Tag: bin

Hi all, I am trying to set JupyterHub so that each user group can choose from a different set of available preconfigured packages. I figured out this might be done via venv’s (one for each group), but there are some issues. I installed the new venv, jupyterhub sees it and…

Hey, what’s up? I’m using the CellRanger for scRNA and this problem appears: Generating STAR genome index (may take over 8 core hours for a 3Gb genome)… Jun 07 19:02:11 ….. started STAR run Jun 07 19:02:11 … starting to generate Genome files Jun 07 19:02:11 … starting to sort…

We use lmod and modules to manage software on a RHEL 8.6 computer cluster. In terminal 1, I load R/4.3.0 and check both LD_LIBRARY_PATH and PATH $ ml load GCC/9.3.0 OpenMPI/4.0.3 R/4.3.0 $ echo $LD_LIBRARY_PATH # This has been exported /export/apps/opt/R/4.3.0-foss-2020a/lib64/R/lib:/gpfs0/export/apps/easybuild/software/Java/11.0.2/lib:/gpfs0/export/apps/easybuild/software/OpenMPI/4.0.3-GCC-9.3.0/lib:/gpfs0/export/apps/easybuild/software/UCX/1.8.0-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/hwloc/2.2.0-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/libpciaccess/0.16-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/libxml2/2.9.10-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/XZ/5.2.5-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/numactl/2.0.13-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/binutils/2.34-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/zlib/1.2.11-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib64:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib $ echo $PATH # This has been exported /export/apps/opt/R/4.3.0-foss-2020a/bin:/gpfs0/export/apps/easybuild/software/Java/11.0.2:/gpfs0/export/apps/easybuild/software/Java/11.0.2/bin:/gpfs0/export/apps/easybuild/software/OpenMPI/4.0.3-GCC-9.3.0/bin:/gpfs0/export/apps/easybuild/software/UCX/1.8.0-GCCcore-9.3.0/bin:/gpfs0/export/apps/easybuild/software/hwloc/2.2.0-GCCcore-9.3.0/sbin:/gpfs0/export/apps/easybuild/software/hwloc/2.2.0-GCCcore-9.3.0/bin:/gpfs0/export/apps/easybuild/software/libxml2/2.9.10-GCCcore-9.3.0/bin:/gpfs0/export/apps/easybuild/software/XZ/5.2.5-GCCcore-9.3.0/bin:/gpfs0/export/apps/easybuild/software/numactl/2.0.13-GCCcore-9.3.0/bin:/gpfs0/export/apps/easybuild/software/binutils/2.34-GCCcore-9.3.0/bin:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin…

I’m trying to run Picard CreateSequenceDictionary using the docker image provided by the Broadinstitute (here), but |I’m having troubles when running it, and don’t understand why. I download and run it as: docker pull broadinstitute/picard docker run –rm -v $PWD:/usr/working broadinstitute/picard CreateSequenceDictionary R=ref.fa.gz O=ref.fa.gz.dict But this returns an error: docker:…

[1] ZHAO Xueliang, WANG Shuyi, SUN Ke, SU Qian, WANG Wenlong, LIU Chunxia. Comparative Transcriptome Analysis of Albendazole-susceptible and Resistant Strains of Haemonchus contortus by RNA-Seq [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(9): 1940-1944. [2] YU Yan,…

Building the protein-membrane system in CHARMM-GUI We are now ready to embed the protein structure in the membrane in the proper location and orientation and construct the membrane composition we desire. To do this, we utilized the CHARMM-GUI input Generator, a handy web-based tool to generate GROMACS inputs for the…

There is only one place for most 3D graphs, and that is the trash bin! The large majority of 3D graphs used in general or business context are confusing to interpret and prone to be misread. Popular data visualisation tools such as ggplot for R and Tableau do not even…

Cute June 5, 2023, 4:19pm 1 Dear LAMMPS developers. I generated a cluster and want to use ultrasonic waves to break this cluster.I found the relevant command “fix move” in the lammps documentation and added a simple harmonic force to the wall.It cant run. Maybe I have used this command…

