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Tag: bash
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…
King’s College London hiring Research Associate in Translational Bioinformatics in London, England, United Kingdom
Job DescriptionThis is a Pre-Fellowship for early career researchers wanting to establish a career in MND translational research and become MND research leaders of the future. The postholder will have a leading role in an exciting new project funded by Motor Neurone Disease Association and MND Scotland. The project is…
Using ColabFold to predict protein structures | by Natan Kramskiy | Jan, 2024
A few hours before the CASP14 (14th Critical Assessment of Structure Prediction) meeting, the latest biannual structure prediction experiment where participants build models of proteins given their amino acid sequences, this image went viral on twitter. Ranking of participants in CASP14, as per the sum of the Z-scores of their…
Amplifybio, LLC Sr./Scientist, Bioinformatics in South San Francisco, CA | 892968472
Are you passionate about significantly improving the future of medicine? Do you believe that people are the most important asset of any company? If so, join AmplifyBio! AmplifyBio is a company dedicated to building an integrated environment where clients can access technologies, platforms, capabilities and safety testing for the scale…
AssertionError: Torch not compiled with CUDA enabled – Jetson Orin Nano
I know the solution for this error is here: AssertionError: Torch not compiled with CUDA enabled and also here too: Torch not compiled with cuda enabled over Jetson Xavier Nx I think, I have the correct software stacks according to those solutions or I have whatever software stacks are compatible…
Bioinformatics scientist | GENOMINES
Job Description Who we are Genomines is a young biotechnology company based in Paris and Saclay, specialized in sustainable extraction of Nickel from plants. The mission of Genomines is to usher in a new era of sustainable mining by using genetically enhanced plants to extract metals from soil (agromining). Through…
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…
Senior Bioinformatics Scientist in Chicago, IL for University of Chicago (UC)
Details Posted: 19-Dec-23 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Chicago, IL Job Description: Development of an integrated data warehouse for symbiote including clinical, microbiome sequence, and metabolomic data. Management of DFI Biobank, MMF, and HMMF data within the Symbiote platform. Functional analysis of…
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…
Business Analytics with LangChain and LLMs | by Naser Tamimi | Dec, 2023
GENERATIVE AI A Step-by-Step Tutorial on Using LangChain to Query SQL Databases with Human Language Image by the author (generated via Midjourney) Many businesses have a lot of proprietary data stored in their databases. If there’s a virtual agent that understands human language and can query these databases, it opens…
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….
Senior Bioinformatics Scientist @ University of Chicago
Department BSD DFI – Translational Informatics About the Department The Duchossois Family Institute focuses on the role of commensal bacteria in enhancing disease resistance and is using genomic and metabolomic platforms to characterize the microbiome and its metabolites. Computational and bioinformatic expertise is required to understand how commensal bacteria impact…
DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea
Description This version is to stay up to date with the improvements and increase in 16S rRNA gene sequences (SSU) added to the GTDB release 214.1. Please read this post for the stats on the updates. gtdb.ecogenomic.org/stats/r214 . There has been no change to the RDP-RefSeq reference database If anyone…
Two uloop variables? – LAMMPS
m.adibi December 18, 2023, 9:39am 1 Greetings, I am trying to define a lammps input script that gets a list of forcefield files and for each forcefield file it runs simulations in multiple temperatures. One way to do this is to make an outer Uloop for force field files and…
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…
Bioinformatics Analyst I-II in Seattle, WA for Fred Hutchinson Cancer Center
Details Posted: 17-Dec-23 Location: Seattle, Washington Type: Full-time Salary: Open Overview Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington. With a…
Unix and Shell Scripting for Bioinformatics course
News:Unix and Shell Scripting for Bioinformatics course 0 Dear all, There are still a few seats available for our online course on Unix and Shell Scripting for Bioinformatics! Dates: 15-19 January 2024 Course Overview: Dive into the world of high-throughput biology Master essential Unix commands for data analysis Connect to…
