Tag: bash

bash: /snp-frequency-diff.pl: Permiso denegado

bash: /snp-frequency-diff.pl: Permiso denegado 1 Cordial greetings. Trust you are all well. I would love to have your help please. Im trying to execute this command: perl </home/anderson/bioinformatica/Ensayo_poolseq/popoolation2_1201>/snp-frequency-diff.pl –input pools_all.sync –output-prefix pools_all_delta –min-count 2 –min-coverage 5 –max-coverage 32,39,32,31 But I keep getting this error: bash: /snp-frequency-diff.pl: Permiso denegado I have…

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PacBio hiring Scientist II, Field Applications Bioinformatics Support in Georgia

PacBio’s single molecule, real-time DNA sequencing platforms are transforming the future of medicine, basic science, and agriculture. Our mission is to transform the way humankind acquires, processes, and interprets data from living systems through innovative tools for biological research. To extend our team, we are looking for a bioinformatics field…

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nVidia 525 + Cuda 11.8 + Python 3.10 + pyTorch GPU Docker image

It is a base environment for torch with GPU support (including 3090Ti!) that can be used for working with AI models. This image requires nvidia-driver-525 and nvidia-docker2 installed on host. It needs 30GB on disk! Dockerfile FROM nvidia/cuda:11.8.0-devel-ubuntu22.04 ENV PYTHONUNBUFFERED=1 # SYSTEM RUN apt-get update –yes –quiet && DEBIAN_FRONTEND=noninteractive apt-get…

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email – Troubleshooting slurm e-mail settings

I am trying to setup a slurm installation and I have advanced towards the e-mail stage. So far I do not receive any mails. I have a working setup using msmtp-mta and msmtp. When I batch a script the slurmctld log shows email msg to **@**: Slurm Job_id=73 Name=example_script.sh Began,…

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sagemath package currently absent from bookworm

Successfully built Sagemath 9.6 on Bookworm (“apt dist-upgrade”-ed as of 25 January 2023) using the following script. (It seems to have partially built 9.7, and that build might be fixable by an interested someone.) The important piece seems to be ./configure –without-system-gcc –without-system-pari –without-system-singular to avoid the version conflicts reported…

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Bioinformatics Programmerother related Employment listings

Quick Apply Full-time 2 hours ago Full Job Description Job Summary Blue Marble Space Institute for Science (bmsis.org) is seeking a mid-level or senior Bioinformatics Programmer with experience in analyzing large-scale epigenomics, genomics, transcriptomics, proteomics, and metabolomics data to support the GeneLab Project at NASA Ames Research Center (genelab.nasa.gov/).The Bioinformatics…

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Mugsy not working

Mugsy not working 0 hello, I have installed mugsy using bioconda and it was installed without any error. Now I can see mugsy in my enviroment but whenever I do source activate mugsy it says “-bash: activate: No such file or directory”, but when I do conda activate mugsy, it…

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Postdoctoral Research Fellow – Epigenomics/Bioinformatics in Cincinnati, OH for Cincinnati Children’s Hospital Medical Center

Details Posted: 26-Jan-23 Location: Cincinnati, Ohio Salary: Open Categories: Academic / Research Description A computational postdoctoral position in bioinformatics and epigenomics (computational/experimental) is available in Dr. Yaping Liu’s lab in the Division of Human Genetics. One of the research directions in Dr. Liu’s group is to study single-cell multi-omics data…

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Running command in docker container results in directly shutting down the docker container

Im currently struggling to run a container and execute a command within this container.I’m trying to use NanoSNP (github.com/huangnengCSU/NanoSNP), which is an image available from dockerhub. After fulling this docker, the following command would be sufficient to run the the container: docker run \ -v “${INPUT_DIR}”:”${INPUT_DIR}” \ -v “${OUTPUT_DIR}”:”${OUTPUT_DIR}” \…

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Sr. Bioinformatics Scientist Job – Karkidi

Job Description Catalytic is looking for a proactive, driven, and talented Bioinformatics Engineer who is motivated by the challenge to deliver highly available, secure, and scalable enterprise bioinformatics software. This mid-level position is a key member of our engineering team who will enable us to continuously deliver quality bioinformatics and…

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Bedtools give different output

Bedtools give different output 1 Hello, I have converted a gene annotation file using bedtools and used another bed file containing regions under selective sweeps. My goal is the find how many genes are inside the interval of the selective sweep regions. I have a converted gene annotation file called…

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cluster computing – Is it possible to execute post-script after slurm job execution?

