Tag: bash

Hi Uri, Thank you for the patch! Yet something to improve: [auto build test ERROR on staging/staging-testing] url: github.com/intel-lab-lkp/linux/commits/Uri-Arev/staging-fbtft-fix-checkpatch-pl-struct-should-normally-be-const/20220520-012948 base: git.kernel.org/pub/scm/linux/kernel/git/gregkh/staging.git 4d0cc9e0e53e9946d7b8dc58279c62dfa7a2191b config: arm64-randconfig-r011-20220519 (download.01.org/0day-ci/archive/20220520/202205200821.nJQ0IfFt-lkp@xxxxxxxxx/config) compiler: clang version 15.0.0 (github.com/llvm/llvm-project e00cbbec06c08dc616a0d52a20f678b8fbd4e304) reproduce (this is a W=1 build): wget raw.githubusercontent.com/intel/lkp-tests/master/sbin/make.cross -O ~/bin/make.cross chmod +x ~/bin/make.cross # install arm64 cross compiling tool…

Given two separate wdl arrays, my command section will do some modifications to each array and place the output into two separate bash arrays. Finally, I want to output the two separate bash arrays in the output section of the wdl task to be used in other tasks within the…

Most popular tags python javascript html java css reactjs c# php r sql arrays pandas c++ android jquery DataFrame python-3.x node.js c mysql list flutter JSON ios typescript sql-server swift string angular regex laravel excel django dictionary dart bash numpy postgresql loops oracle vba linux angularjs function for-loop spring spring-boot…

<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg&#8221; –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg&#8221; width=”60%”></img></a> # What is nf-core\? [Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class=”fa fa-twitter” aria-hidden=”true”></i>@gau](https://twitter.com/gau/) | [<i class=”fa fa-github” aria-hidden=”true”></i>@maxulysse](https://github.com/maxulysse/) [Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/) Sweden — ## Overview – 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/) – 🧬 [NGI](https://ngisweden.scilifelab.se/) – 🍬 [Nextflow](https://www.nextflow.io/) – 🧙 [nf-core](https://nf-co.re/) — ##…

Details Posted: 03-May-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Provides technical expertise in the selection, validation, and implementation of the appropriate internal and external data analytic and bioinformatic solutions needed to analyze specimens, process and integrate data, and…

chinmay5 (Chinmay5) April 29, 2022, 12:48pm #1 Sorry for the naive question but I am confused about the integration of distributed training in a slurm cluster. Do we need to explicitly call the distributed.launch when invoking the python script or is this taken care of automatically? In other words, is…

How to remove everything before a specific character in a column 2 I have a big tsv file with 4 columns in the following format: ERR435678 contig_1 /home/results/file1.txt /home/results/file1.txt ERR435678 contig_2 /home/results/file2.txt /home/results/file2.txt ERR435678 contig_3 /home/results/file3.txt /home/results/file3.txt How can I manipulate only the elements of the third column in a…

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

** Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing ** The NeuroGenomics and Informatics (NGI) Center lead by Dr. Carlos Cruchaga at Washington University School of Medicine is recruiting a Bioinformatics Scientist to work on Whole Genome and Whole Exome Sequencing. We are seeking an experienced, self-motivated, self-driven scientist…

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

Hi, I have an issue with pam_slurm_adopt when I moved from 21.08.5 to 21.08.6. It no longer works. When I log straight to the node with root account : Apr 8 19:06:49 magi46 pam_slurm_adopt[20400]: Ignoring root user Apr 8 19:06:49 magi46 sshd[20400]: Accepted publickey for root from 172.16.0.3 port 50884 ssh2:…

Personalis, Inc. is a leader in advanced cancer genomics for enabling the next generation of precision cancer therapies and diagnostics. The Personalis NeXT Platform® is designed to adapt to the complex and evolving understanding of cancer, providing its biopharmaceutical customers and clinicians with information on all of the approximately 20,000 human genes,…

I had a similar issue with Slurm Version 20.11.7I had a virtual environment created with the systems python3, which was Python 3.6.8When activating the venv on the logging-node calling an installed module worked fine, but from within the following shell script for example it did not and resulted in ModuleNotFound:…

This won’t work. What happens when you run sbatch myscript.sh is that slurm parses the script for those special #SBATCH lines, generates a job record, stores the batch script somewhere. The batch script is executed only later when the job runs. So you need to structure you workflow in a…

LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…

You + Helix Helix is a place where innovators and doers gather in order to drive significant progress in population genomics. We have come together to work at the intersection of clinical care, research, and genomics.   If you’re excited by the idea of making a meaningful impact and joining a…

Hey, I have a script that extract features from a large fasta file (1767 MB) using biopython. I am sending it as a bash job via ssh remote server. The job is running for two days now.. Is there a way to optimize my script? I think maybe the problem…

Hi all, I wanted to ask whether anyone has ever come across the problem I have. In my project we need to run few tools on multiple genes. I have written python script that chooses right genes, runs tools and then aggregates results. The problem I have is that after…

GROMACS version:2022+cp2k interface basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?Thank you in advance I am taking that error : Command line:gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt Compiled SIMD: AVX_256, but for this host/run AVX2_256 might…

I’m trying to run an array job with the configuration below. My nodes have 4 cpu, but the scheduler is only allocating two jobs per node. How can I get it to allocate four jobs per node? When I add #SBATCH –ntasks-per-node=4, it’s even worse – I get one task…

Hello, I’m trying to setup my first CycleCloud cluster, but I keep getting error in the initialization phase. In particular, it complains about not finding nodes for “nodearray hpc”. The full error message: CycleCloud Version: 8.2.0-1616 Cluster: Test2 (version 8.2.x) ============================== Status: Error [Software Configuration] (retrying) Start Time: 2022-03-13T17:31:29.377Z Description:…

Tutorial to learn the steps involve in the installation of Jupyter Notebook on Debian 11 Bullseye using command terminal. What is Jupyter Notebook? The Jupyter Project is a non-profit initiative that aims to develop and provide open-source software and open standards for interactive work. One of the most famous products…

I want to run it from a bash script but it is not accepting string input with spaces. It works with single words or hyphenated words. However the python command is correct and is working fine when I am running it directly from terminal. commands.txt python generate.py -p “Flower girl”…

The protocol presented here describes a complete pipeline to analyze RNA-sequencing transcriptome data from raw reads to functional analysis, including quality control and preprocessing steps to advanced statistical analytical approaches. Welcome to the protocol of high-throughput transcriptome analysis for investigating host-pathogen interactions. This protocol is divided in the following steps….

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…

Job description A Postdoctoral Research Associate (PDRA) – Computational biology position is available in the Centre for Gene Therapy and Regenerative Medicine, King’s College London. This is an exciting opportunity to join an interdisciplinary team of scientists working on a Wellcome Trust funded research programme aimed at studying the mammalian…

container_name: omnisciserver image: omnisci/omnisci-ee-cuda:v5.9.0 – /var/lib/omnisci:/omnisci-storage – /var/lib/omnisci/data/omnisci_import/jhub_omnisci_dropbox:/jhub_omnisci_dropbox # If using binary encryption, uncomment the below line to override the default # command that uses startomnisci, noting that you must have an existing OmniSci # data directory and run initdb before making this change. # command: /bin/bash -c “/omnisci/bin/omnisci_web_server –config…

When I tried to use samtools to split a bam file based on different chromosomes, I used this command: samtools view input.bam -b chr21 | chr21.bam However, I get error messages like this: -bash: chr21.bam: command not found [W::hts_idx_load3] The index file is older than the data file: input.bam.bai How…

I am using slurm to submit jobs to the university supercomputer. My matlab function has one parameter: function test(variable_1) and my slurm file is (I am not sure if it is correct. I know how to define the value of the parameter in the slurm file, but I would like…

Hi threre, I was testing the MPS on Slurm19.05.5 with 4 A100 in compute node. In my opinion, the 4 A100 will be used.  But I found that only the first GPU was used. like below: the job script: #!/bin/bash #SBATCH -J date #SBATCH -p NVIDIAA100-PCIE-40GB #SBATCH -n 1 #SBATCH…

Example: how to create temporary folders in a slurm script hpc script #!/bin/bash #SBATCH –job-name=sand_min #SBATCH -N 1 #SBATCH -n 1 ##SBATCH –gres=gpu:1 #SBATCH –partition=shortq7 #SBATCH –exclude=node[007,041,046],nodeamd[010-014],nodeeng[009-010],nodegpu001,nodenviv[100001-100002,100004-100015] #SBATCH –mail-type=ALL #SBATCH –time=6:00:00 echo “NODE NAMES = “$SLURM_NODELIST echo “CUDA_VISIBLE_DEVICES = “$CUDA_VISIBLE_DEVICES date # # Load the necessary modules, etc… # module…