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,…
[slurm-users] Slurm versions 23.11.1, 23.02.7, 22.05.11 are now available (CVE-2023-49933 through CVE-2023-49938)
Slurm versions 23.11.1, 23.02.7, 22.05.11 are now available and address a number of recently-discovered security issues. They’ve been assigned CVE-2023-49933 through CVE-2023-49938. SchedMD customers were informed on November 29th and provided a patch on request; this process is documented in our security policy. [1] There are no mitigations available for…
Bioinformatics/Genomics Senior Consultant in , for The Ohio State University
Details Posted: 13-Dec-23 Type: Full-time Salary: Open Categories: Information Technology Staff/Administrative Scope of Position: The James Molecular Pathology Laboratory performs clinical molecular diagnostics testing and uniquely spans across the research and clinical missions of The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital (OSUCCC-James). The OSUCCC-James is committed…
Running cellranger on multiple files when R1 and R2 fastqs are in multiple subfolders
Running cellranger on multiple files when R1 and R2 fastqs are in multiple subfolders 0 Hi, I have downloaded a public dataset and would like to run cellranger count on it. The main folder is CNP000460, containing multiple samples, such as CNS0094872, this sample folder has several associated subfolders, each…
Data Science Community & Internal Support Lead
Your role You will provide project leadership and coordination to shape data science-related internal support activities and training programs, spanning programming, consulting in complex data analysis, and specialised courses. Engaging with both the scientific community at EMBL and external representatives, your work will enhance training and consulting offerings across EMBL…
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…
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…
Snakemake rule error
Snakemake rule error 0 I have the following rule in snakemake: rule low_coverage_contig_reads: input: bam=”data/processed/bam_files/bam/{sample}_{fraction}.bam.bai”, output: r1=”data/processed/clean_reads/low_cov/low_cov_{sample}_{fraction}_R1.fq.gz”, r2=”data/processed/clean_reads/low_cov/low_cov_{sample}_{fraction}_R2.fq.gz” threads: 8 params: bam=”data/processed/bam_files/bam/{sample}_{fraction}.bam” log: log1=”logs/{sample}_{fraction}_low_coverage_reads.log”, shell: “”” (samtools coverage {params.bam} | awk ‘NR > 1 && $7 < 10 {{print $1}}’ | tr ‘\\n’ ‘ ‘ | samtools view -u {params.bam}…
Autocompleting paths within scripts
Autocompleting paths within scripts 1 Hello community, I am changing my remote file system to something more organized (based on Johny Decimal). This means that I have to go through the task of editing the paths in my scripts. I am now using vscode to connect to the remote server,…
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…
Ada Nicodemou shows off her trim pins in glistening frock as she leads the arrivals at Channel Seven Christmas bash alongside Sam Mac
By Marta Jary For Daily Mail Australia Published: 06:56 GMT, 9 December 2023 | Updated: 11:01 GMT, 9 December 2023 Ada Nicodemou was ready for a festive good time on Saturday night. The Home and Away star was among the celebrities heading in to the Channel Seven Christmas bash in Sydney. …
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…
Postdoctoral Position in Genomics – Tcheandjieu Lab, US
Postdoctoral Position in Genomics: The Tcheandjieu Lab at the Gladstone Institutes/UCSF is inviting applications for a Postdoctoral position in Genomics. This role offers an exciting opportunity to work on diverse biobanks, utilizing genomic and multi-omic approaches to enhance our understanding of cardiovascular diseases. Located in the heart of Silicon Valley,…
Cannot connect to the server, what am I missing? – JupyterHub
The hub on the host severed directly on my machine (not via docker image). I run the jupyterhub with command arg –debug, and got the terminal infomation as follows: root@DESKTOP-L60P4Q8:~/my_docker/main# jupyterhub –debug -f ../jupyterhub_config.py [D 2023-12-07 23:00:23.417 JupyterHub application:908] Looking for ../jupyterhub_config in /root/my_docker/main [D 2023-12-07 23:00:23.417 JupyterHub application:929] Loaded…
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…
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…
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…
Fetching subsets with slow5curl and samtools
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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…
vcftools
vcftools 1 Hi, I tried this code but I couldn’t get any output. Please guide me to resolve this issue bash for i in {1..2} do vcftools –LROH –vcf Pakistan.total.vcf –out ${i} –chr i done vcftools • 41 views • link updated 2 hours ago by Barista ▴ 10 •…