I was trying to deploy spark on kubernetes after some try and following this guide dev.to/akoshel/spark-on-k8s-in-jupyterhub-1da2 I successfully ran the example pi by using spark-submit from local system and it worked beautifully and I was able to see the pod in completed status. /opt/spark/bin/spark-submit \ –master \ –deploy-mode cluster…

Hi everyone, I want to perform a simulation with a piston on fused silica. I have tried read the fused silica file, extend the dimensions of the simulation box and create atoms of the piston in the upper part of the box (blank region) but it gave an error. So…

Hello! I would really appreciate help with installing a JupyterLab extension for all JupyterHub users. I’ve read various threads including this but (aside from using Lab) it seems my environment is configured differently. We are using Ubuntu 22.04 LTS, with JupyterHub being run as a service by root (ExecStart=/root/.pyenv/shims/jupyterhub -f…

@Emrebel have you tried nanoGPT??? Whoa @draglord I just ran the openwebtext (so called clone of OpenAI’s chatGPT) dataset (smallest init_from=gpt2 and also gpt2-xl) for few minutes training run (max_iters=100 only haha) and asked “What is OpenAI”, “What is your name”, and the sample “What is the answer to life,…

KAUST Professor Mario Lanza and his co-researchers have successfully designed the world’s first 2D microchip using synthetic materials. Despite fabrication challenges, the team successfully created a chip functioning as a high-performance, low-power neural network element, opening doors for the advancement of microchip technology. Credit: © 2023 KAUST; Mario Lanza The…

I am trying to bring this small dataset (1496 cells, 43MB) from cellxgene. 1 R SeuratDisk h5ad to h5seurat and then to seurat. library(SeuratDisk) SeuratDisk::Convert(“local.h5ad”, dest = “local.h5seurat”, overwrite=TRUE) g <- SeuratDisk::LoadH5Seurat(“local.h5seurat”, meta.data=FALSE, misc=FALSE) Validating h5Seurat file Initializing RNA with data Adding counts for RNA Adding feature-level metadata for RNA…

Hi folks! I have a list of NCBI assembly accession numbers, and I’m trying to return species name (latin and common) plus taxid. A few weeks ago, I wrote a bit of code that appeared to do the trick. #!/usr/bin/env python import csv from Bio import Entrez Entrez.email=”kwh1@wi.mit.edu” def get_organism_taxonomy(accession):…

How to calculate TPM from featureCounts output 0 I would like to find the TPM counts for the GSE102073 study. When i downloaded the raw data from GEO, the raw data are featureCounts output. First part of the file: # Program:featureCounts v1.4.3-p1; Command:”/data/NYGC/Software/Subread/subread-1.4.3-p1-Linux-x86_64/bin/featureCounts” “-s” “2” “-a” “/data/NYGC/Resources/ENCODE/Gencode/gencode.v18.annotation.gtf” “-o” “/data/analysis/LevineD/Project_LEV_01204_RNA_2014-01-30/Sample_JB4853/featureCounts/Sample_JB4853_counts.txt” “/data/analysis/LevineD/Project_LEV_01204_RNA_2014-01-30/Sample_JB4853/STAR_alignment/Sample_JB4853_Aligned.out.WithReadGroup.sorted.bam”…

Author links open overlay panelJin Ju Kim a 1, Hoon Je Seong a b 1, Timothy A. Johnson c, Chang-Jun Cha a, Woo Jun Sul a, Jong-Chan Chae d Show more doi.org/10.1016/j.jhazmat.2023.131761Get rights and content ABSTRACT Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming…

GROMACS version: 2022.3GROMACS modification: No Hello everyone. I am currently using GROMACS ver. 2022.3 patched with PLUMED ver. 2.8.1., and I’ve been trying to replicate the gREST simulations from Oshima et al. (J. Chem. Inf. Model. 2020, 60, 11, 5382–5394) using GROMACS. In the paper, the authors perform gREST simulation…

DOI: 10.18129/B9.bioc.flowBin     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see flowBin. Combining multitube flow cytometry data by binning Bioconductor version: 3.13 Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing…

