baseline0.qzv Based on previous posts on the…
Topaz GPU issue -pytorch issue? – Particle Picking
Hi all, I am trying to install topaz on ubuntu.CUDA version is 11.7 First attempt:conda create -n topaz python=3.6conda activate topazconda install topaz=0.2.4 cudatoolkit=11.2 -c tbepler -c pytorch -c conda-forge which topaz/home/mjmcleod/eman2-sphire-sparx/envs/topaz/bin/topaz Put this path into cryosparc and ran.It would run, but would not use GPU. Attempt 2: Realized I…
Starting Server for Non-Default Users in JupyterHub: 500 Internal Server Error – JupyterHub
I am encountering an issue with starting a server for non-default users in JupyterHub. When attempting to start a server for a user named “mahdi” (or any other non-default user), I receive the following error message in the JupyterHub container logs: [I 2023-09-20 07:40:15.461 JupyterHub provider:659] Creating oauth client jupyterhub-user-mahdi…
Cannot install OpenCV in the same conda environment as PyTorch
I have a conda enviornment named ‘pytorch-train’ where I have PyTorch with all CUDA related packages. When I try to install OpenCV in this environment it takes forever to solve the environment and it never reaches the end of the solving process. The command for installing pytorch in my case…
Elusive syntax error in Snakefile
Elusive syntax error in Snakefile 0 Hi, I’m quite new to snakemake and was trying to write a little workflow to analyze some nanopore data. However, it keeps returning an invalid syntax error caused by this rule rule alignment: input: “{base_out}/2.TRIMMING/{sample}.trimmed_and_clean.fastq.gz” output: “{base_out}/3.ALIGNMENT/{sample}.ngmlr.bam”, “{base_out}/3.ALIGNMENT/{sample}.ngmlr.bai” resources: partition: “EPYC” runtime: 5760 mem_mb:…
issue with qiime dada2 denoise-ccs – Technical Support
Hi,I have 24 clean CCS read datasets and i want to get amplicon sequence variants by running dada2.I got one issue when running dada2 denoise-ccs with QIIME2. When i am running dada2 in qiime2 with all 24 samples:The command I used was: qiime dada2 denoise-ccs –i-demultiplexed-seqs reads_qza/ccs_reads.qza –p-min-len 1200 –p-max-len…
Error executing process > consensus_classification in NanoCLUST
Error executing process > consensus_classification in NanoCLUST 1 Hello, I’m trying to run NanoCLUST with my 16S sequence data. I run it on a Linux ubuntu 20.04 machine. When I use the command: nextflow run main.nf -profile docker –reads “*.fastq” –db “db/16S_ribosomal_RNA” –tax “db/taxdb/” I get the following terminal output:…
How to use PyTorch on Holoscan AGX dev kit? – Holoscan SDK
We are installing the PyTorch on Holoscan SDK with AGX Orin platform, but we failed to enable the CUDA acc. on PyTorch, following are the steps we’ve tried: conda install pytorch==1.11.0 torchvision==0.12.0 torchaudio==0.11.0 cudatoolkit=11.3 -c pytorch our CUDA version is 11.6:NVIDIA-SMI 510.73.08 Driver Version: 510.73.08 CUDA Version: 11.6 we install…
I can’t install qiime2 – User Support
debug.txt (182.2 KB)The attachment appears when I run the conda env create -n qiime2-2023.7 –file qiime2-2023.7-py38-linux-conda.yml command in Ubuntu 22.04.3 LTS (GNU/Linux 6.2.0-32-generic x86_64) I don’t know how to solve the error. Can anyone help me? My anaconda version is conda 22.9.0 Hello @a17370910195, Welcome to the forums! In that…
Problem with custom extensions and PyTorch installation using Anaconda
MFML September 16, 2023, 11:10am 1 I installed PyTorch using conda in a fresh environment on my Manjaro linux OS as described in “Get Started” / “Start Locally”, using the given command: conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia This worked fine, given that torch.cuda.is_available() returns True…
python – Sentence-transformers installlation in offline Kaggle competition
In a Kaggle competition, submissions must be offline. Therfore, I need to download some packages, like sentence-transformers. I have downloaded the source code from github and uploaded it, I followed this tutorial But I receive this error (knowing that all dependencies are already satisfied) Building wheels for collected packages: sentence-transformers…
How to create virtual environment with OpenCv and Pytorch to execute your program on GPU – Jetson Nano
A98 September 16, 2023, 12:33pm 1 This is my solution of this question. My sequence of actions: 1.Anaconda installation: Clicked on: Archiconda3-0.2.3-Linux-aarch64.sh It downloaded to /Download folder In terminal: gerardg@Nvidia:~$ cd Downloads gerardg@Nvidia:~/Downloads$ bash Archiconda3-0.2.3-Linux-aarch64.sh @yannickdeicaza I see a bash shell at Archiconda With just conda-forge I have HDF5 tools…