Postdoctoral Fellowship in bioinformatics and genetic epidemiology – University of Copenhagen – job portal
Job Portal Postdoctoral Fellowship in bioinformatics and genetic epidemiology A two-year postdoctoral fellowship is available at the Section for Computational and RNA Biology, Department of Biology, University of Copenhagen. The position will be available from April 1st, 2024 or thereafter. The specific projects involve analyzing…
Advanced use of LAMMPS
This lesson provides an overview of some more advanced techniques and uses of LAMMPS. Specifically, we will be discussing: Measuring and improving LAMMPS performance: Strong vs weak scaling for a range of systems. Smarter domain decomposition. Accelerators, and what they do. Running LAMMPS from Python. Analysing systems through reruns. Advanced…
systemd autopkgtest regression on arm64 and s390x on mantic
Is seems the container fails to boot. From a bad run: 9109s autopkgtest [10:39:17]: test tests-in-lxd: [———————– 9145s 2023-11-28T10:39:50Z INFO Waiting for automatic snapd restart… 9259s lxd 5.19-8635f82 from Canonical** installed 9288s Creating autopkgtest-prepare-jhI 9475s Retrieving image: metadata: 100% (323.81MB/s) Retrieving image: rootfs: 1% (3.53MB/s) <SNIP> Retrieving image: rootfs: 100%…
Entry Bioinformatics Professional Cancer Research job with University of Colorado Anschutz Medical Campus
Entry Bioinformatics Professional – Cancer Research – 31970 University Staff Description University of Colorado Anschutz Medical Campus Department: Pediatrics – Hematology, Oncology, and Bone Marrow Transplant Job Title: Entry Bioinformatics Professional – Cancer Research Position: # 00817933 – Requisition: # 31970 Job Summary: The Entry Bioinformatics Professional utilizes applied or…
The Anthropological and historical reasons why Nagas are not Indians and Indians not Nagas | MorungExpress
Kaka D Iralu The following article is made up of excerpts from a paper presented at the international conference on Armed Conflicts in Eastern India held at Shillong from December 1-2, 2006. The original 10-paged paper was entitled, “An anthropological and historical analysis of the Indo-Naga war”. In this just…
Senior Bioinformatics Software Engineer – Land A Remote Job From Top Employers
The Center for Applied Bioinformatics (CAB) at the St. Jude Children’s Research Hospital (SJCRH) is seeking a creative Software Engineer with a strong background in bioinformatics to join our development team to create and maintain our vital analytical infrastructure. The new hire will work closely with a team of computer…
DS Group hiring Bioinformatician in London, England, United Kingdom
Bioinformatician – Deep Learning, Python, PyTorch, GWAS, RNA At the company, a leading agbiotech start-up, safeguarding the future of food is at the heart of what drives and inspires every member of the team. With a mission to accelerate the development of more productive, sustainable, nutritious, and climate-resilient food sources,…
Postdoctoral Researcher in Alzheimer’s disease Genetics, Multi-Omics, and Imaging Biomarkers, St Louis, MO, USA
Location: Department of Neurology, NeuroGenomics and Informatics Center, Washington University in St. Louis Description The Washington University School of Medicine, Department of Neurology, has an opening for a post- doctoral research associate to join the Belloy lab in the NeuroGenomics and Informatics Center (NGI). The successful candidate will be involved…
Visualize and explore eventalign data against reference
Visualize and explore eventalign data against reference 0 Hi all, Is anyone aware of a tool (GUI or python/R/bash package) to explore eventalign nanopore data (or fast5 raw data) with the corresponding alignment to a reference genome? Kind of like viewing how reads in a bam file align against a…
Running STAR on fastq file generated from a RNA-seq experiment
Running STAR on fastq file generated from a RNA-seq experiment 1 Hi, I am new to bioinformatics, especially on the command line. I am trying to run STAR alignment on pairs of fastq.gz files from several samples generated as part of an RNAseq experiment. My goal is to perform splice…
Redirect loop detected. Notebook has jupyterhub version unknown (likely < 0.8), but the Hub expects 4.0.2 - JupyterHub
Thanks very much for your help. I changed the jupyterhub_config.py to this: c.Spawner.args = [“–allow-root”] And run the jupyterhub, and there is the terminal information: I 2023-11-27 17:01:45.679 JupyterHub app:2859] Running JupyterHub version 4.0.2 [I 2023-11-27 17:01:45.679 JupyterHub app:2889] Using Authenticator: jupyterhub.auth.PAMAuthenticator-4.0.2 [I 2023-11-27 17:01:45.679 JupyterHub app:2889] Using Spawner: jupyterhub.spawner.LocalProcessSpawner-4.0.2…
Species coverage in the NCBI protein NR database ?