The short answer is that there is no such option in Slurm. If post-script.sh can run on a compute node, the best option would be if it is short: to add it at the end of the job submission script if it is long; to submit it in its own…

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Bug#1029556: espeak-ng: autopkgtest regression

Source: espeak-ng Version: 1.51+dfsg-9 Severity: serious tags: patch Hello, autopkgtests started to fail I presume since llvm-default change. To fix, you need to depend on clang-rt when you use fsanitize=fuzzer) clang++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/tmp/autopkgtest-lxc.4x6n726o/downtmp/build.8AY/src=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tests/dummy.o tests/dummy.cpp /bin/bash ./libtool –tag=CXX –mode=link clang++…

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Setup And Use JupyterHub (TLJH) On AWS EC2

[embedded content][embedded content]Video Tutorial   A Jupyter Notebook is an open source application used throughout academia and industry. The interactive computing application consists of cells that render explanatory text written using the Markdown syntax and cells that execute programming code (including Python, R, Julia, and Scala). This means that notebooks…

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cluster computing – How to show the status of all job steps defined in a sbatch script, including those not yet created due to resource contention

I’m using SLURM sbatch to launch a bunch of parallel tasks in a cluster. The total amount of cores that I need to run all tasks in parallel exceeds the total amount of cores that my sbatch script asks for, so some job steps won’t run until others have finished….

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Esox Biologics hiring Head of Bioinformatics in London, England, United Kingdom

Esox Biologics is curating the UK’s most comprehensive aquatic pathogen database. Our next-generation sequencing platform is revealing the total microbial landscape across aquatic farms by genotyping the unculturable majority of microorganisms through de novo whole-genome sequencing. You will join a team that works alongside farmers, veterinarians and government bodies, to assist in the…

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Python for loop of sbatch submitted to SLURM only runs for one iteration, help? : SLURM

I am submitting a Python script to my school’s HPC and having difficulty. The for loop runs fine on the login node, but as soon as I submit it to the HPC, it only will run the first iteration and then stops. Does anyone know how to remedy this? Does…

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Sr. Scientist, Bioinformatics jobs | Hydrogen Group

Summary The ideal candidate will collaborate with biologists and software engineers to develop and improve bioinformatics algorithms for characterizing solid tumors, immuno-oncological targets, and tumor targeting therapies for cancer. This position will report into the Director, Bioinformatics. Responsibilities Design, develop, and apply computational and statistical methods to model complex biological…

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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science Job in Nevada, Molecular Biology Career, Full Time Jobs in University of Nevada, Reno

Postdoctoral Scholar – Bioinformatics/Biomedical Data Science R0127900 University of Nevada, Reno – Main Campus 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…

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DevSecOps Engineer (Contract) | EU-Startups

To cure diseases, you need data. Inspire People are partnering with Lifebit, a market leader in connected data to bring precision medicine to Governments and world-leading pharma institutions and, to meet client demand and have opportunities for contract DevSecOps Engineers who are proactive and collaborative, with skills using Terraform, Kubernetes,…

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Redirect Stdout From twoBitToFa in Bash

Hi there, I’ve been going round and round trying to figure out a way to redirect stdout to use with seqtk. I’ve read many posts that are similar, so I am confident the answer is out there, but since I’m having such a hard time I figured I might as…

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Post-doctoral Fellow in Bioinformatics and Statistical Analysis job with THE UNIVERSITY OF HONG KONG

Work type: Full-time Department: School of Biological Sciences (26000) Categories: Academic-related Staff Applications are invited for appointment as Post-doctoral Fellow in Bioinformatics and Statistical Analysis of Molecular Data in the School of Biological Sciences (Ref.: 518683), to commence in January 2023 or as soon as possible thereafter for two years. Applicants should possess a Ph.D. degree in…