#!/usr/bin/env perl # Generate error.c # # Usage: ./generate_errors.pl or scripts/generate_errors.pl without arguments, # or generate_errors.pl include_dir data_dir error_file use strict; my ($include_dir, $data_dir, $error_file); if( @ARGV ) { die “Invalid number of arguments” if scalar @ARGV != 3; ($include_dir, $data_dir, $error_file) = @ARGV; –d $include_dir or die “No such…

#!/bin/sh # Measure heap usage (and performance) of ECC operations with various values of # the relevant tunable compile-time parameters. # # Usage (preferably on a 32-bit platform): # cmake -D CMAKE_BUILD_TYPE=Release . # scripts/ecc-heap.sh | tee ecc-heap.log set –eu CONFIG_H=‘include/mbedtls/config.h’ if [ –r $CONFIG_H ]; then :; else echo…

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…

Mini Review – Journal of Brain and Neurology (2023) Volume 6, Issue 2 Harry Warner* Department of Neurosciences *Corresponding Author: Bin Kayano Department of NeurosciencesUniversity of ExeterUnited KingdomE-mail:h.m.warner@exeter.ac.uk Received:24-Apr-2023, Manuscript No. AAJBN-23-97950; Editor assigned:27-Apr-2023, PreQC No. AAJBN-23-97950(PQ); Reviewed:11-May-2023, QC No. AAJBN-23-97950; Revised:15-May-2023, Manuscript No. AAJBN-23-97950(R); Published:22-May-2023, DOI:10.35841/ aajbn-6.2.146 Citation: Warner…

(if you are only interested in the problem, then go to “What if in short?”) What kind of stupid question? I’m doing work and before that I built all graphics with x and I don’t want to change the style. And now I need a histogram, but it does not…

I would like to create a plot using plotly::ggplotly(). This works just fine. library(ggplot2) #> Warning: package ‘ggplot2’ was built under R version 4.2.2 p <- mtcars |> ggplot() + geom_histogram( aes( x = disp, text = after_stat(count) ) ) #> Warning in geom_histogram(aes(x = disp, text = after_stat(count))): Ignoring…

Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…

I am trying to run scripts on a remote server with DataSpell, so I am trying to configure a remote interpreter. I follow these instructions and I get the error Cannot Save Settings: SSH Python x.x.x user@IP : Python x.x.x (path/to/interpreter) can’t be used as a workspace interpreter As a…

Here’s another beginner BioPython question from me… I’m running some genome assemblies for someone who has some new Illumina sequence data and also had done some sequencing a few years ago. They have some Sanger and 454 sequences (a couple thousand sequences with a couple thousand base pairs for each)…

The inchworm process failed. Trinity running error. 0 Hello everyone, I’m trying to perform a de novo transcriptome using Trinity and having many issues. The last time I got the inchworm error attached. ******************************************************************** ** Warning, Trinity cannot determine which version of Java is being used. Version 1.7 is required….

Hi everyone, I have a following configuration: cryosparc_master running on a local workstation (where I have sudo) a university HPC cluster with wonderful GPUs (where I don’t have sudo) I want to connect the HPC cluster as a separate lane for our local cryosparc. However, when I try using example…

YOLO refers to the paper published in May 2016. The YOLOv5, a version of the model in the You Only Look Once (YOLO) family of computer vision models, is on Pytorch and all the previous models used the darknet implementation. Our goal is to use the YOLO for logo detection, even…

After hitting my head a lot (Brazilian expression for trying several times), I found a mechanism provided by the plugin itself. It consists of two steps: Create ${project.baseDir}/.openapi-generator-ignore defining the paths to be ignored: # github.com/OpenAPITools/openapi-generator/blob/master/docs/customization.md#ignore-file-format # # Use this file to prevent files from being overwritten by the generator….