Hi Biostars, I am currently trying to build a Eukaryote version of the NCBI NR database and I am not really sure that I fully understand how the NR is implemented. Here is the code that I’m using to do so : #!/usr/bin/bash ############## # DOWNLOAD FULL NR ############## baseURL=”https://ftp.ncbi.nlm.nih.gov/blast/db/”…
python – PyTorch distributed from two ec2 instances hangs
# env_vars.sh on rank 0 machine #!/bin/bash export MASTER_PORT=23456 export MASTER_ADDR=… # same as below, private ip of machine 0 export WORLD_SIZE=2 export GLOO_SOCKET_IFNAME=enX0 export RANK=0 # env_vars.sh on rank 1 machine #!/bin/bash export MASTER_PORT=23456 export MASTER_ADDR=… # same as above export WORLD_SIZE=2 export GLOO_SOCKET_IFNAME=enX0 export RANK=1 # on rank…
How to run python experiments with Slurm and Conda? | by Hitesh Vaidya | Nov, 2023
source: getyarn.io/yarn-clip/368e3529-f540-4cfa-af28-d40a2ca2b99d As data scientists and researchers, efficiently managing multiple machine learning experiments is fundamental to our work. Tools like Slurm and Conda offer powerful capabilities that streamline the execution of experiments on high-performance computing clusters while ensuring environment consistency and reproducibility. In this blog, we will take a look…
Tools for Efficient Retrieval from GEO and SRA Databases | by Denis Odinokov, MBBS, MSc, PMP | Nov, 2023
Image by Gerd Altmann from Pixabay For downloading data and standardized metadata from GEO (Gene Expression Omnibus) and SRA (Sequence Read Archive), several bioinformatics and command-line tools and scripts are available, primarily hosted on GitHub. ARA: An automated pipeline developed for better sampling of NCBI SRA database records, allowing full…
[Hiring] QA Engineer Release Manager @Lifebit Biotech Ltd at Lifebit Biotech Ltd
Nov 22, 2023 – Lifebit Biotech Ltd is hiring a remote QA Engineer Release Manager. 📍Location: Europe. At Lifebit, we carve our own path. We’re open-source pioneers and our driving mission is to revolutionise bioinformatics and biomedical data analysis forever. Our product, Lifebit CloudOS, is the world’s first federated genomics…
[slurm-users] Dynamic MIG Question
Hello All, I am currently working in a research project and we are trying to find out whether we can use NVIDIAs multi-instance GPU (MIG) dynamically in SLURM. For instance: – a user requests a job and wants a GPU but none is available – now SLURM will reconfigure a…
Senior Bioinformatics Support Specialist – it-jobs-switzerland.ch
This is a version of the job ad optimized for mobile devices. Show original job ad The Position ROLE SUMMARY: Creates, reviews, and maintains training content and training documentation for job-oriented training in cooperation with regional training centers. Training are executed and supported for end customers, first-level support, regional trainers,…
Bioinformatics Scientist – Madison, Wisconsin, United States