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CSIRO hiring CSIRO Postdoctoral Fellowship in Anti-Viral Bioinformatics in Canberra, Australian Capital Territory, Australia

Acknowledgement of CountryCSIRO acknowledges the Traditional Owners of the land, sea and waters, of the area that we live and work on across Australia. We acknowledge their continuing connection to their culture and pay our respects to their Elders past and present. View our vision towards reconciliation The Opportunity Do…

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Bioinformatics Programmer 4 (Hybrid) – 120485

UCSD Layoff from Career Appointment: Apply by 12/13/22 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 12/22/22. Eligible Special Selection clients should contact their Disability Counselor for assistance. This position will remain posted until a suitable candidate has been…

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Bioinformatics Software QA Engineer (Remote Option) at Genentech

The Position Genentech, a member of the Roche group and founder of the biotechnology industry, is dedicated to pursuing groundbreaking science to discover and develop medicines for people with serious and life-threatening diseases. To solve the world’s most complex health challenges, we ask bigger questions that challenge our industry and…

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TDF to bed graph — IGV on command line

TDF to bed graph — IGV on command line 0 Hi all, I’m trying to convert some TDF files to bedgraph files so that I can do a genomic leftover on them (as far as I can tell, I can’t lift over TDF files). This google group answer here (groups.google.com/g/igv-help/c/RcZw5YB5SOQ)…

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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts

Hi, running Rsubread 2.8.2/2.12.0 or featureCounts 2.0.3/2.0.1, I stumbled over two issues when allowing ambiguous read assignment (-O/allowMultiOverlap) 1) regarding assignment via minimum fractional overlap (–fracOverlap) using featureCounts stand-alone binary. 2) when combined with –/largestOverlap and –/fraction using Rsubread featureCounts function or the stand-alone binary. to 1) Assume a read…

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Post-doctoral Fellow in the Department of Clinical Oncology job with THE UNIVERSITY OF HONG KONG

Work type: Full-time Department: Department of Clinical Oncology, School of Clinical Medicine (21600) Categories: Academic-related Staff Applications are invited for appointment as Post-doctoral Fellow in the Department of Clinical Oncology, School of Clinical Medicine (Ref.: 517408) (to commence as soon as possible for one to two years, with the possibility of renewal subject to satisfactory…

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Research Associate, Bioinformatics (Cancer Science Institute, NUS) job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description A Bioinformatics position is available immediately at the Cancer Science Institute (a part of The National University of Singapore) in the laboratory of Dr. Sriram Sridharan. The research will focus in the broad area of replication stress, DNA damage and genome integrity.  This is an exciting opportunity to…

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Postdoc position Infectious Disease Epidemiology

The lab of professor Moradigaravand at KAUST has an opening for one postdoctoral fellowship in Bioinformatics (postdoc.kaust.edu.sa), as part of the KAUST Smart Health Initiative, to investigate the genetic basis of key clinical features of bacterial infections. This position suits recent PhDs, MD/PhDs, with a career interest in computational biology,…

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Sbatch How Submitted Location Using Jobid With Code Examples

Sbatch How Submitted Location Using Jobid With Code Examples With this piece, we’ll take a look at a few different examples of Sbatch How Submitted Location Using Jobid issues in the computer language. scontrol show job your_job_id_234533 We learned how to solve the Sbatch How Submitted Location Using Jobid by…

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java – I am unable to execute the fastqc command in HPC cluster

I am trying to run fastqc for fastq.gz files in RNA-seq Data analysis and I have written a PBS script. However, I am encountering the following error Can’t exec “java”: No such file or directory at /home/paksls/Atreya/software/FastQC/fastqc line 307 I have written the following script: #!/bin/bash #PBS -l nodes=1:ppn=6,pmem=10240MB,walltime=04:00:00 #PBS…

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miRDeep2 for small RNA sequencing

miRDeep2 for small RNA sequencing 1 Hello, I am using the following tutorial for microRNA profiling: drmirdeep.github.io/mirdeep2_tutorial.html I was able to follow it until the patching step which is: bash patchme.sh However the next step where we install the miRBase reference file gives an error as follows: mirdeep2_patch abhaykanodia$ mirbase.pl…