I am an undergraduate who’ll graduate in 2 years. I think I want to get a PhD in computational chemistry (although not sure where, might want to study in the US), and I’ve had around 5 months of research experience in computational chemistry in an research internship. However, I’ve only…

I want to use snakemake to do bowtie2 mapping of split read files to a reference genome, and I’d like that rule to be integrated in the general workflow. For that purpose, I first defined a rule to create a bowtie index rule build_bowtie_index: input: referenceGenomeFasta output: expand(“{name}.{index}.bt2”, index=range(1,5), name…

<p><strong>Want to participate to the outstanding new area of agro-genomics ? To put into the practice how the genetic diversity and genome-assisted breeding in crops contribute to provide healthy and high quality food in a sustainable way to humankind? Strong in bioinformatics and interested in working with very large datasets…

find_te_ins is designed to find Transposon Element (TE) insertions using long reads (nanopore), by alignment directly. (minimap2) Install $ git clone github.com/bakerwm/find_te_ins.git&#13; $ cd find_te_ins Change the following variables upon your condition: genome_fa and te_fa in line-10 and line-11; $ bash run_pipe.sh run_pipe.sh Prerequisite minimap2 – 2.17-r974-dirty, align long…

Hello everybody, I have a question quite different about similar topic addressed on: Post not found I tried Paul’s bash script in the web indicated above (fastq_lane_merging.sh) adapting to my filename organization data being: #!/bin/bash for i in $(find ./ -type f -name “*.fastq.gz” | while read F; do basename…

It is certainly possible the ‘error’ is the input file 2. However, both try: routines are weird and if this is the real code it would fall over. Something isn’t quite right however, which I’ll touch on at the end. What the code is supposed to say is: try: load…

For a slurm job, the environment variable $SLURM_JOB_NUM_NODES gives the number of nodes requested. Is there a similar variable that gives the run time requested? I couldn’t find the answer and I have tried $SLURM_JOB_TIME, $SLURM_TIME and $SLURM_SUBMIT_TIME, but none of these works. Ultimate goal is to let the script…

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

Your message dated Sat, 22 Jan 2022 21:52:05 +0100 with message-id <f98ce279-5828-d2b5-8b7c-88287a3ab…@debian.org> and subject line Re: Bug#997845: bug 997845 has caused the Debian Bug report #997845, regarding growlight: autopkgtest regression: log repeats until it times out to be marked as done. This means that you claim that the problem has…

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

Running test job with srun works: wayneh@login:~$ srun -G16 -p v100 /home/wayne.hendricks/job.sh 179851 Linux dgx1-1 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 179851 Linux dgx1-2 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Submitting the same with sbatch does…

JOB OVERVIEW: The main role of this position is project coordination, timeline management, and requirement gathering. To this end, the Bioinformatics Specialist analyzes and refines business and user requirements, and coordinates with developers to facilitate bioinformatics solutions through the entire SDLC, from discovery, design, development, and validation. The Bioinformatics Specialist…

The role This is a full time Research Associate position based in the Donoghue, Pisani and Williams Labs of the Palaeobiology research group in the Schools of Earth and Biological Sciences, located in the Life Sciences Building. The role is funded through to the end of February 2023 on a…

Running Jobs on Titan Table of Contents Titan’s Job Scheduler – SLURM Documentation Translating to SLURM commands from other workload managers Basic SLURM Commands squeue sinfo scontrol sbatch scancel Titan’s Environment Module System – LMOD Listing all available modules on Titan Loading a module into your environment Listing all modules…

SUMMARY We are seeking a talented and motivated Senior Bioinformatics Scientist who will be an integral member of the Sequencing team contributing to the support and development of ground-breaking next-generation sequencing (NGS) products. As a member of Roche’s Sequencing and Life Science (SLS), Scientific Support and Applications team, you will…

7 1 4 genbank,MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from…

I want to run three instances of GROMACS mdrun on three different nodes. I have three temperatures 200,220 and 240 K and I want to run 200 K simulation on node 1, 220 K simulation on node 2 and 240 K simulation on node 3. I need to do all…

