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Tag: bin
Scaling of MD with domain decomposition on JUWELS Cluster – Developers discussions
GROMACS version: 2024-dev-20240201-787d96c7a9-unknownGROMACS modification: YesI’m conducting some performance tests on the JUWELS Cluster, trying to see the improvement in performance that DD can bring within a single node. GROMACS build infoHere, GROMACS was built using GCC v11.4.0, uses OpenMP and OpenMPI v4.1.5, and builds its own FFTW v3.3.8. JUWELS Cluster…
Short tandem repeat mutations regulate gene expression in colorectal cancer
A novel STR panel for human protein-coding genes To explore STR mutations in CRC, we first annotated STRs in the introns, exons, and promoter sequence of all protein-coding genes in the GRCh38 reference genome (“Methods”). We discarded STR loci for which genotyping was expected to be inaccurate due to genomic…
Investigation of the Flipping Dynamics of 1, N6-Ethenoadenine in Alkyladenine DNA Glycosylase
dataset posted on 2024-02-09, 02:43 authored by Bin Liu, Yanping Qi, Xiaowei Wang, Xin Gao, Yuan Yao, Lu Zhang Alkyladenine DNA glycosylase (AAG) is an essential enzyme responsible for maintaining genome integrity by repairing several DNA lesions damaged by alkylation or deamination. Understanding how it can recognize and excise the…
Error in neigh_modify configuration – LAMMPS Beginners
Dear community of LAMMPS users I am simulating a complex system consisting of a biomolecule (1876 atoms), a nantube of an oxide (4200 atoms) and a box of water (30000 atoms) and I get the following error: ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_half_bin_newton.cpp:156) I am…
Problems rendering a quarto qmd file through jupyter in VS Code – JupyterHub
bj631 January 19, 2024, 10:45pm 1 I’m trying to preview a .qmd file using quarto with jupyter in VS Code. There is a little banner in the bottom right corner that shows up when trying to render the .qmd that says ” command ‘quarto.preview’ not found “. It is a…
Can’t Access Multiple GPUs when Using PPPM GPU Acceleration – LAMMPS
Dear developers and user, I’m running the simulation using an unmodified LAMMPS (2 Aug 2023) version. I want to use multiple GPUs and CUDA API to accelerate the PPPM alogrithm. However, I can’t access more than one GPU when running program. I have tried numerous ways to solve this problem,…
Classifier and Heuristic Quality Filtering
While the following steps can be run manually using the commands given, we also provide a SLURM script in the examples folder that follows the same procedure. It must be filled in with the necessary parameters described below before running. The classifier-based filtering approach we have implemented follows closely to…
Division of the box into smaller regions – LAMMPS General Discussion
Hi, I’d like to divide my simulation box into smaller boxes (regions).Specifically, I want to have 24 smaller boxes on each axis (24x24x24). In the region command, apart from defining the boundaries of each region separately, is there any faster way to divide the cell into 24 regions on each…
Genomic insights into Plasmodium vivax population structure and diversity in central Africa | Malaria Journal
Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article CAS PubMed PubMed Central Google Scholar Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…
Problem with DRAGEN RNAseq hashtable directory
Problem with DRAGEN RNAseq hashtable directory 1 Dear all, Recently I wrote a code to work with DRAGEN and RNAseq pipeline. I use this command: /opt/edico/bin/dragen -f -l \ -r refdir \ -1 ${forward} \ -2 ${reverse} \ -a ${gtf} \ –output-dir output/${sample} \ –output-file-prefix ${sample} \ –RGID ${sample}_group_id \…
Having Trouble Loading Required Packages : Lazy-Load database is corrupt – General
Hi, I am very new to R-Studio but a few months I had taken an 8-week course in which I was taught to use R-Studio for academic purposes. I recently decided to review some of the exercises we were provided with. However, I have now started to have trouble loading…
rstudio – Cannot deploy R-shiny app due to “fribidi was not found”
Local app runs fine, but I keep encountering this error when attempting to publish it. I have already installed fribidi & harfbuzz using brew install fribidi & brew install harfbuzz on my Mac, but I am still encountering the error. I am using: Installing urltools (1.7.3) … Using cached urltools….