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Senior Clinical Bioinformatics Scientist – Medical Center, New York, United States

Senior Clinical Bioinformatics Scientist 525626 Medical Center Institute for Genomic Medicine Full Time Grade 104 Job Type: Officer of Administration Bargaining Unit: Regular/Temporary: Regular End Date if Temporary: Hours Per Week: 35 Salary Range:   Position Summary The Precision Genomics Laboratory (PGL), a partnership between the Department of Pathology and…

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Bioinformatics Training Project Manager at European Molecular Biology Laboratory (EMBL)

About the team/job Are you passionate about computational training in life sciences and wish to focus your career on the management and coordination of training programs? We are looking for a team member who will coordinate a new multi-organization project (BioNT) funded by the European Commission, embedded in the Data…

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Research Associate, Bioinformatics(Cancer Science Institute, NUS) job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description A Bioinformatics position is available immediately at the Cancer Science Institute (a part of The National University of Singapore) in the laboratory of Dr. Sriram Sridharan. The research will focus in the broad area of replication stress, DNA damage and genome integrity.  This is an exciting opportunity to…

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Number of sequences in RefSeq.

Number of sequences in RefSeq. 2 Dear colleagues I can not understand. When I download all the genomic sequences from the refseq database, after counting, I see that there are much fewer records than presented in the release (123394 organisms ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release214.txt). What am I doing wrong? 1. wget ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt 2….

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Integrated Resources, Inc ( IRI ) hiring Bioinformatics Data Scientist in Mississauga, Ontario, Canada

Location: Mississauga, ON Duration: 12+ Months Who We Are Looking ForWe are looking for an experienced Bioinformatics Data Scientist, with a proven track record of generating insights and building predictive models from biological data.For this position, we will consider applicants focused on Data Science applied to biological data with 3…

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[Internship] Bioinformatics Intern, Fall 2022 at Harmonic Discovery (United States)

About Us Based in NYC, Harmonic Discovery is a biotechnology company leveraging biology, medicinal chemistry, and machine learning to create a new generation of therapeutics for oncology and autoimmune disorders. We look for passionate innovators, radical thinkers, and collaborative builders. It’s time to integrate our understanding of biology and chemistry…

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Setting root folder to shared folder – Zero to JupyterHub on Kubernetes

peppie August 23, 2022, 10:20am #1 I have a homemade Kubernetes Cluster with an NFS configured on each node + shared with developpers. It is used for shared storage of code and data. I configured JupyterHub using the Zero to JupyterHub tutorial with Helm chart, which is running correctly and…

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Running parfor on SLURM limits cores to 1 – MATLAB Answers

Hello, I’m trying to run some parallelized code (through parfor) on a university high performance cluster. In order to make sure parallelization is working correctly, I set up a single node with 32 cores via “srun –pty -t 00:30:00 -n 32 -N 1 /bin/bash -l”, which I verify does start…

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Bash script to automate htseq-count

Hi everyone- I am trying to write a script to automate htseq-count on a large number of samples. The script runs but then throws the following error: “Please provide 2 arguments”. Does anyone see something obvious I am missing: #!/bin/bash for samples in *.sam do gtf = “Galaxy135-\[Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.29.gtf\].gtf” echo $sample …

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mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

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Bioinformatics_-_Writing_your_first_Bash_script.stamped_doc.pdf – Bioinformatics – Writing your first Bash script [00:00:00.00] [MUSIC

Bioinformatics – Writing your first Bash script[00:00:00.00] [MUSIC PLAYING][00:00:07.45] Hello, I’m Victoria Offord. And in this video, I’ll be walking you through how towrite and execute your very first Bash script. Now, all a Bash script is, is just a text file thatcontains one or more Bash commands. In order…

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Job Application for C++ Software Developer in Bioinformatics and Big Data at NIH-NCBI

Overview Black Canyon Consulting (BCC) in partnership with Medical Science and Computing (MSC) is searching for a C++ Software Developer in Bioinformatics and Big Data to support the National Center for Biotechnology Information (NCBI).  This opportunity is full time and onsite at the NCBI in Bethesda, MD and/or remote work. NCBI,…