ANGSD-wrapper prefers the regions file to be formatted as chr_name:start_position-end_position. Below, we will create a toy BED file as an example and show how we can go from BED file format to ANGSD-wrapper’s regions file format. Create toy BED file Let’s create an example BED file. You can run the…

Github repository  02-04 February 2022  SciLifeLab Solna, Tomtebodavägen 23b, Stockholm, Sweden This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 45 hours, including the online lectures (15 hours)…

A click-based command line interface for QIIME 2. Installation and getting help Visit qiime2.org to learn more about q2cli and the QIIME 2 project. Enabling tab completion Bash To enable tab completion in Bash, run the following command or add it to your .bashrc/.bash_profile: ZSH To enable tab completion in…

In the dependency checking script, the bash builtin command -v is used for checking whether BioPerl is installed. However, this command will always succeed as long as Perl is installed, as it does not execute the command. Consider changing e.g., github.com/abhijeetsingh1704/AcetoScan/blob/70f0428e4fffbff6af17ce5a83b26ce24abd0f29/AcetoScan_MacOS/scripts/AcetoScan_software_check.sh#L48 into if ! perl -MBio::SeqIO -e ‘printf “%vdn”, $Bio::SeqIO::VERSION,…

The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If you need assistance or have questions regarding the application process, please contact…

DepartmentDepartment of Histology and Embryology  – Faculty of MedicineDeadline 28 Feb 2022Start date Jully 2022Job type full-timeJob field Science and research Medical Faculty of Masaryk University, Brno, Czech Republic, invites excellent scientists to apply for Postdoc position in Bioinformatics in Stem Cell Neurobiology   Description: The Department of Histology and Embryology is…

Hi, I was relatively recently told about slurm, however, as usual, I did not have time to go into details and had to quickly write scripts and subsample them “to not waste time”. Well, since recently, constantly goes out of timeout and scripts “do not finish” as simply not enough…

$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi (base) bash-4.2$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi [+] /opt/intel/cmake (external cmake-3.20.0-3teotjsa6webcsazofydfkk2v3pn2hb6) [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/alsa-lib-1.2.3.2-yctbppr2tcdayclbt32xjgagmmwbct2v [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/libiconv-1.16-ilxedtsoqggtmtbrjxehh6ojznmtdni3 [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/yasm-1.3.0-7y4fvxshqkmikii3cvelccaiajj4dboc [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/zlib-1.2.11-k24vg36ubsrvwfgrdipndmpqn4eo5jq7 ==>…

Department Department of Histology and Embryology – Faculty of Medicine Deadline 28 Feb 2022 Start date Jully 2022 Job type full-time Job field Science and research Medical Faculty of Masaryk University, Brno, Czech Republic, invites excellent scientists to apply for Postdoc position in Bioinformatics in Stem Cell Neurobiology   Description: The Department of…

CSIRO Postdoctoral Fellowship in Pathogen Genomics and Bioinformatics – Job posted on PostdocJobs.com CONNECT WITH US :    CSIRO Postdoctoral Fellowship in Pathogen Genomics and Bioinformatics Job Number: Date Posted: Dec 23, 2021 Application Deadline: Open Until Filled Job Description Acknowledgment of Country   CSIRO acknowledges the Traditional Owners of the…

We are hiring a bioinformatics specialist interested in developing a clinical decision support for implementation of genetics in clinical settings. The person will be responsible of building analytical pipelines forpatients’ genomic, demographic, and individual data, as well as working with our senior software engineer tointegrate our knowledge base with existing…

I am currently partnered with a large biotech that is based in the San Francisco Bay Area. They are seeking a Bioinformatics Associate to join the team researching human genetics. This position would report directly into the Scientists and will be responsible for analyzing genome scale data through in-depth longitudinal…

Hello all, I am new to JupyterHub and trying to integrate it with LTI as an authenticator. We have our own course provider platform like edX and Canvas so we are doing custom configuration in the jupyterhub_config.py. However, I am partially successful in doing so because when I launch my…

[*] I have been trying to follow the GATK Best Practice Workflow for ‘Data pre-processing for variant discovery’ (gatk.broadinstitute.org/hc/en-us/articles/360035535912). This has all been run on Windows Subsystem for Linux 2 on the Bash shell. I started off with FASTQ files from IGSR (www.internationalgenome.org/data-portal) and performed alignment with Bowtie2 (instead of…