Shocking Support for Bin Laden Emerging Among Young Americans Is Called the Fruit of America’s Educational Priorities
A new poll is sounding alarm bells for the future of liberty as young Americans express growing support for Osama bin Laden and the 9/11 attacks. It’s the fruit of an education system with an increasingly hard-left bent, one that casts Western Civilization as the world’s repository of evil. J.L….
installing DESeq2 on Windows
installing DESeq2 on Windows 0 I have a problem with installing DESeq2 on Windows. The problem started with installing libraries that DESeq2 uses so I’m installing them individually. I do it by: ‘BiocManager::install(‘zlibbioc’)’ . I got an error that suggests that is something wrong with compilation: C:\rtools43\x86_64-w64-mingw32.static.posix\bin\windres.exe: can’t popen `C:\rtools43\x86_64-w64-mingw32.static.posix\bin\gcc.exe…
[ccp4bb] Several Positions available at EMBL Grenoble
Dear All, We have several job openings at EMBL Grenoble */Full-Stack Developer / * www.embl.org/jobs/position/GR00219 */Research Technician/* www.embl.org/jobs/position/GR00220 /*Structural Biology Data Platform Developer*/ www.embl.org/jobs/position/GR00221 <www.embl.org/jobs/position/GR00221> Best wishes — _________________________________________________________ Jose A. Marquez, Senior Scientist Head of the Crystallization Facility European Molecular Biology Laboratory, Grenoble. Delivery address: EMBL, 71, Avenue des…
r – ggplot2 stacked bar chart with total proportions for the heights of bars and fill as proportion of each species
This code makes a bar plot that displays the proportion of fish with ingested microplastics across several 5-year bins. I also want it to display the proportion of each species by stacking different colors. My problem with the plot produced with this code is that it adds up the proportions…
Bwa-mem2 indexing not working down stream
Bwa-mem2 indexing not working down stream 0 I am using bwa-mem2 to create my index and to map my reads to the reference genome. This is my indexing code #!/bin/bash #SBATCH -J index #SBATCH -A gts-rro3 #SBATCH -N 1 –ntasks-per-node=24 #SBATCH –mem-per-cpu=8G #SBATCH -t 1:00:00 #SBATCH -o index.out cd $SLURM_SUBMIT_DIR…
132releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.1.1_1 in configure
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere3/data/132releng-armv7-default/1dd4264fe4a8/logs/py39-pytorch-2.1.1_1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=132releng-armv7-default&build=1dd4264fe4a8 Log: =>> Building misc/py-pytorch build started at Tue Dec 19…
mpi – Slurm error ” Allocation requested cores/tasks must be in quarter increments “
Hi I am using the bridges2 supercomputer in PSC for running jobs, when I am trying to submit the job using the script below, I am getting the error sbatch: error: Allocation requested cores/tasks must be in quarter increments of EM node resources (24, 48, 72, 96) sbatch: error: Batch…
Lipid vesicle(CHARMM Gui files) simulation in GROMACS – User discussions
GROMACS version: 2022.1 and 2020GROMACS modification: Yes/NoHere post your questionHello, I am trying to simulate Lipid based vesicle in GROMACS on Frontera super-computer. The following command I am using to run the simulation. But I am getting error messages. Since I am new I don’t understand the error message perfectly….
‘Resources’ object has no attribute ‘tmpdir’
Snakemake error AttributeError: ‘Resources’ object has no attribute ‘tmpdir’ 0 I have built a Snakemake pipeline which has been designed for paired-end reads. I have made a trial with single-end reads, and got this error. I am not sure it is related to the change of reads design, and to…
Detecting small- and medium-length copy number variants by whole-genome sequencing
Gains and losses of genetic material can be almost any size: a single base pair or an entire chromosome spanning tens of millions. As genomic analysis technologies have evolved, researchers have separated these often medically relevant variants into bins based on their size and the methods used to detect them….
Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir
Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…
Trim Your Bin: free program to help local businesses reduce waste
The City of Casey has partnered with Frankston City Council and Mornington Peninsula Shire Council to deliver a program to help businesses reduce waste, save money and help the environment. If you are a business in Casey, you can join the Trim Your Bin program. The program is free and…
Ray on Vertex AI: Let’s get it started | by Ivan Nardini | Google Cloud – Community | Dec, 2023
Figure 1 — Image from author At Next 2023, Google Cloud announced Ray on Vertex AI, a managed service that provides scalability for AI and Python applications using Ray.As a Vertex AI developer, you may be wondering: As a Vertex AI developer, you may be wondering: What is Ray? Why…