NVIDIA-open-gpu-kernel-modules 535.43.02 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of NVIDIA-open-gpu-kernel-modules-535.43.02.tar.gz (30 May 19:11, 12892666 Bytes) About: open-gpu-kernel-modules is the source release of the NVIDIA Linux open GPU kernel modules. Hint: According to a NVIDIA technical blog post this code…

Make a BedGraph file 1 I have a simple BED file displays repetitive elements localization (this file was obtained using RepeatMasker). Here are the first few rows:: 2L 840 882 Simple_repeat 2L 2763 2796 Simple_repeat 2L 3409 3498 DNA/Helitron 2L 5405 5432 Simple_repeat 2L 8844 9132 LINE/unknown Now, I would…

ERROR running Cuffmerge in reference based RNA-SEQ analysis? 0 I am using cufflinks for the reference based RNA-Seq analysis. During the step of cuffmerge I was shown an error that I have attached below. can anyone please help me out solving this problem. Command used: cuffmerge -g ../../../../Reference_files/PGSC_DM_V403_genes.gtf -s ../../../../Reference_files/potato_dm_v404_all_pm_un.fasta…

I have problem with installing qiime2-2023.2 with conda on a server running linux system. I ran command conda env create -n qiime-2023.2 –file qiime2-2023.2-py38-linux-conda.yml. But it turned out to report the error info ERROR conda.core.link:_execute(952): An error occurred while installing package ‘bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0’.,and below for the detailed error info. At first…

Brief overview of inference approach Mutations occur during viral replication within infected individuals and these have the potential to be transmitted. During the epidemiological spread of an emerging virus or viral lineage, the virus population (distributed across infected individuals) thus accrues mutations and diversifies genetically. This joint process of viral…

ABySS Process Killed 0 Hi everyone! Name is Sam and I’d like to ask for help on my contig assembly using ABySS. I’ve been trying to assemble a contig from paired sequences using ABySS in WSL. I started with a basic script as follows: abyss-pe k=21 B=2G name=A1k21 in=’A1_1.fastq A1_2.fastq’…

How to collapse leaves with the same name in ETE3 tree? 3 I’m trying to collapse leaves that have the same name in ETE3’s tree. I think I almost got it. Two leaves in my example (A. thaliana) have been combined into a single leaf, but not named. I would…

I am using Limma for downstream analysis of mass spectrometry proteomic data. I am comparing differential protein expression between healthy controls (n= 40) and two disease subtypes (disease_1 n= 59, disease_2 n= 41). I have an ‘intensities’ matrix with the log2 transformed LFQ expression for 1300 proteins in rows with…

Number Of Bins In R. To create the bins for a continuous vector, we can use cut function and store the bins in a data frame along. Web it’s best to use the ntile() function when you’d like an integer value to be displayed in each row as opposed…

Software description This open source code provides an implementation of the AlphaFold v2.0 system. It allows users to predict the 3-D structure of arbitrary proteins with unprecedented accuracy. AlphaFold v2.0 is a completely new model that was entered in the CASP14 assessment and published in Nature (Jumper et al. 2021)….

I have used the instructions such as ‘nvidia-smi -c 3’ or ‘nvidia-smi -i 0 -c 3’. But they seem have no effect. The following is my script in slurm. But the GPU my job runs on is still shared with other people. #!/bin/bash #SBATCH -o job.%j.out #SBATCH –partition=GPU3 #SBATCH –qos=low…

yzs May 26, 2023, 3:42pm 1 Hi, I’m experiencing performance degradation when trying to compile from source, and I’m wondering if there are some details I’m missing. Using pytorch v2.0.0 as an example, I used both cuda 11.7 and cudnn 8.5 (consistent with builder/install_cuda.sh at main · pytorch/builder · GitHub…

** *Dear all,* * We are excited to announce the release of the new version of the PISA software, developed at PDBe, based on the jsPISA implementation from CCP4. This new version, PISA-lite, developed in collaboration with the CCP4 core team, enables the calculation of macromolecular interaction data for every…

I like this question a lot. Firstly I don’t know singularity, but I know Docker and it will be similar. docker exec is very similar. So for example the reasons are likely as follows: media could be empty and hence no output. the Python script may not be in /proc…

The CHPC uses Slurm to manage resource scheduling and job submission. Users submit jobs on the login node. The queueing system, also known as the job scheduler, will determine when and where to run your jobs. Slurm will factor in the computational requirements of the job, including (but not limited…