This blog post was contributed by Ankit Sethia, PhD, and Timothy Harkins, PhD, at NVIDIA Parabricks, and Olivia Choudhury, PhD,  Sujaya Srinivasan, and Aniket Deshpande at AWS. This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It…

I’m a beginner k8s user, I’m trying to recreate this docker-compose SLURM cluster with kubernetes. First I converted the docker-compose.yaml file into k8s yaml file in order to use kubectl apply -f . to create pods and services. I’m using minikube on my computer with the none driver (like this…

University of Calgary Home Prospective Students Current Students Alumni Community Faculty & Staff Home Information for Candidates Opportunities by Type Opportunities by Faculty/Unit Home Information for Candidates Opportunities by Type Opportunities by Faculty/Unit Share this Job: Postdoctoral Scholar in Microbiology and Bioinformatics, Cumming School of Medicine Job ID: 24643 Updated:…

Blast command line pipeline not working 0 Hello, I am running now a local blast pipeline using MacOs. The goal here is to take interval of the 5 best hits and then extract the SNP variants from multiple vcf.gz files. But I am facing an error which I cannot solve….

snakemake truncating shell codes 0 I’m trying to change the chromosome number notation from [0-9XY] to Chr[0-9XY] using the samtools reheader in the shell command of the snakemake. rule rename: input: os.path.join(config[“input”], “{sample}.bam”), output: os.path.join(config[“output”], “new_sample/{sample}_chr.bam”) log: os.path.join(config[“log”], “samtools/{sample}”) shell: “samtools view -H {input} | sed -e ‘s/SN:([0-9XY]*)/SN:chr1/’ -e ‘s/SN:MT/SN:chrM/’…

Hello, I am trying running an assembly with MaSuRCa but am getting an error at the step: “Computing super reads from PE”. here’s the output with the error: [xxxx@vic Bovidae]$ cd Assembly_test/ [xxxx@vic Assembly_test]$ ls assemble.sh guillaumeKUnitigsAtLeast32bases_all.fasta.tmp masurca_assembly.o4302352 meanAndStdevByPrefix.pe.txt pe_data.tmp quorum_mer_db.jf work1 environment.sh guillaumeKUnitigsAtLeast32bases_all.jump.fasta masurca_config.txt pe.cor.fa pe.renamed.fastq super1.err ESTIMATED_GENOME_SIZE.txt masurca_assembly.e4302352…

Problem : ( Scroll to solution ) I am running multiple array jobs using slurm. For a given array job id, let’s say 885881, I want to list the count of failed and completed number of jobs. Something like this: Input: <some-command> -j 885881 Output: Let’s say we have 200…

Hi Lucas, got a weird one for you. If I change the caller from hapotypecaller to freebayes, I get the error below. It’s doubly strange because it seems to occur well before freebayes would be used in the pipeline. [Sat Dec 11 11:13:02 2021] rule samtools_stats: input: dedup/111D03-1.bam output: qc/samtools-stats/111D03-1.txt…

Easy Swagger UI for your Flask API Flasgger is a Flask extension to extract OpenAPI-Specification from all Flask views registered in your API. Flasgger also comes with SwaggerUI embedded so you can access localhost:5000/apidocs and visualize and interact with your API resources. Flasgger also provides validation of the incoming data,…

We are seeking a postdoctoral bioinformatician in the Department ofRenal Medicine, Centre for Genetics and Genomics (www.ucl.ac.uk/nephrology/research/centre-genetics-and-genomics).  Working with clinical and non-clinical colleagues, the post holder will design, develop and perform analyses of large-scale genomic data (eg from the 100,000 Genomes Project) to answer clinically relevant questions about the causes…

The role This is a full time Research Associate position based in the Donoghue, Pisani and Williams Labs of the Palaeobiology research group in the Schools of Earth and Biological Sciences, located in the Life Sciences Building. The role is funded through to the end of July 2024 on a…

I’m using the software plink2 (www.cog-genomics.org/plink/2.0/) and I’m trying to iterate over 3 variables. This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file. The idea is to iterate over…