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in WORLDWIDE

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. This opportunity is…

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Postdoctoral Research Fellow /Associate – Epigenomics/Bioinformatics in Cincinnati, OH for Cincinnati Children’s Hospital Medical Center

Details Posted: 11-Aug-22 Location: Cincinnati, Ohio Salary: Open Categories: Academic / Research Description Computational postdoctoral positions in bioinformatics and epigenomics (computational/experimental) are available at Dr.Yaping Liu’s lab in the Division of Human Genetics. One of the research directions in Dr. Liu’s group is to study single-cell multi-omics data to understand…

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Setting up Aspera Connect (ascp) on Linux and macOS

This tiny tutorial cover setting up Aspera Connect (binary is called ascp) which might be used to download sequencing data, e.g. with download links provided by sra-explorer.info, see also sra-explorer : find SRA and FastQ download URLs in a couple of clicks Setting up Aspera Connect is simple and was…

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Cornell Virtual Workshop: Execution: idev (at TACC)

TACC also offers their idev command (for interactive development) as a convenient way to initiate interactive work on their compute nodes, via Slurm. It works very much like srun and even takes many of the same options. But by making a few assumptions, idev shortens the path for you…

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Computational Biologist, Clinical Bioinformatics – Remote job in Boston, Massachusetts at Dana-Farber Cancer Institute

Computational Biologist, Clinical Bioinformatics – Remote Job Details Job ID: 26821 Location: 450 Brookline Ave, Boston, MA 02215 Category: Clinical Research Employment Type: Full time Work Location: Full Remote: 4-5 days remote/wk Overview The NGS Bioinformatics Group at Dana-Farber Cancer Institute seeks a Computational Biologist to work on Profile, our…

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Transition from Woody with Ubuntu 18.04 and Torque to Woody-NG with AlmaLinux8 and Slurm

2022-07-17 Valued Tier3 HPC users of NHR@FAU, as briefly announced in the HPC Cafe in June, we now started with switching from Woody with Ubuntu 18.04 and Torque to Woody-NG (“Woody Next Generation”) with AlmaLinux8 as operating system and Slurm as batch system. Woody-NG uses the same operating system as…

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Mapping reads using kallisto – rna seq analysis

Mapping reads using kallisto – rna seq analysis 0 Hi, I’m trying to map reads to a reference genome using kallisto for rna seq analysis with terminal on mac and the following command keeps loading for hours and won’t run. I’m not exactly sure where I’ve gone wrong. kallisto index…

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why the syntax error comes when i use the same command in loop in bash linux

hi, I am using awk to sort a tsv file with command: awk -F “\t” ‘{ if(($3 => 95) && ($13 >= 95) && ($11 <= 1e-5)) { print } }’ FILENAME| sort -k1,1 -k12,12gr -k11,11g -k3,3gr | sort -u -k1,1 –merge > SORTED_FILENAME It is working fine when i…

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German Cancer Research Center in the Helmholtz Association (DKFZ) hiring Postdoc in Bioinformatics, Medical Informatics or Biostatistics in Brussels, Brussels Region, Belgium

Offer DescriptionThe German Cancer Research Center is the largest biomedical research institution in Germany. With approximately 3,000 employees, we operate an extensive scientific program in the field of cancer research. Together with university partners at seven renowned partner sites, we have established the German Cancer Consortium (DKTK). For the partner…

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Open Rank Bioinformatics Software Engineer I and Bioinformatics Engineer II in Baltimore, MD for University of Maryland, Baltimore

Open Rank Bioinformatics Software Engineer I and Bioinformatics Software Engineer II The Institute for Genome Sciences (IGS), Informatics Resource Center, is recruiting for a Open Rank Bioinformatics Software Engineer I and Bioinformatics Software Engineer II position. This position will be filled as either the Bioinformatics Software Engineer I or II.IGS…

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Issue with streamlit as dependency when deploying my package to Bioconda repository – Using Streamlit