Job Summary: The Bioinformatics Scientist will develop, adapt, and implement computational and bioinformatics pipelines for established and novel approaches, depending on the current demands of the service. The Bioinformatics Scientist will be responsible for project management, data delivery, and communication of results to clients as required. As we are a…
TF Footprinting using HINT ATAC module from RGT
I was successful in running the first three commands of HINT ATAC as shown below following this tutorial github.com/sufyazi/sufyazi.github.io/wiki/TF-Footprinting-Tutorial-using-HINT-ATAC-module-from-RGT-toolbox rgt-hint footprinting –atac-seq –paired-end –organism=mm10 –output-location=/XXX –output-prefix=Afootprints A.mRp.clN.sorted.bam A.mRp.clN_peaks.narrowPeak rgt-hint footprinting –atac-seq –paired-end –organism=mm10 –output-location=/XXX –output-prefix=Afootprints B.mRp.clN.sorted.bam B.mRp.clN_peaks.narrowPeak rgt-motifanalysis matching –organism=mm10 –input-files Afootprints.bed Bfootprints.bed But when I ran the command below…
How to filter .fasta file based on conditional statement
How to filter .fasta file based on conditional statement 2 Hi all, I have a .fasta file resulting from vsearch clustering. The sequences in the .fasta file look like: >centroid=211650b5-4541-47e4-a7a4-3659962f9818;seqs=2236 GAGATGATGATGATATAATT the “seqs” parameter in the sequence header, reflects the number of reads of that cluster consensus that was present…
Automation Script for installing virtual environment with installation of tensor flow and PyTorch on mac os metal | by Vineeth Krishna | Nov, 2023
TensorFlow, TensorFlow-Metal, and PyTorch are powerful deep learning frameworks widely used in various applications. To effectively manage these frameworks and their dependencies, it’s recommended to work within a virtual environment. A virtual environment isolates the project’s dependencies from the global Python environment, preventing conflicts and ensuring compatibility. This article provides…
132amd64-default][science/votca] Failed for votca-2023 in package
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/beefy16/data/132amd64-default/5b346a1c0cc2/logs/votca-2023.log Build URL: pkg-status.freebsd.org/beefy16/build.html?mastername=132amd64-default&build=5b346a1c0cc2 Log: =>> Building science/votca build started at Tue Nov 21…
How to overlap patient VCF with ClinVar database annotation using bedtools?
How to overlap patient VCF with ClinVar database annotation using bedtools? 1 Hello, I’m trying to help a colleague who is trying to add ClinVar databases clinical significance column to VCF samples that she analysed. More specifically, we are trying to add overlapping/common variant annotation so that if the variant…
JupyterHubSingleUser – Failed to connect to my Hub at http://127.0.0.1:8081/hub/api – JupyterHub – Jupyter Community Forum
After updating the base notebook image to Quay (base-notebook:2023-10-31) getting these connection errors in single user server spawn. Earlier used version jupyter/base-notebook:2023-04-14 this working without any errors. (python3.10 version used in working docker image) Environment:Used helm chart version “3.0.3” to deploy the 4.0.2 version of application on AWS EKS Cluster….