Plugin error from fragment-insertion: – Technical Support
HiI am running the Parkison mice sample data, and I have updated the Qiime2, and my computer have enough capacity. But I still met this problem. Could you please help me deal with it? Plugin error from fragment-insertion: Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-6m4if51o/a3c55eab-dffc-426e-8521-3d193cab2fc0/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/tmp/qiime2-archive-0s212g0k/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta’,…
python – Mageck-Vispr problem to visualize results
I’m trying to run the tool vispr in able to visualize the results of the mageck-vispr run. I have installed everything as explained on the website within a conda environment. Unfortunately, when running the command vispr server results/ESC-mle.vispr.yaml I receive the following error Traceback (most recent call last): File “/sw/mambaforge/10/envs/mageck-vispr/bin/vispr”,…
Server Crashing: Epyc 7402P with Nvidia Tesla A100s Ubuntu 20.04 – Hardware
Swamp7 September 13, 2023, 3:35pm #1 Seeing if someone could give me some guidance on troubleshooting a new AL/DL Epyc 7402P server with Dual Nvidia Tesla A100 40GB GPUs. This is my first Epyc server (moving from Xeon E5-2680 v3s…I know very old but they work for GPU servers very…
After installing Jupyter Hub and Jupyter Lab on CentOS 7, how do I use them on Windows?
After installing Jupyterhub in CentOS 7 Master account, I want to set up analysis environments and use Jupyter Lab in each account. I want to connect with Jupyter lab from windows-based computer, so people don’t need to log-in to CentOS 7, they just need to write password in Jupyter Lab…
Running python script in slurm using conda environment
Running python script in slurm using conda environment 3 Hello everyone! I am trying to run slurm using python in the environment, but the base is overwriting it and due to which the tool is not running. #!/bin/bash #SBATCH –ntasks-per-node=1 #SBATCH –mem-per-cpu=100G #SBATCH –time=100:00:00 #SBATCH –job-name=celloracle #SBATCH –output=celloracle-%J.log # Load…
Creating a PyTorch/TensorFlow Code Environment on AMD GPUs – AMD lab notes
Goal: The machine learning ecosystem is quickly exploding and we aim to make porting to AMD GPUs simple with this series of machine learning blogposts. Audience: Data scientists and machine learning practitioners, as well as software engineers who use PyTorch/TensorFlow on AMD GPUs. You can be new to machine learning,…
http – Struggling to install PyTorch on windows 10 with anaconda 3.26.0 python 3.11.4 – Stack Overflow
I have tried numerous ways to install PyTorch: !pip install torch –index-url=https://pypi.org/simple/ !pip cache purge !conda install pytorch torchvision torchaudio cudatoolkit=10.2 -c pytorch !pip install torch and i have had no luck! i am new to this so im not sure if thi si s a simple fix but i…
Cellfinder singularity container – Usage & Issues
cyril_vl (Cyril) September 8, 2023, 2:18pm 1 Hi, We’re trying to get cellfinder to work inside a singularity container on our HPC. Currently, we’re just converting the default docker container using singularity’s conversion feature, and running our pipeline. This keeps on giving the following error message no matter what we…
python – Cannot import Optuna after installing Pytorch
Optuna is clashing with some other module and can’t import – I think pytorch is to blame. The error when importing optuna is: TypeError: dataclass_transform() got an unexpected keyword argument ‘field_specifiers’ It was working fine until I installed pytorch, but I can’t find any reason why they would clash, I’ve…
Sana Biotechnology, Inc. hiring Bioinformatician in Cambridge, Massachusetts, United States
About The RoleSana Biotechnology is growing, and we are hiring new team members who believe in the potential of engineered cells as medicines, who want to challenge status quo, and who lead with the desire to work on novel ideas. The CNS team is seeking a highly trained and motivated…
How to Optimize Your DL Data-Input Pipeline with a Custom PyTorch Operator | by Chaim Rand
PyTorch Model Performance Analysis and Optimization — Part 5 Photo by Alexander Grey connected Unsplash This station is nan 5th successful a bid of posts connected nan taxable of capacity study and optimization of GPU-based PyTorch workloads and a nonstop sequel to portion four. In portion four, we demonstrated really…
PyTorch Installation-RTX 3060 – PyTorch Forums