You can access the various parameters using the SLURM environment variables. A complete list of the environment variables are found on the SLURM webpage. input-environment-variables output-environment-variables Here is an example of how to print information regarding these parameters using SLURM environment variables: Say we have a test.sh with the following…

Hello everybody, I am observing an interaction between the –mem-per-gpu, –cpus-per-gpu and –gres settings in sbatch which I do not understand. Basically, if the job is submitted with –gres=gpu:2 the –mem-per-gpu and –cpus-per-gpu settings appear to be observed. If the job is submitted with –gres=gpu:a100:2 the settings appear to be ignored…

Cutadapt error: too many parameters. 0 Hi biostars community! I am having issues to loop cutadapt over gunzipped samples. This is the script I am using: #!/bin/bash #SBATCH –account GRINFISH #SBATCH -c 8 #SBATCH –mem 96g #SBATCH –output logfile.out #SBATCH –error logfile.err # This script performs trimming for PE sequences…

I am having trouble launching a SLURM job calling a mpirun subprocess from a python script. Inside the python script (let’s call it script.py) I have this subprocess.run: import subprocess def run_mpi(config_name, np, working_dir): data_path = working_dir + “/” + config_name subprocess.run( [ “mpirun -np ” + np + “…

Abyss taking a Long time to run 0 I am trying to do genome assembly of a chicken using Abyss with the following command- abyss-pe k=64 np=8 j=8 name=assembly_female in=’s1.fastq s2.fastq’ However, even after three hours, the process is still stuck in the same place like this- /home/mkkk/.conda/envs/abyss-env/bin/mpirun -np 8…

GROMACS version: 2021.4GROMACS modification: Yes/No Hi, I am getting this error while installing gromacs 2021.4 please help me with it. I configured cmake as follows: cmake … -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DGMX_MPI=ON -DGMX_GPU=CUDA -DGMX_SIMD=AVX2_256 -DCMAKE_PREFIX_PATH=/usr/local/gromacs2021 -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs2021 -DBUILD_SHARED_LIBS=ON -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-11.7 after this I am getting an error as follows: [ 92%] Building…

I am trying to fine tune a T5 model for more accurate summarization, but my loss is very high and does not change with each epoch. I have tried increasing the learning rate, but the model still does not train. It seems like there is some issue with the code…

Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article  PubMed  PubMed Central  Google Scholar  Bankevich A, Nurk S,…

Hello I am new to the vertex AI. I have created a binary classfication model using hugging face Pytorch model (ROBERTA).  Now I am following the google vertex AI documentation to deploy but I am facing somer errors while deploying. ERROR 2023-05-22T08:08:18.241378784Z usage: torchserve [-h] [-v | –start | –stop]…

I’m trying to run docker for alphafold but it says that there is no ‘/home/administrator/alphafold/run_alphafold.py’ in the directory even if it does exist Code I’m trying to run python3 docker/run_docker.py \ –fasta_paths=your_protein.fasta \ –max_template_date=2022-01-01 \ –data_dir=/data8/Alphafold_database\ –output_dir=/data8/Alphafold_output_dir OBS: this is just a test to know if docker is working (your_protein.fasta…

GROMACS version: 2022.3, 2022.5, 2023.1GROMACS modification: NoHello, I’ve been having issues, trying all three of these GROMACS distributions. I’m running on an HPC, and I have included the basic error logs for the outputs of cmake and make check for the blank run after logging into the HPC. After gcc-7.5.0…

samtools installed but error message: Library not loaded: @rpath/libcrypto.1.0.0.dylib 1 I would like to convert input.sam to output.bam but I get following error message: kk$ samtools view -bS input.sam > output.bam dyld[88970]: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/kk/opt/anaconda3/bin/samtools Reason: tried: ‘/Users/kk/opt/anaconda3/bin/../lib/libcrypto.1.0.0.dylib’ (no such file), ‘/Users/kk/opt/anaconda3/bin/../lib/libcrypto.1.0.0.dylib’ (no such file), ‘/usr/local/lib/libcrypto.1.0.0.dylib’…