Hello,I am opening an issue here for a problem that I don’t think you guys can solve, but you never know. I recently developped a Python tool, and I need to get it onto the Bioconda repository . To do this, I have created a recipe that I must know…

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Senior Software Developer (commencing immediately) at European Molecular Biology Laboratory (EMBL)

Contract Type: Staff Member Location: EMBL-EBI, Hinxton near Cambridge, UK Job Function: Senior Technical Officer (gr. 6-8) Contract Duration-Length of Time (years/months): 1 year (until grant-end date of 30/10/2023) Contract Duration-Is this renewable to 9 years?: No Advertised Grade-Grading: Grade 6 (monthly salary starting at £3,143.06 after tax plus benefits) About the team/job We are seeking…

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parallel downloads from SRA with SRA toolkit or other ways to speed up downloads

parallel downloads from SRA with SRA toolkit or other ways to speed up downloads 0 Is there a way to parallelize downloads from NCBI using SRAToolkit on a HPC cluster? I tried using GNU parallel but I can not actually tell if the downloads are doing anything: cat < /home/ptellier/scratch/phillip/data/escc_data/SRA_accessions.txt…

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Jobs on jobactive hiring Postdoctoral Bioinformatician in Single Cell and Spatial Omics Data Analysis in Adelaide, South Australia, Australia

Full-Time, 2 Year Contract Salary range $95,000 – $110,000 At the South Australian Health and Medical Research Institute (SAHMRI), we are committed to achieving innovative, ground-breaking health and medical research that fundamentally improves the quality of life for all people. The South Australian Genomics Centre (SAGC) is a multi-institutional, national…

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fix checkpatch.pl struct should normally be const — DRI Development

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…

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How can you put a bash array into a wdl variable?

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…

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Recent questions tagged fasta – Q&A

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…

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nf-core presentation – HackMD

<!– .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/) — ##…

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Director of Bioinformatics in Chicago, IL for University of Chicago (UC)

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…

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Distributed training on slurm cluster – distributed

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…

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How to remove everything before a specific character in a column

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…

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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

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…

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Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing

** 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…

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Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

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…

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[slurm-users] Issues with pam_slurm_adopt

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:…

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Bioinformatics Pipeline Development Engineer II at Personalis, Inc

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,…

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Problem with Python environment and Slurm (srun/sbatch)

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:…

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[Solved] Use Bash variable within SLURM sbatch script

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…

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LAMMPS Patch Release 24 March 2022

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…

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BioInformatics Product Manager at Helix (remote)

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…

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Optimize a script that extract features from Fasta file using biopython

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…

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Running bash commands from within python script : bioinformatics

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…

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Nvt.mdp killed in 7 min – User discussions

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…

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How do I get SLURM to allocate jobs to all CPUs

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…

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Error in creating cyclecloud cluster (No nodes found for nodearray hpc)

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:…

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Install Jupyter Notebook on Debian 11 Bullseye Linux

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…

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Unable to run python script from bash scripts with string arguments : SLURM

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”…

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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

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….

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in PEORIA, IL

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…

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Research Associate job with KINGS COLLEGE LONDON

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…

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JupyterLab Installation and Configuration – HEAVY.AI Docs

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…

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bam – samtools view command not found error

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…

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Passing a parameter into a slurm script (matlab)

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…

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[slurm-users] mps on A100 only zero-index GPU was used when there is four GPUs

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…

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how to create temporary folders in a slurm script hpc script code example

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…

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Do I meet the basic requirements needed to study a PhD in computational chemistry? : comp_chem

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…

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Processing two lists of files with snakemake

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…

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PostDoc Plant Bioinformatics job with SKOLKOVO INSTITUTE OF SCIENCE AND TECHNOLOGY

<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…

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Find Transposon Element insertions using long reads (nanopore), by alignment directly. (minimap2)

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…

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Merging compressed fastq files based on a conditions defined in a csv file

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…

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bash – Python argparse error

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…

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Slurm environment variable for requested time

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…

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Senior Bioinformatics Software Developer – Bethesda

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…

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log repeats until it times out)

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…

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H2O is an in-memory platform for distributed, scalable machine learning

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…

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