How to entry user-selectable page with Dockerlized Jupyterhub – JupyterHub
I am currently building JupyterHub on single machine using Docker, and I want users to access a page where they can select the Docker image they want upon logging in, like the below page. But whenever I log in using any account, the system always redirects me to the JupyterLab…
Binning the rare biosphere
Hello everyone. I would like to start a discussion here. Recently, I responded to a question on Seqanswers regarding the binning of rare microbes from shotgun metagenomes (www.seqanswers.com/forum/applications-forums/metagenomics/324515-software-recommendation-for-metagenome-assembly-for-low-abundance-bacteria). I suggested an idea for an appropriate pipeline for this task, but unfortunately, it did not gain much attention. Nevertheless, I tried…
40 years of success and the future of Danum Valley | Daily Express Malaysia
THE late 1980’s was the beginning of the important phase of heightening research and conservation activities at Danum Valley in Lahad Datu, Sabah. It was also the era where the unlogged area and portion of the Yayasan Sabah Concession area were still very large. Consequently, the Danum Valley Conservation…
Functional alterations and predictive capacity of gut microbiome in type 2 diabetes
Diversity and compositional analyses Regarding clinical differences (Table 1), T2DM individuals (mean 69.6 (± 12.3 sd) years) were significantly (p value < 0.01; Wilcoxon rank-sum test) older than the controls (46.9 (± 17.3 sd) years), showed higher BMI (mean 30.9 (± 7.01 sd) vs. mean 26.3 (± 6.12 sd) than the control…
Binary location in Linux .deb package – General
The Linux .deb package contains the rstudio binary in a non-standard location, namely /usr/lib/rstudio/rstudio. This is problematic for packaging RStudio, because package maintainers need to copy (or symlink) the binary to a standard location like /usr/bin or /usr/local/bin. Arch Linux is currently hitting this issue. RStudio is available in the…
Undefined reference to mbedTLS functions – Nordic Q&A – Nordic DevZone
Hi all! So I’m trying to use mbedTLS methods in my project. I got it to work on SDK v1.9.0 but when upgrading to v.2.4.0 I get a lot of “undefined references” to methods regarding mbedTLS.I see that there is some other issues regarding this but those haven’t solved my…
Research Biologist (Computational/Bioinformatics)/Microbiologist (Research Associate) Job in Columbia, MO
Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. **ANNOUNCEMENT IS OPEN…
installing R studio server on Ubuntu 22.04 LTS occour dependency problems : Package libclang-dev is not installed – General
I am installing the R studio server on my Ubuntu22.04 LTS, when sudo gdebi rstudio-server-2023.09.1-494-amd64.deb error occours Reading package lists… Done Building dependency tree… Done Reading state information… Done Reading state information… Done RStudio Server RStudio is an integrated development environment (IDE) designed to support multiple languages, including both R…
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Mouse breeding and husbandry All experimental procedures related to the use of mice were approved by the Institutional Animal Care and Use Committee of the AIBS, in accordance with NIH guidelines. Mice were housed in a room with temperature (21–22 °C) and humidity (40–51%) control within the vivarium of the AIBS…
Conserved and divergent gene regulatory programs of the mammalian neocortex
Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…
Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles
Rignot, E., Jacobs, S., Mouginot, J. & Scheuchl, B. Ice-shelf melting around antarctica. Science (80-) 341, 266–270 (2013). Article ADS CAS Google Scholar Wadham, J. L. et al. Ice sheets matter for the global carbon cycle. Nat. Commun. 10, 1–17 (2019). Google Scholar Adusumilli, S., Fricker, H. A., Medley, B.,…
Installing JupyterHub via Stackable Demo on K8s | by Alex McLintock | Dec, 2023
docs.stackable.tech/home/stable/demos/jupyterhub-pyspark-hdfs-anomaly-detection-taxi-data So, this is an article in an ongoing series where I investigate the deployment tools of Stackable.tech This firm supplies supported versions of many open source data engineering tools to easily build data platforms on Kubernetes (k8s) clusters. These can be on your own premises, in a data centre,…
[llvm-bugs] [Bug 75428] clang crash when build IPEX code.
Issue 75428 Summary clang crash when build IPEX code. Labels clang Assignees Reporter xuhancn The error msg: “`cmd Stack dump: 0. Program arguments: /usr/bin/clang++ -DAT_PARALLEL_OPENMP=1 -DUSE_C10D_GLOO -DUSE_DISTRIBUTED -DUSE_RPC -DUSE_TENSORPIPE -Dintel_ext_pt_cpu_EXPORTS -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/aten -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/tpp -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/libxsmm/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/build/Release/csrc/cpu/csrc/cpu/cpu_third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/include -I/home/xu/anaconda3/envs/ipex_cpu/include/python3.12 -I/home/xu/anaconda3/envs/ipex_cpu/include -I/home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include/torch/csrc/api/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/src/../include -isystem /home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include -fPIC…