Why Upgrade? Upgrade Objectives Python ≥ 3.8, ≤ 3.11 CUDA ≥ 11.7.0 CUDNN ≥ 8.5.0.96 Pytorch ≥ 2.0.0 “We expect that with PyTorch 2, people will change the way they use PyTorch day-to-day”“Data scientists will be able to do with PyTorch 2.x the same things that they did with 1.x,…

doi: 10.2217/pgs-2023-0029. Online ahead of print. Abdullah Alsulaiman  1 , Hoyin Chu  2   3 , Mohammed Al-Jumaan  1 , Mohammed Alyahya  1 , Yousef Al Marzooq  1 , Fatmah Almulhim  1 , Chittibabu Vatte  1 , Areej Alnimer  1 , Afnan Almuhanna  1 , Amein Al-Ali  1 , Saud H AlDubayan  2   3   4   5 Affiliations…

Source: astra-toolbox Version: 2.1.0-2 Severity: important Tags: ftbfs sid Justification: fails to build from source Control: block 1036676 with -1 … /usr/bin/nvcc -Wno-deprecated-gpu-targets -gencode=arch=compute_50,code=sm_50 -gencode=arch=compute_60,code=sm_60 -gencode=arch=compute_70,code=sm_70 -gencode=arch=compute_75,code=sm_75 -gencode=arch=compute_80,code=sm_80 -gencode=arch=compute_86,code=sm_86 -gencode=arch=compute_86,code=compute_86 -I../build/linux/../../include -DASTRA_CUDA -c ../build/linux/../../cuda/2d/par_bp.cu -Xcompiler -fPIC -DPIC -o cuda/2d/.libs/par_bp.o ../build/linux/../../cuda/2d/par_bp.cu(36): error: texture is not a template 1 error detected in…

I would run the following code for multiple fastq files in a folder. In a folder I have different fastq files; first I have to read one file and perform the required operations by activating the miniconda , then store results in a separate file. fastq and then read second…

I’m training on mask2former_beit_adapter_large_896_80k_ms model with custom dataset and I have 2 issues that I’m having hard time to figure them out. I tried running train.py but after each epoch, when validation starts, it is slower than training speed which I thought it was weird and not sure what’s the…

Ggplot Histogram Bin Number. Web heatmap of 2d bin counts. Check that you have ggplot2 installed. r How to change the bin separate for histogram in ggplot2? Stack – image credit : stackoverflow.com Web a histogram is a plot that can be used to…

Hello. Recently I installed eks cluster with torchserve following the tutorial github.com/pytorch/serve/tree/master/kubernetes/EKS, but having troubles uploading a motel. When I try to upload a model via: curl -X POST “http://$HOST:8081/models?url=http%3A//54.190.129.247%3A8222/model_ubuntu_2dd0aac04a22d6a0.mar” curl -X POST “http://$HOST:8081/models?url=http://54.190.129.247/8222/model_ubuntu_2dd0aac04a22d6a0.mar” I am getting the following error: { “code”: 400, “type”: “DownloadArchiveException”, “message”: “Failed to download archive…

I was using R in RStudio under a conda environment with various bioconductor packages. But suddenly I ran into this error when I tried to load a package: ImportError: /home/user/anaconda3/envs/dmcgb/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.30′ not found (required by /lib/x86_64-linux-gnu/libLLVM-13.so.1) It is not the first time that I have this error so I…

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Phenotype and organism model references for a large list of genes 1 Hi all. I have to generate table for about 3500 genes with following columns: 1) references to each gene; 2) pathological features 3) reference to the organism model, e.g. MGI number for mouse Are there any databases/softwares, which…

Hello, I am having trouble running the GPU version of guppy on a cluster using SLURM. I have two guppy scripts called guppy_pass1.sh and guppy_pass2.sh. In the pass 1 script I basecall to get look at the ‘raw’ data without additional filtering/trimming. In the pass 2 script I basecall to…