Director of Bioinformatics Research Location:  Remote Status:  Full-time ExemptReports to:  VP Bioinformatics & BiostatisticsDirect Reports:  Build and lead a team consisting of bioinformatics research scientists that support internal business development client engagements, as well as, external academic partner research projects and biopharma sponsored bioinformatics services Who we are M2GEN is…

Job Description Summary We are looking for a highly driven and talented software engineer to join the DRAGEN verification Team. The team focuses on developing tools to analyze large genomic datasets, setting up a CI/CD and automated testing infrastructure and improving the databases and websites that we use for the…

Question: How do I view data in pymol via Ipymol for visualisation in a Jupyter notebook? 1 I am analysing protein data using Python programming language and Jupyter notebook. In the Terminal I have put an alias in a hidden file on the home directory entitled .bash_profile, in order to…

Hi, This is my first post. :-) Where can I find the ‘smap’ gui for Cenos7 ? I can’t seem to locate the package that provides this. I didn’t get any results with ‘yum whatprovides smap’. In contrast, ‘yum whatprovides sview’ gives me ‘slurm-gui’. Shouldn’t smap be part of…

Are you wondering how you can leave your mark and impact the betterment of humanity? Through collaborative innovation, Illumina is fueling groundbreaking advancements in oncology, reproductive health, genetic disease, microbiology, agriculture, forensic science, and beyond.   Position Summary: We are looking for a highly driven and talented bioinformatics engineer or software…

Running SortMeRNA on Multiple Files 0 Hi all, I am VERY new to SortMeRNA (I’m a PhD student taking a bioinformatics class that has been very poorly taught). I have 27 paired samples for a total of 54 samples named like this: SRR13711719_1_val_1.fq SRR13711719_2_val_2.fq. So the format is _1_val_1.fq and…

install pytorch in jetson nano Done! Getting Started with Jetson Nano In this tutorial, you will learn how to set up the NVIDIA ® Jetson ™ Nano and install everything you need to use the full power of the tiny embedded board. Git – Version Contol…

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

We are currently searching for a Bioinformatics Scientist to provide support services to satisfy the overall operational objectives of the National Human Genome Research Institute (NHGRI), The primary objective is to provide services and deliverables through performance of support services. This opportunity is full-time, and it is on site in…

bash script not a valid identifier 2 I am trying to run bash script, but it gives this error ( `$fastq’: not a valid identifier). #!/bin/bash database=”kraken2_database” fastq=”fastq_dir” for $fastq in $(ls *_R1.fastq.gz | sed ‘s/_R1.fastq.gz//’) do kraken2 –db $database –threads 8 –memory-mapping –use-names –confidence 0.1 –report taxonomy_reads/${fastq}_kraken2.tax –paired ${fastq}_R1.fastq.gz…

Bash script to help with print Name of reads that only have query subsequence or its verse complement and position of first occurance of this subsequence in read and output of all this in tab separat 0 Create bash script that receives name of fastq fastq file and query subsequence…

query sequence is input sequence or its reverse complement 0 >sp|O14920.1|IKKB_HUMAN RecName: Full=Inhibitor of nuclear factor kappa-B kinase subunit beta; Short=I-kappa-B-kinase beta; Short=IKK-B; Short=IKK-beta; Short=IkBKB; AltName: Full=I-kappa-B kinase 2; Short=IKK2; AltName: Full=Nuclear factor NF-kappa-B inhibitor kinase beta; Short=NFKBIKB; AltName: Full=Serine/threonine protein kinase IKBKB MSWSPSLTTQTCGAWEMKERLGTGGFGNVIRWHNQETGEQIAIKQCRQELSPRNRERWCLEIQIMRRLTH PNVVAARDVPEGMQNLAPNDLPLLAMEYCQGGDLRKYLNQFENCCGLREGAILTLLSDIASALRYLHENR IIHRDLKPENIVLQQGEQRLIHKIIDLGYAKELDQGSLCTSFVGTLQYLAPELLEQQKYTVTVDYWSFGT LAFECITGFRPFLPNWQPVQWHSKVRQKSEVDIVVSEDLNGTVKFSSSLPYPNNLNSVLAERLEKWLQLM LMWHPRQRGTDPTYGPNGCFKALDDILNLKLVHILNMVTGTIHTYPVTEDESLQSLKARIQQDTGIPEED QELLQEAGLALIPDKPATQCISDGKLNEGHTLDMDLVFLFDNSKITYETQISPRPQPESVSCILQEPKRN LAFFQLRKVWGQVWHSIQTLKEDCNRLQQGQRAAMMNLLRNNSCLSKMKNSMASMSQQLKAKLDFFKTSI…