amir_mm (amir) September 7, 2023, 7:25pm 1 Hello, I have been working diligently to install Pytorch but I haven’t been successful so far. Here’s the summary of my situation:Using NVIDIA RTX 3060 GPU (with the latest updates).Installed CUDA 11.7, cuDNN 8.9.3, running Python 3.8.17 on my conda environment.Correct Paths are…
Building Pytorch – Missing Symbols – deployment
Cyberes September 7, 2023, 6:09am 1 I’m working on compiling PyTorch in my Dockerfile and running into a strange issue where the compiled libtorch.so only contains 4 symbols: ~ $ nm -D /opt/conda/lib/python3.9/site-packages/torch/lib/libtorch.so w _ITM_deregisterTMCloneTable w _ITM_registerTMCloneTable w __cxa_finalize w __gmon_start__ Compare that to the libtorch.so from pip: U __cxa_allocate_exception…
Installation – environment file not found – Technical Support
rjay428 (Rylee Jensen) September 5, 2023, 10:34pm 1 Hi all! Brand new to QIIME2 and with the Python environment as well. I’m running into an issue during the installation process that is close to what is posted on here, but I haven’t been able to figure out this exact problem….
Use kaggle kernel inside kaggle notebook
I want to use this command !kaggle kernels output iliasparalikas/dcgan -p . to download the outputs of the previous notebook to this one so i can continue training.It works fine in my local machine, but when I try to use it i get this error Traceback (most recent call last):…
Step-by-Step Guide to Setup Pytorch for Your GPU on Windows 10/11
In this competitive world of technology, Machine Learning and Artificial Intelligence technologies have emerged as a breakthrough for developing advanced AI applications like image recognition, natural language processing, speech translation, and more. However, developing such AI-powered applications would require massive amounts of computational power far beyond the capabilities of CPUs…
Building mosdepth on macOS
This is just a tiny tutorial on how to build mosdepth on Mac. There is currently no version for Mac available at conda (hope that changes soon, edit (3/2021): it did change, see anaconda.org/bioconda/mosdepth), and from what I’ve read building from source was a pain so far, still these simple…
Are packages installed with `conda` located in the same place as the ones installed through RStudio? – RStudio IDE
My data science projects typically involve both Python and R and multiple co-authors. We tend to use conda environments to keep track of package versioning. Whenever I’m using R, my workflow is the following: Activate the respective conda environment for that given project; Launch that respective project file (“open Project.Rproj”)…
python – Run command when creating Conda environment with Snakemake
I presume that downloading script produces some output. I would split your rule into two rules, one specifically for downloading and the other only for running the annotation. The downloading rule will have declared only the output directive, which would be the input for the second rule. rule download_genome: output:…
Installing CLOCCS and Using it to Parameterize the Experiments
Transcript To begin, download the CLOCCS alignment repo by entering the command into the terminal. Create a conda environment using the conda.rec. yml file by entering the command into the terminal in the folder where the CLOCCS alignment repo was cloned. Double-click the cloccs_v2023. jar file located in the CLOCCS…
Conversion of Time Points to Lifeline Points Using the Python Conversion Functions and the CLOCCS Parameters
Transcript To begin, activate the Conda environment by entering the command into the terminal. Use the command to open an interactive Python notebook. Create a new Python notebook in the desired folder, providing an appropriate name. Then import the Python file containing the alignment functions by running the command in…
r – Python libraries not available in rstudio
I’m new to using R and Rmarkdown, and I am trying to use numpy in a python chunk of an .rmd file. I tried to install numpy but its not available to use. I’ve set my python environment in R to the system environment but I’m still not able to…
installation of Numpy >= 1.6 not found
Help with Error: Required version of NumPy not available: installation of Numpy >= 1.6 not found 1 Hi all, seurat_combined <- FindClusters(seurat_combined, resolution = 0.1, algorithm = 4) library(reticulate) py_install(“leidenalg”) leidenalg<- import(“leidenalg”) py_install(“numpy”) py_install(“pandas”) I don’t know how to install Numpy 1.6 in R. Would you please have a suggestion…
Trouble importing Pytorch from a MATLAB code – MATLAB Answers