LP pseudo-atom is not supported
Hi, I want to perform MMPBSA for complex file Command: gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv Error: [INFO ] Starting gmx_MMPBSA v1.6.2 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1…
Single-cell analysis of chromatin accessibility in the adult mouse brain
Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…
The landscape of genomic structural variation in Indigenous Australians
Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…
Checking my installation via serial mode of testing – LAMMPS Installation
I have installed LAMMPS 02Aug 2023 version and now from the bench directory I am running the test cases. I loaded the environmental modules and the path where lmp_nompi is oocated, but it ended up with following: /apps/lammps-2Aug2023/02082023/bench$ mpirun -np 4 /apps/lammps-2Aug2023/02082023/bin/lmp_mpi -in in.rhodo /apps/lammps-2Aug2023/02082023/bin/lmp_mpi: error while loading shared libraries:…
Bug#1058580: flint: autopkgtest regression
Source: flint Version: 3.0.1-1 Severity: serious tracker.debian.org/pkg/flint Migration status for flint (2.9.0-5 to 3.0.1-1): BLOCKED: Rejected/violates migration policy/introduces a regression Issues preventing migration: ∙ ∙ autopkgtest for flint/3.0.1-1: amd64: Regression or new test ♻ (reference ♻), arm64: Regression or new test ♻ (reference ♻), armel: Regression or new test ♻…
How does the cull values get used in the jupyerhub helm chart – JupyterHub
Shi_Jin December 12, 2023, 4:48am 1 First of all, everything is working and I am just puzzled at how it works. According to github.com/jupyterhub/zero-to-jupyterhub-k8s/blob/f11f8ea8ea857917f59b7f9a1b79a9570e21e622/jupyterhub/values.yaml#L653-L668, I am able to specify my own cull values like cull: timeout: 600 every: 60 users: true adminUsers: true And when I installed the jupyterhub helm…
Script Error using TRAVIS.Core.pl script within TRAVIS transcriptome viral scanner
Script Error using TRAVIS.Core.pl script within TRAVIS transcriptome viral scanner 0 Hi, I’m new to bioinformatics, and I’m trying to run the TRAVIS Transcriptome virus scanner on my sequences. When running the Core script, I see this error message pop up. Is this a script error that I should report…
Meet Single’s Inferno season 3 cast
The Single’s Inferno season 3 cast are officially here, hoping to find love on the Netflix series. Following the success of seasons 1 and 2, the hottest and most flirty singles search for love on a deserted island. The only way to escape? To match for a romantic night in…
Opening singleuser instance in browser in JupyterHub API-only mode – JupyterHub
Hello, I’m trying to run JupyterHub in API-only mode. I got to the part where I start the user’s instance through API, however, when I try to navigate to the URL printed out by the Hub console, this is what happens: This is the URL I get redirected to: 127.0.0.1:50585/hub/api/oauth2/authorize?client_id=jupyterhub-user-milos%2540milos.com&redirect_uri=%2Fuser%2Fmilos%40milos.com%2Foauth_callback&response_type=code&state=eyJ1dWlkIjogIjYyYTI2NzA0MmU2NTQzNmY5NmU0NmY5MjQxNTYzZmQwIiwgIm5leHRfdXJsIjogIi91c2VyL21pbG9zQG1pbG9zLmNvbS9sYWI_dG9rZW49In0…
pytorch-cluster: FTBFS: ImportError: Failed to load PyTorch C extensions:
Source: pytorch-cluster Version: 1.6.1-2 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu…@debian.org Usertags: ftbfs-20231212 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > debian/rules clean > dh clean –buildsystem pybuild > dh_auto_clean -O–buildsystem=pybuild > I: pybuild…
What is the troubleshoot for this error: conversion of .SRA to FASTA file on command prompt?
I am getting this error message after using the following code: C:\sratoolkit.3.0.7-win64\sratoolkit.3.0.7-win64\bin>fastq-dump –fasta SRR1658345 Error: 2023-12-11T06:08:04 fastq-dump.3.0.7 err: timeout exhausted while waiting condition within process system module – failed SRR1658345 ============================================================= An error occurred during processing. A report was generated into the file ‘C:\Users\Hp/ncbi_error_report.txt’. If the problem persists, you may…
Unable to start Model Training with Ray Train on SLURM Cluster – Ray Libraries (Data, Train, Tune, Serve)
I’d like to set up a Slurm cluster with a master + n worker nodes, then run a HPO framework which runs the training (done with Ray Train) in a spawned process. Each spawn process is on a separate node. When I have 2 interactive SLURM nodes I am able…