Socat not found in the /usr/bin folder in MacOS 0 I have installed socat using brew install socat on my Mac and then tried to connect to the cluster. But it does not connect. It throws the following error message: zsh:1: no such file or directory: /usr/bin/socat kex_exchange_identification: Connection closed…

Source: ptl Version: 2.3.0-1 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of ptl the autopkgtest of ptl fails in testing when that autopkgtest is run with the binary packages of ptl from unstable. It passes when run with only packages from testing. In…

how to do basic statistics for bam files 1 Hi Bistar teams, I have unpaired Exom-seq data. I did the quality control and alignment. Now my files are in bam format and I would like to do some basic statistics like fragment size, coverages, mismatches, Gaps , duplicates etc ….

This repository contains a PyTorch implementation of the Pose Residual Network (PRN) presented in our ECCV 2018 paper: Muhammed Kocabas, Salih Karagoz, Emre Akbas. MultiPoseNet: Fast Multi-Person Pose Estimation using Pose Residual Network. In ECCV, 2018. arxiv PRN is described in Section 3.2 of the paper. Getting Started We have…

How to count fastq reads 9 ‘wc’ is faster than awk #yourfile.fastq echo $(cat yourfile.fastq|wc -l)/4|bc #yourfile.fastq.gz echo $(zcat yourfile.fastq.gz|wc -l)/4|bc for fasta files: grep -c “^>” file.fasta for fastq files: grep -c “^@” file.fastq for fastq files: awk ‘{s++}END{print s/4}’ file.fastq Here is the fancy script in bash: #!/bin/bash…

Results change using ete3 0 Hi all, i’m running ete3 evol to detect positive selection in a list of orthologs. I realized something strange, I get different results if I run with lots of orthologs vs. just a couple. This is strange because I’m running it using a bash loop…

Bioinformatics is branch of data science that merges biology, computer science and statistics to solve biological problems. It involves taking biological data, such as sequence data or metabolomics, and using an informatics approach. For this week’s column, I interviewed Kelsey Florek, a senior genomics and data scientist at the Wisconsin State…

Job:Ph.D. Bioinformatics Specialist (Long-Term Contract) – NIH/NIEHS – Research Triangle Park, NC 0 Kelly Government Solutions is a strategic supplier and business partner to the federal government and its key suppliers. We are seeking an individual to work as a Ph.D. Bioinformatics Specialist at the National Institutes of Health in…

Getting errors trying to run rmats 1 Hi, I am trying to use rmats for splice variation analysis through ssh using slurm after loading rmats module, these are commands that I tried and errors they produced rmats –s1 $PWD/control.txt –s2 $PWD/pdac.txt –gtf mm10/mm10.refGene.gtf Python programming language version 3.6.8 loaded. GNU…

Run multiple times samtools and sed for a big number of bam files in folder 1 How can we execute the following commands with bash for a big amount of bam files in a folder samtools view -H in.bam > header.sam sed -i s/SN:/SN:chr/ header.sam sed -i s/SN:chrMT/SN:chrM/ header.sam samtools…

This page aims to allow the user to submit a job using the Slurm resource manager and scheduler which is responsible for allocating resources. Resource intensive applications should always be run via Slurm. It is assumed that you are already familiar with Slurm. If not, you can read the Slurm…

Pylomin (PYtorch LOw-Memory INference) is a deep learning optimization library for low-memory inferencing in PyTorch. Motivation The scale of deep learning models has grown exponentially in recent years, which has greatly increased the difficulty of product deployment. Image source: Microsoft Research Blog The goal of this library is to enable…

Position as Postdoctoral Research Fellow available at the Department of Biosciences. The appointment is a fulltime position and is made for a period of three years, and devoted to carrying out a project entitled URGE-3D, funded by the Norwegian Research Council. No one can be appointed for more than one…

Fq file to table 1 Hello all! I am looking for different ways to convert fq file to tabular format. I mean from this: @name AGTC some_text HHJH to this: @some_name AGTC + HHHH every four strings in one row How can I do it with Python/R and in bash/awk?…