Tag: zsh

I know that this question is available in this page, but I have tried most of them, and I just can’t make it works. How can I set an external program as blast permanently using Sys.setenv for my personal functions in R I’m using a MacOS with R4.1.1 and RStudio…

Hello, I’m trying to run gget alphafold on my M1 mac, but am encountering the following error: zsh: illegal hardware instruction I noticed other threads (143) that comment on the difficulty of running tensorflow with m1 hardware and was wondering if this might be the issue? I checked to see…

The relevant bedtools option seems to be -c: -c For each entry in A, report the number of overlaps with B. – Reports 0 for A entries that have no overlap with B. – Overlaps restricted by -f, -F, -r, and -s. We can get the number of overlaps per…

STAR solo segmentation fault after ‘started Solo counting’ 1 Dear all, I have some 10x v3 single cell rna seq fastq files that I am trying to map to hg38 human genome using STAR aligner and generate read counts. However, I am getting the following error and hope that some…

ADMIXTURE ABORTS WITHOUT REASON 0 Hello! I am trying to run admixture with the command line admixture –cv all_cg_gersamples.bed 2 It aborts with the following output. Please what am I getting wrong? ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information…

ivanllam (Ivan Lam) February 2, 2023, 4:29am 1 Hi all, I aim to install QIIME2-2022.11 on Mac. I encounter the following error similar to (Error to install qiime2-2022.2 with conda). The recommendation involve a Mac with a M1 chip, but my Mac is working with a Intel Core-i9. May I…

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…

bwa , 2 files fastq to 1 sam 1 i have this problem, please, help me, I’m trying it too from Mac OS Catalina I am creating a sam file, with 2 fastq files, using bwa I apply the following command bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz > V350019555_L03_B5GHUMqcnrRAABA-556.sam…

conda samtools 0 It gives me error when installing samtools I installed curl -O repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh sh Miniconda3-latest-MacOSX-x86_64.sh conda install -c bioconda samtools zsh: command not found: conda javierpalomares@JAVIERs-Air ~ % samtools conda • 184 views Login before adding your answer. Read more here: Source link

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…

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….

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…

Hi everyone, I’m new to Kaggle and I’m trying to use it for my Bachelor’s degree thesis. However when I try to activate my conda environment it runs into an error: CommandNotFoundError: Your shell has not been properly configured to use ‘conda activate’. To initialize your shell, run $ conda…

Hi everyone, I’m pretty new at this stuff, especially with Kaggle, and I’m trying to activate a conda environment with the conda activate command. However, it comes out with this error: CommandNotFoundError: Your shell has not been properly configured to use ‘conda activate’. To initialize your shell, run $ conda…

CUT&RUN pipeline – zsh: command not found: sbatch (MacOS terminal) – how to fix this? 1 Dear all, I apologise in advance if this issue has been addressed before and I just did not find it in here. Also, I am not a bioinformatician/programmer/computer person at all… I have been…

Samfile error: dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib 1 I’ve downloaded samfiles using conda For converting sam to bam I used the command samtools view -S -b /Users/dhee/Desktop/SRR12304924.s > /Users/dhee/Desktop/SRR12304924.bam In getting an error as dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/dhee/miniconda3/bin/samtools Reason: image not found zsh: abort samtools view…

Samfiles 1 I’ve downloaded samfiles using conda For converting sam to bam I used the command samtools view -S -b /Users/dhee/Desktop/SRR12304924.s > /Users/dhee/Desktop/SRR12304924.bam In getting an error as dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/dhee/miniconda3/bin/samtools Reason: image not found zsh: abort samtools view -S -b /Users/dhee/Desktop/SRR12304924.s Samfiles • 36…

fasted 0 I’m using a m1 Mac and I’ve installed fastqc using homebrew and also from the official website www.bioinformatics.babraham.ac.uk/projects/fastqc/ but I’m not able to run the command line(./fastqc) on terminal this is the output I get zsh: permission denied: ./fastqc and my fastqc does not show file option to…

FYI, FreeBSD users can now install all the bioinformatics software referenced by the Biostar Handbook via FreeBSD ports. Everything except bedGraphToBigWig can be installed simply by running pkg install biostar-tools bedGraphToBigWig is part of ucsc-userapps, which cannot be redistributed for licensing reasons, so there is no binary package. However, the…

If you are on a Mac then this is not the right executable. You will need to download Mac executable from here: hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ You may still run in to library errors if you are using latest BigSur OS. Your best bet is to use conda to install. conda install -c…