Hi, I’m getting an error when I’m trying to Import Pytorch from MATLAB. I’m using Windows 10, and MATLAB version is R2021a Update5. Here is how to reproduce this error. Create a conda environment with Python version 3.8: conda create -n torch python=3.8 Activate the enviornment and donwload pytorch (pytorch.org/):…
Need help building Pytorch for old GPU
Hello everyone,I tried to build Pytorch from source on Linux for NVIDIA Quadro K600. After building it, CUDA is not available. Here is what I did: git clone –recursive github.com/pytorch/pytorch cd pytorch git submodule sync git submodule update –init –recursive conda install cmake ninja pip install -r requirements.txt conda install…
gladiaio-torchaudio 2.1.0a0 on PyPI – Libraries.io
The aim of torchaudio is to apply PyTorch to the audio domain. By supporting PyTorch, torchaudio follows the same philosophy of providing strong GPU acceleration, having a focus on trainable features through the autograd system, and having consistent style (tensor names and dimension names). Therefore, it is primarily a machine…
cudnn error – Avseetvr
28 mai 2020 — Error occurs after about 583 episodes (8 hours) or 1,150,000 steps, where each step involves a forward pass through the LSTM model. My code also …Please ensure that you can successfully run this code before you test the project. If it does not work, it is more…
Pytorch Domain Library for Recommendation Systems
TorchRec (Beta Release) TorchRec is a PyTorch domain library built to provide common sparsity & parallelism primitives needed for large-scale recommender systems (RecSys). It allows authors to train models with large embedding tables sharded across many GPUs. TorchRec contains: Parallelism primitives that enable easy authoring of large, performant multi-device/multi-node models…
linux – TensorFlow GPU Detection Issue in DataSpell on Ubuntu 22.04 with Nvidia 1080 GPU
I have successfully configured TensorFlow on a fresh Ubuntu 22.04 installation, following the instructions provided in the official TensorFlow documentation link. I have setup CUDA® Toolkit 11.8 cuDNN SDK 8.6.0 in my conda enviroment and I have my nvidia drivers installed. My system is using a Nvidia 1080 GPU, and…
DADA2 denoising not working (First return error 9 then 1 after increasing memory to 16 GB) – Technical Support
Did not find the exact answer to this on the forum; new to QIIME2, apologies. QIIME2-2023.5, running in Conda through university’s central Linux-based system Apply DADA2 denoising qiime dada2 denoise-paired –i-demultiplexed-seqs paired-end-demux.qza –p-trunc-len-f 280 –p-trunc-len-r 220 –p-n-threads 24 –o-representative-sequences rep-seqs-dada.qza –o-table table-dada2.qza –o-denoising-stats dada-stats.qza –verbose R version 4.2.3 (2023-03-15)Loading required…
Failed installation of OpenMS
Failed installation of OpenMS 0 I have been trying to install OpenMS on my Ubuntu system. This is the command I’m using: conda install -c bioconda openms I keep getting this error: ————————————————————————————————————————————————————————————— Collecting package metadata (current_repodata.json): failed CondaHTTPError: HTTP 000 CONNECTION FAILED for url <conda.anaconda.org/conda-forge/noarch/current_repodata.json> Elapsed: – An HTTP…
How to install solo-sc or use hashsolo from scvi? – scvi-tools
When I attempt to install solo in conda environment lately, I have been encountering the following error. pip install solo-sc Collecting solo-sc Using cached solo-sc-1.3.tar.gz (18 kB) Preparing metadata (setup.py) … done Collecting ConfigArgParse (from solo-sc) Obtaining dependency information for ConfigArgParse from files.pythonhosted.org/packages/6f/b3/b4ac838711fd74a2b4e6f746703cf9dd2cf5462d17dac07e349234e21b97/ConfigArgParse-1.7-py3-none-any.whl.metadata Using cached ConfigArgParse-1.7-py3-none-any.whl.metadata (23 kB) Collecting pandas…
Jupyterhub 4.0.x with jupyter-collaboration – JupyterHub
Hi, Did anyone have success of using the latest Jupyterhub with jupyter-collaboration extension? For some reason I get WebSocket errors when trying to use the server link with a token in a private browser window. This worked previously with Jupyterhub 3.1.1. Here a quick test: Dockerfile: FROM jupyter/minimal-notebook:hub-4.0.2 RUN pip…
CondaError: Downloaded bytes did not match Content-Length – Technical Support
HI,I’m trying to install QIIME2 using miniconda3 using the exact command provided in the website using Linux systemdocs.qiime2.org/2023.5/install/native/using these provided steps : Updating Miniconda After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda: conda update conda Installing wget conda install wget Install…
What is PyTorch and use cases of PyTorch?