Optimizing Language Model Training: A Practical Guide to SLURM | by Viktorciroski | Nov, 2023
In the dynamic world of deep learning, pushing the boundaries of language models often bumps into the memory limits of individual GPUs, like the NVIDIA GeForce RTX 3090. With 24 GB of GDDR6X memory, it’s a powerhouse, but models such as Llama 2 can still stress these resources, causing headaches…
Senior Scientist, Bioinformatics II job with AbbVie
AbbVie’s Genomics Research Center Computational Genomics is looking for a highly motivated computational biologist (Senior Scientist II, Bioinformatics) to join a team of bioinformatics scientists investigating aging and age-related diseases. AbbVie’s GRC is a center of excellence for bioinformatics, functional genomics, and human genetics. The GRC works across all R&D…
[Kernel-packages] [Bug 2007050] Autopkgtest regression report (initramfs-tools/0.142ubuntu15.1)
All autopkgtests for the newly accepted initramfs-tools (0.142ubuntu15.1) for mantic have finished running. The following regressions have been reported in tests triggered by the package: initramfs-tools/0.142ubuntu15.1 (armhf) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-…
STAR output
STAR output 1 Hello, I am trying to map with STAR but it is not clear to me why I am not getting the SAM/BAM mapping file, could you help me? [epola@mazorka alignment_STAR]$ ls -lh total 13M -rw-rw-r– 1 epola epola 13M Nov 17 12:34 SRR22164928SJ.out.tab -rw——- 1 epola epola…
Molecular Analyst – 1744 – Job at Advanced Systems Design, Inc. in Jacksonville, FL
Advanced Systems Design is seeking a Molecular Analyst/Bioinformatician for our client located in Jacksonville, FL. Sorry, remote work will not be considered or negotiated for this position. Job Overview: The Molecular Analyst/bioinformatician will provide technical skills in bioinformatics and molecular sequencing analysis and reporting for the Florida Newborn Screening Program….
Trying to spawn pods in other namespace – Zero to JupyterHub on Kubernetes
Hello manics, thank you for your quick response and the tips on further debugging!In the default setting everything works fine, I can even use a profile as long as I dont use the kubespawner_override.namespace option. Here are the logs from the profile+namespace setting with the debug logging:Hub: [I 2023-11-16 19:58:45.827…
View All Jobs/Careers – Emory Healthcare/Emory University Assistant Bioinformatics Scientist in Atlanta, Georgia, United States
Discover Your Career at Emory University Emory University is a leading research university that fosters excellence and attracts world-class talent to innovate today and prepare leaders for the future. We welcome candidates who can contribute to the diversity and excellence of our academic community. Description The Division of Behavioral Neuroscience…
University of Michigan hiring Bioinformatics Specialist in Ann Arbor, MI
How to Apply Applications are welcomed and encouraged from all qualified individuals regardless of background and identity. To apply, please complete the application on the U-M Careers site. A one page cover letter is required for consideration for this position and should be attached as the first page of your…
Internship: Master’s Thesis in Bioinformatics & Data Science, Italy – 2024 at GSK – Siena
Posting Title: Master’s Thesis in Bioinformatics & Data Science Intern Help us get ahead of disease together with our Vx Computational Design team Education required: Knowledge in Informatics, Computational Biology, Mathematics, Physics, Computer Science, or related fields and interest in biological research problems. Familiarity with Artificial Intelligence and Machine Learning…
CCMB Bioinformatics Mol Bio & Bioinformatics Research
“Breaking News: Exciting Job Openings at CCMB for Bioinformatics and Mol Bio Research! Apply Now!” CCMB Bioinformatics Mol Bio & Bioinformatics Research CCMB Bioinformatics Mol Bio & Bioinformatics Research. Interested and eligible applicants can check out all of the details on the same below: A leading research institution, CSIR-CENTRE FOR…
Senior Bioinformatics Scientist @ Storm3
⚡ Senior Bioinformatics Scientist (HUMAN GENETICS) 🧪 Healthtech Start-Up 📌 Remote (US) 💰 $150K Base + Bonus + Impressive equity Are you interested in joining a revolutionary Biotech start-up that is using their ground-breaking AI platform to change the way we discover drugs? This established start-up with over $30M in…