MetaSPAdes genome assembly (shotgun metagenome singleend) – usegalaxy.org support
Busrak December 11, 2023, 3:31pm 1 Hi friends, Metagenomic single end raw data with cut adapt‘Maximum error rate 0.3’Match times: 1Minimum overlap length:3minimum lenght: 15Max N: 0.3Max expected errors: 30 parameters.Then I aligned the host genome with gallus gallus with BBmap tool. I want to Assembly unmapped read. However, MetaSPAdes…
Navigating TensorFlow Configuration in RStudio: A Guide for Diverse Environments | by Kamrul | Dec, 2023
1. Installing the Right Python Version Recommended Version: Python 3.10.x Optimal balance between new features and stability. Compatible with TensorFlow and avoids many common issues. Installation: Visit the Python website and select a 3.10.x version. Verification: python –version Troubleshooting: Ensure Python is correctly added to your system PATH. 2. Installing…
Bahrain’s genome programme hits 85% target
MORE than 42,000 samples have been collected as part of a nationwide genome project, it has been confirmed. Speaking at the final day of the Manama Health Congress and Expo at Exhibition World in Sakhir, the National Genome Centre’s Dr Fatima Marhoon revealed that almost 85 per cent of the…
SRA toolkit (NCBI) – sra to fasta
SRA toolkit (NCBI) – sra to fasta 1 Dear all, At the moment I’m trying to download sequences from the Sequence Read Archive (SRA) from NCBI and put them into fasta format. For this I downloaded the SRA-toolkit of NCBI and used the following code: set PATH=%PATH%;C:\Users\Admin\Desktop\sratoolkit.2.9.0-win64\sratoolkit.2.9.0-win64\bin prefetch –max-size 100000000…
bash – Running task once in a slurm script with job array
I am running a couple of jobs in parallel using the following slurm script: #!/bin/bash #SBATCH –job-name=”example” #SBATCH –account=”st-me-1″ #SBATCH –array=0-9 #SBATCH –nodes=1 #SBATCH –ntasks-per-node=8 #SBATCH –time=1:00:00 #SBATCH –mem=32000mb # Change directory into the job dir cd $SLURM_SUBMIT_DIR # Load conda environment source ~/.bashrc # Activate conda environment conda activate…
cluster – Slurm nodes randomly dropping
I’ve set up a cluster using Slurm, consisting of a head node, 16 compute nodes, and an NAS with NFS-4 network shared storage. I’ve recently installed Slurm on Ubuntu v22 via apt (sinfo -V reveals slurm-wlm 21.08.5). I’ve tested with some single-node and multi-node jobs, and I can get jobs…
Pytorch installation error – General Topics and Other SDKs
Hi ,i have upgrade my cuda from 11,4 to 12.2 using the following steps:wget developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/arm64/cuda-keyring_1.1-1_all.debsudo dpkg -i cuda-keyring_1.1-1_all.debsudo apt-get updatesudo apt-get -y install cudasudo gedit ~/.bashrcexport PATH=/usr/local/cuda-12.2/bin${PATH:+:${PATH}}export LD_LIBRARY_PATH=/usr/local/cuda-12.2/${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}source ~/.bashrc after that i am ablr=e to clone the pytorch using the following steps: git clone –recursive –branch v2.1.1 github.com/pytorch/pytorch export USE_NCCL=0…
Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic
Seawater samples were collected from surface waters (SRF) and the bottom of the surface mixed layer (BML) in the Eastern Fram Strait region to investigate the distribution of carbohydrates and their utilisation by microbial communities. The ten sites were grouped into three categories based on the underlying seafloor topography (above-slope,…
ncs v2.5.0 linker error when setting CONFIG_BOOTLOADER_MCUBOOT – Nordic Q&A – Nordic DevZone
Hello, I currently have an app using nRF Connect SDK v2.5.0. To enable FOTA I set CONFIG_NCS_SAMPLE_MCUMGR_BT_OTA_DFU and CONFIG_BOOTLOADER_MCUBOOT in my prj.conf (following the documentation instructions). After this building the app fails during linking for 3 different undefined references: [275/280] Linking C executable zephyr/zephyr_pre0.elf FAILED: zephyr/zephyr_pre0.elf zephyr/zephyr_pre0.map : && ccache /home/q/app/zephyr_workspace/toolchains/7795df4459/opt/zephyr-sdk/arm-zephyr-eabi/bin/arm-zephyr-eabi-gcc…
06 – BLAST 1 .pdf – BLAST Bioinformatics for Beginners – 06 Bin He Departments of Biology binhe-lab.org WORKSHOP – PART 1 DINOSAUR? DNA SEQUENCE FROM
Jurassic Park DNA sequence &&)’A dinosaur sequence appears on page °±² of 20Jurassic Park³ by Michael ((+)Crichton ´”*(Ballantyne ”*(Books³ °$!$!²µ¶ 1/In it³ the 1/In,/-Gen’s chief scientist³ )),*Dr¶ -0.Henry Wu³ indicates that the sequence “probably contains instructions to make a single protein ·· say³ a hormone or an enzyme”¶ So what…
Can’t train deep learning models using GPU in PyTorch even with a graphics card? (2023/12 latest version) | by Michael Chen | Dec, 2023
As a Windows user, I’m often plagued by environmental issues. These problems have also led many friends around me to give up on their learning journey. Hence, today I want to share about setting up the environment on Windows to enable PyTorch to utilize GPU for training models. If you…