What is PyTorch? What is PyTorch PyTorch is an open-source deep learning framework that provides a flexible and dynamic approach to building and training neural networks. Developed by Facebook’s AI Research lab (FAIR), PyTorch is known for its “define-by-run” philosophy, which allows developers to create and modify neural network architectures…
CUDA error: driver shutting down using cpu code – autograd
junpu (Junpu Fan) August 16, 2023, 6:17pm 1 I have a custom built pytorch-2.0.1 with cuda12.1 (used pytorch/conda-builder:cuda121) and observed an unexpected cuda shutting down error when using cpu only code with autograd. terminate called after throwing an instance of ‘c10::Error’ what(): CUDA error: driver shutting down CUDA kernel errors…
a cross-platform, efficient, practical and pretty CSV/TSV toolkit
Tool:csvtk – a cross-platform, efficient, practical and pretty CSV/TSV toolkit 2 Hi all, I’d like to share my another practical toolkit, csvtk, after introducing SeqKit yesterday. Introduction Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data sicence. People…
Error in snakemake with working shell script
Error in snakemake with working shell script 0 I want to run fastqc using snakemake. This is my snakemake script. configfile: ‘sample_config.yaml’ configfile: srcdir(‘path_config.yaml’) FASTQC = config[‘FASTQC’] UNZIP = config[‘UNZIP’] rule all: input: fqc1 = expand(“00_QC/{sample}_fastqc.txt”, sample = config[‘sample’]), rule fastqc: input: fq1 = lambda wildcards: config[‘sample’][wildcards.sample][‘fq1’], output: fqc1 =…
Online Bioinformatics tutor job in Lucknow
Lucknow, India TeacherOn.com Part time Looking for a tutor who is well familiar with conda environment, cluster and ricopili installation. I know these but struggling to create an environment based on given file. Please contact if you are extremely familiar with this. Level:…
Perbase base-depth
Perbase base-depth 2 Hi all, I hope everyone is doing great. may I ask if anyone knows how can I get perbase base-depth function? I have followed the instruction in github.com/sstadick/perbase and downloaded it by conda install -c bioconda perbase. The help function shows that only simple-depth function is included…
SRA obtained metagenomic reads appears to corrupt
Hello, I am trying to run SingleM on data obtained using sratoolkit (2.10.7) I used prefetch SRR2103020 to download and fastq-dump –outdir ./fastq –split-e ./SRR2103020/SRR2103020.sra to split. when I check the file : head SRR2103020_1.fastq @SRR2103020.1 D7RS0RN1:177:C12Y0ACXX:3:1101:1404:2079 length=93 AATGTGGACAGCGCCGTCTTCAAACAGGCGCTGTCCAGCTAGCAGCTCAACGCTCCGCGCCGCCGTCTTCGCCGTCTTCAGGCAGGGGGAGAA +SRR2103020.1 D7RS0RN1:177:C12Y0ACXX:3:1101:1404:2079 length=93 @BCFFFDDHHHHHJJJGIJIBHHIJJCH?HBG<GIG@HEGIGFIFG@>CGHHHFFFDD@BB::BD@B??CDBDD@BD@DA@CCDDBD###### @SRR2103020.2 D7RS0RN1:177:C12Y0ACXX:3:1101:1440:2113 length=93 GGTATAAGTTCTATGTGTAATGAACCACAGAGTTATCAAAAAACTCAAGATCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG +SRR2103020.2 D7RS0RN1:177:C12Y0ACXX:3:1101:1440:2113 length=93…
BE Day 2023 – Group 2: scRNASeq Minimal Marker Gene Selection
Abstract Single-cell/nuclei RNA sequencing (sc/sn-RNA-seq) has revolutionized our understanding and discovery of cell phenotypes and states. Marker genes are an integral part of identifying cell types. NSForest is an existing machine learning-based program that utilizes the random forest ensemble learning method to find the minimal marker genes required to identify…