cryptic error with pod5 subset tool
I’m running into a error that I haven’t managed to debug so far. The job runs for a few seconds, and then stops writing files. The errors are not always exactly the same, nor they are happening at the same point of the subsetting process. Here is a representative example,…
python – Docker with Rstudio & conda virtual env – unable to load R packages
I have this dockerfile: # Use the rocker/rstudio image with R version 4.1.2 FROM rocker/rstudio:4.1.2 # Install deps RUN apt-get update && apt-get install -y \ wget \ bzip2 \ bash-completion \ libxml2-dev \ zlib1g-dev \ libxtst6 \ libxt6 \ libhdf5-dev \ libcurl4-openssl-dev \ libssl-dev \ libfontconfig1-dev \ libcairo2-dev \…
Use WSL as terminal in RStudio desktop on Windows
On a Windows machine, I have WSL2 installed and working. I believe I can use the WSL2 shell as my terminal in RStudio desktop (note, I am not trying to run RStudio in WSL2, at least not yet). However, although I have seen screenshots where WSL bash appears as an…
University of Alabama at Birmingham hiring BIOINFORMATICIAN I in Birmingham, Alabama, United States
Position Summary: The primary role is to execute a variety of data management and analysis tasks, ensuring the quality, reproducibility, and efficiency of processes related to high-dimensional data. You will collaborate with study investigators and fellow bioinformatics professionals within the department to contribute to high-quality, reproducible research across various scientific…
132arm64-default][science/votca] Failed for votca-2022.1_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/ampere3/data/132arm64-default/d5268d5f7157/logs/votca-2022.1_1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=132arm64-default&build=d5268d5f7157 Log: =>> Building science/votca build started at Fri Nov 10…
trying to use the API for edirect tool (NCBI)
trying to use the API for edirect tool (NCBI) 1 Hi, I’m new to bioinformatics, so I apologize if my question seems a little bit basic. I wanted to use the tool Edirect to retrieve information about a list of samples that I have generated. I work on a cluster,…
PIGx ChIP-seq pipeline error
Hi Lisa, You also need to modify the gtf annotation file using: sed ‘/^#/d’ annotation_file.gtf > annotation_file_no_header.gtf Best, Alex > On 12. Oct 2022, at 15:07, Bora Uyar <borauy…@gmail.com> wrote: > > You would need to check how your fasta headers look and how the chromosomes are represented in…
bash – How to hold jobs for a user so that a total cpu number isn’t reached in slurm?
I am submitting a bunch of array jobs 4 sets of 5 with 8 cpus each, so 4x5x8=160 cpus total. I would like to keep the running amount to below 100>2x5x8+1x2x8 cpus total, because I need to let others run things. My whole research group is allowed 300 cpus, but…
Llama pytorch profiling – Nsight Compute
Hello, I’m trying to profile an inference of Llama GPT, which recently added cuda support link. The model is ran through a bash script, which creates an appropriate docker container and launches the model within it. However, the profiler is unable to detect any kernel, even though I have confirmed…
Real-time collaboration for jupyterhub – Zero to JupyterHub on Kubernetes
Hi there,I’ve been playing around with RTC extension on jupyterhub recently and I’ve been stuck at creating-collaboration-accounts for a while. It mentions This configuration code runs when jupyterhub starts up, so I included the example code block under hub.extraConfig.’myConfig.py’, then I got this error: TypeError: ‘LazyConfigValue’ object is not subscriptable….
[slurm-users] GraceTime is not working, But there is log.
Hello ~ Please help me. Total GPU : 4 Large qos : 3 (max 3 gpus) Base qos : 2 (max 2 gpus) I have a total of four GPUs, and when a job with a large QoS is using three GPUs and a job with a…
[slurm-users] Unable to submit job (ReqNodeNotAvail, UnavailableNodes)
Hi there, First of all, apologies for the rather verbose email. Newbie here, wanting to set up a minimal slurm cluster on Debian 12. I installed slurm-wlm (22.05.8) on the head node and slurmd (also 22.05.8) on the compute node via apt. I have one head, one compute node, and…
bash – Racon: empty overlap set!
Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then converted from bam to fastq using samtools, then trimmed using nanofilt from there…
Senior Scientist Bioinformatics – AZNJP00026759 Hays Working for your tomorrow
Location – Cambridge, UK Outside IR35 Duration – 12 months Make a more meaningful impact to patients’ lives around the globe. When we put unexpected teams in the same room, we unleash bold thinking with the power to inspire life-changing medicines. In-person working give us the platform we need to…
Reduce PDB doesn’t match Topology File atom – User discussions
GROMACS version: 2023.2GROMACS modification: No I am testing running proteins with mutations through AlphaFold and then passing the PDBs to gromacs to run relaxation. I originally attempted to run this without reducing the molecule, but that definitely didn’t work. Next, I reduced the structure using GitHub – rlabduke/reduce: Reduce –…
ANGSD beagle generation returning empty file
ANGSD beagle generation returning empty file 0 Hello Biostars community, I am struggling quite a bit with ANGSD these days as it seems that no code I provide to the machine is working as intended. I want now to produce a beagle file but the following script is returning me…
python – Attaching Debugger to Slurm compute node using Debugpy
I’m trying to debug code running on a SLURM compute node. I’m using VS Code to connect to the head node where I develop my code. To debug I have first to allocate a node to get access to a GPU. I tried this: stackoverflow.com/a/64700090/14290795 but got an error saying…
Got an error when using chilin
Got an error when using chilin 0 I installed chilin and all the dependencies following the guidance, but when I run bash foxa1 and my own data, I got an error as below: Traceback (most recent call last): File “/chipseq/3.fastqc/chilin/software/mdseqpos/bin/MDSeqPos.py”, line 421, in <module> main() File “/chipseq/3.fastqc/chilin/software/mdseqpos/bin/MDSeqPos.py”, line 385, in…
Snakemake issue with wrappers
I have issues when running a wrapper of BWA mem with Snakemake. The error message “No module named ‘snakemake_wrapper_utils’” appear (see below). However, when checking if the package is installed in Python, I found the following: import snakemake_wrapper_utils print(snakemake_wrapper_utils.__version__) 0.1.0 Did anyone have this problem? Would you know why there…
Epigenetic regulation during cancer transitions across 11 tumour types
Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…
How to extract specific region from multiple bam files and merge the outputs into single bam?
How to extract specific region from multiple bam files and merge the outputs into single bam? 0 I have more than 50 bam files and wanted to extract the reads from a region from all those bam files and merge the outputs into a single bam. I’m using samtools for…
[slurm-users] multiple srun commands in the same SLURM script
Here is my SLURM script: #!/bin/bash #SBATCH –job-name=”gpu_test” #SBATCH –output=gpu_test_%j.log # Standard output and error log #SBATCH –account=berceanu_a+ #SBATCH –partition=gpu #SBATCH –cpus-per-task=1 #SBATCH –mem-per-cpu=31200m # Reserve 32 GB of RAM per core #SBATCH –time=12:00:00 # Max allowed job runtime #SBATCH –gres=gpu:16 # Allocate four GPUs export SLURM_EXACT=1 srun –mpi=pmi2 -n 1 –gpus-per-node 1 python gpu_test.py & srun…
Ivy Farm Technologies hiring Senior Bioinformatician in Oxford, England, United Kingdom
The insights we’ll get using bioinformatics will be essential in fulfilling Ivy Farm’s mission to create the world’s best guiltfree and sustainable meat. And that’s why we’re hiring our first permanent Senior Bioinformatician, as part of our humble community of some 50 scientists; a team where you can make a…
jobs – ‘–dependendy=aftercorr:Submitted’ slurm option unrecognized
I have a script to run in slurm. The script works with job-array aftercorr, or at least that’s what I want it to do. Basically it runs the first Job-array without any issue, however, it does not recognize the command –dependendy=aftercorr. I am quite new with slurm, could you please…
How to install or uninstall “votca-tutorials” on Kali Linux ?
1. Install votca-tutorials package This guide let you learn how to install votca-tutorials package: sudo apt install votca-tutorials Copy 2. Uninstall / Remove votca-tutorials package Learn how to uninstall votca-tutorials package: sudo apt remove votca-tutorials Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of votca-tutorials package Package:…
FASTA File Concatenation
FASTA File Concatenation 0 Hello, I am a beginner in bioinformatics and I am currently doing gene mapping of viral RNA sequences. And I have the following question: How can I concatenate several FASTA files without losing the ID of each one? These files are located in different folders. I…