Gromacs 2023.3 on Apple M3 chip – User discussions
GROMACS version: 2023.3GROMACS modification: No Hi folks I know that there have been several threads on running Gromacs with Apple M1 and M1 or M2 chips (e.g. Error compiling Gromacs 2023’s checks on Mac M2), but I recently got a MacBook Pro with the M3 chip, so I was interested…
Installation error Gromacs 2023.3 – User discussions
GROMACS version:2023.3GROMACS modification: NoHere post your questionI am trying to install the Cuda version of Gromacs. However, I am getting the following error after executing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda. Error : [ 98%] Linking CXX executable …/…/…/bin/argon-forces-integration/bin/ld: /home/saikat/softwares/gromacs-2023.3/build/lib/libgromacs.so.8: undefined reference to srot_’ /bin/ld: /home/saikat/softwares/gromacs-2023.3/build/lib/libgromacs.so.8: undefined reference to strsm_’collect2:…
sparklyr – Databricks Connect v2
Last updated: Thu Dec 7 16:28:19 2023 Intro Databricks Connect enables the interaction with Spark clusters remotely. It is based on Spark Connect, which enables remote connectivity thanks to its new decoupled client-server architecture. This allows users to interact with the Spark cluster without having to run the jobs from…
Charmm36-jul2022.ff – User discussions – GROMACS forums
GROMACS version:GROMACS modification: Yes/NoHere post your question I am trying to generate amylin 2L86.top using CHARMM36-jul2022.ff and TIP3P. Amylin has 37 residues but the last NH2 is considered as residue 38. Although AMBERsb-star-ILDN.ff works with 38 resiues”, Charmm36-jul2022 does not work (see below):Fatal error:Residue type ‘NH2’ not found in residue…
linux – MPI_Init_thread Error When Integrating LAMMPS and Parallel Python in Slurm Script
I am attempting to submit a Slurm script on my school’s clusters, aiming to perform LAMMPS calculations and post-processing with MPI-based parallel Python in a single script. However, I encountered an error. After experimenting, I have distilled the script to its minimal form that consistently triggers the error. my Slurm…
cuda sample build fails on windows with CUDA 12.3, VS 2022
When I tries to build cuda bandwidth test sample, MSB3721 error occurs. MSB3721 “”C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v12.3\bin\nvcc.exe” – gencode=arch=compute_50,code=\”sm_50,compute_50\” – gencode=arch=compute_52,code=\”sm_52,compute_52\” – gencode=arch=compute_60,code=\”sm_60,compute_60\” – gencode=arch=compute_61,code=\”sm_61,compute_61\” – gencode=arch=compute_70,code=\”sm_70,compute_70\” – gencode=arch=compute_75,code=\”sm_75,compute_75\” – gencode=arch=compute_80,code=\”sm_80,compute_80\” – gencode=arch=compute_86,code=\”sm_86,compute_86\” – gencode=arch=compute_89,code=\”sm_89,compute_89\” – gencode=arch=compute_90,code=\”sm_90,compute_90\” –use-local-env – ccbin “C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Tools\MSVC\14.38.33130\bin\HostX64\x64” -x cu -I./ -I../../../Common -I./…
Slurm REST API in AWS ParallelCluster
This post was contributed by Sean Smith, Sr HPC Solution Architect, and Ryan Kilpadi, SDE Intern, HPC AWS ParallelCluster offers powerful compute capabilities for problems ranging from discovering new drugs, to designing F1 race cars, to predicting the weather. In all these cases there’s a need for a human to…
Error while installing Extension Pytorch utils – Support
Hello, dear repositoriesI am having trouble installing Pytorch utils in slicer 5.6.0. When I click the botton “install PyTorch”, it says pytorch will be installed using light-the-torch. After few minutes, I get the error: ModuleNotFoundError: No module named ‘torch’. Detailed error: Traceback (most recent call last): File “C:\Users\jaxni\AppData\Local\slicer.org\Slicer 5.6.0\bin\Python\slicer\util.py”, line…
eciboadaptech/finapi-webform – Packagist
The following pages give you some general information on how to use our APIs.The actual API services documentation then follows further below. You can use the menu to jump between API sections. This page has a built-in HTTP(S) client, so you can test the services directly from within this page,…
python – SLURM: Run Same Parallel Script on Multiple Files
First, you need to be careful with your usage of –ntasks-per-node. The directives for sbatch can be a little bit confusing at first: –nodes — this is the number of nodes that you are requesting for your job. Note: the number of CPUs per node entirely depends on the cluster…
JupyterHub server spawning never completes; new JupyerHub admin – JupyterHub
Hello, I’ve recently started a position responsible for a JupyterHub installation as part of an HPC environment; the old team left without leaving much in the way of documentation, and I’ve never worked on JupyterHub before, so please bear with me. When launching JupyterHub, the system will stay on the…
sequence alignment – BioPython bootstrap is not reliable?