Working with multiple conda environments in RStudio/Quarto – rstudio
I have a Quarto project with 2 .qmd files, each of them located in a folder with an _environment.local file. Like this: Notebook_01/ Notebook_01.qmd environment.local Notebook_02/ Notebook_02.qmd environment.local The _environment.local file in each of the folders has only one line, that indicates the python to be used by reticulate. Each…
Deploy to local endpoint Vertex AI – Health check …
Hello, I am trying the deploy_to_local_endpoint function but without success. The first step is from google.cloud.aiplatform.prediction import LocalModelfrom src_dir.predictor import MyCustomPredictorimport oslocal_model = LocalModel.build_cpr_model({LOCAL_SOURCE_DIR},f”{REGION}-docker.pkg.dev/{PROJECT_ID}/{REPOSITORY}/{IMAGE}”,predictor=MyCustomPredictor,requirements_path=os.path.join(LOCAL_SOURCE_DIR, “requirements.txt”),) /opt/conda/lib/python3.10/subprocess.py:955: RuntimeWarning: line buffering (buffering=1) isn’t supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, ‘wb’, bufsize) This step runs…
rstudio-desktop PackagesNotFoundError: The following packages are not available from current channels – RStudio IDE
I recently got a new computer (MacBook Pro with Apple M2 Max chip). On my previous computer I installed and used RStudio fine in a conda environment using conda install -c conda-forge rstudio-desktop When I try this however, I get the message: PackagesNotFoundError: The following packages are not available from…
PacBio 16S pipeline
QIIME2 analysis pipeline 0. activate conda environment conda activate qiime2-2019.10 1. flip sequences to the same direction mkdir raw_data_rc/ mkdir raw_data_cat/ parallel -j 8 ‘seqtk seq -r {} > raw_data_rc/{/.}_rc.fastq’ ::: rawdata/*.fastq parallel -j 8 –link ‘cat {1} {2} > raw_data_cat/{1/.}_cat.fastq’ ::: rawdata/*.fastq ::: raw_data_rc/*_rc.fastq 2. trim primers mkdir trimmed_reads/…
using R and RStudio on linux (ubuntu 23.04)
I’m looking to start working with R and RStudio on my ubuntu installation. I am having problems with updating/installing my packages, sudh as DESeq2. According to this post it is because r-base installs packages into protected os files. I have followed this posts recommendation but I have not had success….
Not detecting GPU RTX 4000 – Opacus
HelloI am trying to install pytorch in Ubunut Mint 21 and use it with RTX 4000. First I’ve installed all drivers and cuda (from cuda_12.2.1_535.86.10_linux.run). Here are some outputs (local user – not root): $ nividia-smiMon Aug 7 08:50:44 2023±————————————————————————————–+| NVIDIA-SMI 535.86.05 Driver Version: 535.86.05 CUDA Version: 12.2 ||—————————————–±———————±———————+| GPU…
Cant install Pytorch on JetsonNano P3450 – Jetson Nano
Hello.I tried to install Pytorch to execute my programm on gpu, but i couldnt.I used instructions:docs.nvidia.com/deeplearning/frameworks/install-pytorch-jetson-platform/index.html Below are pre-built PyTorch pip wheel installers for Jetson Nano, TX1/TX2, Xavier, and Orin with JetPack 4.2 and newer. Download one of the PyTorch binaries from below for your version of JetPack, and see…
Optimizing the parameters k in Abyss
Optimizing the parameters k in Abyss 0 I want to do genome assembly of chicken. I am trying to optimize the kmer value for AByss using this tutorial and code – #!/bin/bash for k in `seq 50 8 90`; do mkdir k${k} abyss-pe np=16 -C k${k} name=chicken k=$k in= ‘/home/zsiddiki/…