I think this is a bug. It seems to work if you do this, creating an equivalent Alignment object instead of a MultipleSeqAlignment to give the bootstrap step: from Bio.Align import Alignment alignment2 = Alignment(list(alignment)) consensus_tree = bootstrap_consensus(alignment=alignment2, times=50, tree_constructor=constructor, consensus=majority_consensus) bootstrap_consensus calls bootstrap_trees, which makes however many randomly shuffled…
tensorflow – CuDNN using wrong CUDA version
I’m re-doing my CUDA/CuDNN setup on a new profile on Ubuntu 22.04.3 because Keras raised an error with libcublasLT I couldn’t fix. For project compatibility, I need to use TF 12.12 with CUDA 11.8 and CuDNN 8.6. I’m working on a machine with multiple CUDA versions already installed. $ cd…
Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Fig 1. rrnI-dependent expression of HspA in V. vulnificus MO6-24/O strains. (A) Schematic representation of the allele-specific RT-PCR analysis analyzing the relative amounts of I-rRNA or G-rRNA. (B) The number of I-rRNA or G-rRNA amplicons and other rRNAs amplified from the cDNA of the MO6 WT, MO6+rrnG, and MO6+rrnI strains…
How to use Nextflow to call scripts from different environments?
How to use Nextflow to call scripts from different environments? 0 I have the following conda environments: wf-preprocess_env wf-assembly_env Each environment has unique dependencies installed. I have 3 scripts: preprocess.py which I use with wf-preprocess_env environment assembly.py and assembly-long.py which I use with wf-assembly_env How can I use Nextflow to…
Sorted bam files are empty after sorting them from bam
Sorted bam files are empty after sorting them from bam 0 Hi, I have been working with all my DNA analysis files in parallels but I got to a point where I had about 15 files get stuck on one step. Specifically, I notice something is wrong because the files…
Calculate GC content for entire chromosome
If you’re comfortable using Python, I’ve created a script that calculates the GC content and GC-skew for each contig, scaffold, or chromosome in a fasta file. This is specifically designed for generating data for a circos plot. To use the script, make sure you have Biopython installed in your conda…
UAE university vies for international recognition in AI education and research
Mohamed bin Zayed University of Artificial Intelligence (MBZUAI) was founded in 2019 as part of the national strategy for AI in the United Arab Emirates (UAE), with a single campus located in Masdar City in Abu Dhabi. The university is another example of how committed the UAE is to…
Fetching subsets with slow5curl and samtools
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Java error while running HiCDC overview code
Hey folks! I am trying to run the code provided in the HiCDC overview (github.com/mervesa/HiCDCPlus#diff_int). Everything runs as expected (as shown in the Github code) but at the moment of trying to save the output of HiCDCPlus_parallel() into a .hic file with hicdc2hic() I run into an error I am…
Panic: Could not run ‘torchvision::roi_pool’ with arguments from the ‘CUDA’ backend – Jetson Nano
Hi, Team! I have such errors, when I run my code in docker container: root@de87551d73cf:/app/src# ./main WARN[0032] CUDA is valid WARN[0044] CUDA is valid INFO[0044] Forwarding… [W TensorImpl.h:1156] Warning: Named tensors and all their associated APIs are an experimental feature and subject to change. Please do not use them for…
Nvcc fatal : Host compiler targets unsupported OS. (GPU=MX150, CUDA, Win 11 Pro, VS 2022/17.8.2) – CUDA Setup and Installation
Hello Folks, I’m working with the CUDA samples found here: github.com/NVIDIA/cuda-samples When I go to build in Visual Studio 2022, I get hit with this error: nvcc fatal : Host compiler targets unsupported OS. The whole commandline instruction is the following: —-BEGIN COMMAND—– “C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v12.3\bin\nvcc.exe” -gencode=arch=compute_50,code=”sm_50,compute_50″ -gencode=arch=compute_52,code=”sm_52,compute_52″…
4 Fastq files for a single run generated by 10X
4 Fastq files for a single run generated by 10X 0 Hello, I have a question about the 10X generated Fastq files. As I know 10X platforms can generate up to 4 Fastq files as R1, R2, I1 and I2. I need to use Fastq files and align them with…
locuszoom error
locuszoom error 1 Hi there, I downloaded locuszoom in it’s entirty from their github page. I have everything in order but when I attempt to run the following I get an error: locuszoom_test/bin/locuszoom –metal chr7.snx13.marker.locuszoom.metal –ld chr7.imputed.concat.sorted.nomono.80.recode.maf01.pheno.vcf.2.ld.locuszoom.input –refsnp rs1533245 –prefix chr7.snx13.rs1533245 /share/hennlab/progs/locuszoom_test/bin/../src/m2zfast.py:82: SyntaxWarning: invalid escape sequence ‘\d’ RE_SNP_1000G = re.compile(“chr(\d+|[a-zA-z]+):(\d+)$”);…
sagemath crashes on start (output in messagem body)
Package: sagemathVersion: 9.5-6Severity: importantFile: /usr/bin/sage Dear Maintainer, I can’t start sage on console. Starting it, I get the following: $ sage┌────────────────────────────────────────────────────────────────────┐│ SageMath version 9.5, Release Date: 2022-01-30 ││ Using Python 3.11.6. Type “help()” for help. │└────────────────────────────────────────────────────────────────────┘ Error in sys.excepthook:Traceback (most recent call last):File “/usr/lib/python3.11/pathlib.py”, line 1251, in is_dirreturn S_ISDIR(self.stat().st_mode)^^^^^^^^^AttributeError: ‘str’…
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
I am mapping RNA-Seq data using STAR, using multi-sample two-pass mapping. I first mapped all samples with one-pass then concatenated their SJOut files and filtered junctions. I launched the second mapping by using this SJOut file. I used this command to generate genome : ` /home/STAR-2.7.10b/bin/Linux_x86_64/STAR \ –runThreadN 10 \…
linux – How to install sox for PyTorch audio?
I want to run PyTorch code on Linux. I start a virtual machine on AWS with AMI Deep Learning PyTorch, but, surprisingly, PyTorch is not installed. So I run: python3 -m pip install torch torchaudio When I load a WAV file, I get this error: RuntimeError: Couldn’t find appropriate backend…
Error in blast+
Error in blast+ 0 Hello, I have a problem with creating a local database (blast+) I downloaded NCBI BLAST and then put a fasta file in the bin folder. Later I opened this folder in PowerShell and wrote a command “makeblastdb -in ownBLASTdb.fasta -out DataBase -dbtype prot -parse_seqids”. I got…
140releng-powerpc64le-quarterly][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/140releng-powerpc64le-quarterly/84b4661ec108/logs/py39-pytorch-2.0.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=140releng-powerpc64le-quarterly&build=84b4661ec108 Log: =>> Building misc/py-pytorch build started at Sun Dec 3…
140releng-powerpc64le-quarterly][biology/cytoscape] Failed for cytoscape-3.6.1 in build
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/140releng-powerpc64le-quarterly/84b4661ec108/logs/cytoscape-3.6.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=140releng-powerpc64le-quarterly&build=84b4661ec108 Log: =>> Building biology/cytoscape build started at Sat Dec 2…
RStudio doesn’t work on Debian 12 with R version 4.3.2 – General
Hello, From the download website, it seems RStudio support Debian 12. I have installed R 4.3.2 R version 4.3.2 (2023-10-31) — “Eye Holes”Copyright (C) 2023 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain…
Spending 30 Minutes on TikTok a Day Significantly Increases the Chances of Holding Antisemitic and Anti-Israeli Beliefs, Study Finds
Shocking new data indicate that using TikTok a mere 30 minutes a day increases the chance of holding “antisemitic or anti-Israel” views by 17 percent, a number far above the same correlation on other social media platforms. That’s the latest research from a data scientist, Anthony Goldbloom, who founded a…
Using metagenome assembly and binning to identify and mitigate contamination in a genome
Hi everyone, This may be a silly question, but I am interested if using metagenome assembly and binning is a valid method of determining if a sample contains a mixture of species. Similarly, can metagenomics be used to identify and remove contamination from a single genome? For some background, I…
Identification of constrained sequence elements across 239 primate genomes
De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…
AutoDock Vina 1.2.0: new docking methods, expanded force field, and Python bindings
J Chem Inf Model. Author manuscript; available in PMC 2023 Nov 28. Published in final edited form as: PMCID: PMC10683950 NIHMSID: NIHMS1947068 Jerome Eberhardt aDepartment of Integrative Structural and Computational Biology, Scripps Research, La Jolla, 92037, California, USA Diogo Santos-Martins aDepartment of Integrative Structural and Computational Biology, Scripps Research, La…
Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m5C at GCU motifs
Introduction Oxford Nanopore Technologies (ONT) direct RNA sequencing (Fig 1A) enables detection of RNA modifications. A modified base produces an altered electrical current and/or dwell time relative to a canonical base that can be detected with algorithms (Garalde et al, 2018; Smith et al, 2019; Workman et al, 2019). Figure…
nrfConnect 2.5.0: mbedTLS fails to compile (calloc()) – Nordic Q&A – Nordic DevZone
Hi there: we’ve just updated from nrfConnect 2.3.0 to nrfConnect 2.5.0 and mbedTLS (which seems to have been modified in nrfConnect 2.5.0) now fails to link (in platform.c) because it needs and is unable to find calloc(): /home/arm_embedded_gcc-10-2020-q4-major/bin/ld.bfd: modules/mbedtls/libmbedTLSBase.a(platform.c.obj):/home/nrfconnectsdk-v2.5.0/modules/crypto/mbedtls/library/platform.c:56: undefined reference to `calloc’ As you can see, we are just compiling…
A two-kinesin mechanism controls neurogenesis in the developing brain
Reduced Kif13b expression increases the ratio of neurons to progenitors in the developing rat brain To compare the roles of Kif13B vs. Kif1A in rat brain cortical development, we injected embryonic day 16 (E16) rat embryos in utero with an empty GFP control plasmid, or shRNAs designed for knockdown of…