R-Studio is a family of powerful and cost-effective undelete and data recovery software for experienced data recovery professionals. Empowered by the new unique data recovery technologies, R-STUDIO is the most comprehensive data recovery solution for recovery files from NTFS, NTFS5, ReFS, FAT12/16/32, exFAT, HFS/HFS+ (Macintosh), Little and Big Endian variants…

I wan to run a code using multiprocessing in a server with slurm architecture. I want to limit the number of cpus available and that the code creates a child process for every of them. My code could be simplified in this way: def Func(ins) : ### things… ### return…

Hello!I tried to install qiime2-2023.2 with miniconda3 under Windows Subsystem for Linux but met error message.The error message was below.ERROR conda.core.link:_execute(740): An error occurred while installing package ‘bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0’.Rolling back transaction: doneclass: LinkErrormessage:post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0location of failed script: /home/elaine/miniconda3/envs/qiime2-2023.2/bin/.bioconductor-genomeinfodbdata-post-link.sh==> script messages <== ==> script output <==stdout:stderr: QIIME is…

Hello I am new to the vertex AI. I have created a binary classfication model using hugging face Pytorch model (ROBERTA).  Now I am following the google vertex AI documentation to deploy but I am facing somer errors while deploying. ERROR 2023-05-22T08:08:18.241378784Z usage: torchserve [-h] [-v | –start | –stop]…

Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa 1 Hi I am trying to add ancestral allele to 1000 Genomes Phase3 VCF files. I have used the “human_ancestor_GRCh37_e59.tar.bz2” files for ancestral allele input file. The steps I have used are: cat human_ancestor_3.fa | sed ‘s,^>.*,>1,’ | bgzip…

GROMACS version:2023.1GROMACS modification: NoHere post your question System: Ubuntu on WSL2 with Windows 11 I try to cmake gromacs using the following tags: cmake .. -DGMX_GPU=CUDA -DGMX_CUDA_TARGET_SM=”75″ -DGMX_CUDA_TARGET_COMPUTE=”75″ -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_BUILD_OWN_FFTW=ON -DGMX_PYTHON_PACKAGE=ON But the configure returns an error with the following statement: Traceback (most recent call last): File “<string>”, line 1,…

R-Studio is a family of powerful and cost-effective data recovery and undelete utilities. Empowered by the new unique data recovery technologies, it is the most comprehensive solution for data recovery from FAT12/16/32, NTFS, NTFS5 (created or updated by Windows 2000), and Ext2FS (LINUX file system) partitions. It functions on local…

Error in running Abyss assembler for chicken genome assembly 0 I have a Fasta file of the chicken genome sequence which size is 54 GB. I am trying to do the assembly of this chicken genome using Abyss using the following code- abyss-pe k=32 B=25G name=assembly in=’merged_female.fa’ I gave B=25G…

GROMACS version: 2022.4 GROMACS modification: No Hi, I am trying to use gromacs through a bash loop to automatically run through all my folders and sub-folders; and rename the output with the same of the folders and sub-folders. I have used this script on an external computer cluster through a…

DUBAI, 12th May, 2020 (WAM) — The Emirates Down Syndrome Society in Dubai has confirmed that the country’s first self-advocacy program for people with Down syndrome, launched in its third phase, continues to achieve its goals. It was established to raise the voice of assertive people with Down syndrome, enabling…

Send slurm-users mailing list submissions to         slurm…@lists.schedmd.com To subscribe or unsubscribe via the World Wide Web, visit         lists.schedmd.com/cgi-bin/mailman/listinfo/slurm-users or, via email, send a message with subject or body ‘help’ to         slurm-use…@lists.schedmd.com You can reach the person managing the…

hello everyone i installed jupyter in my cluster but it seems that cm-jupyterhub.service cant start from the error that i got i think its about jupyter cant find its module file can someone check with me because i dont know where to start to fix this systemctl status cm-jupyterhub.service ●…

Prokka installation – compilation aborted 0 Hi, I installed Prokka using this code posted at github.com/tseemann/prokka sudo apt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl sudo cpan Bio::Perl git clone github.com/tseemann/prokka.git $HOME/prokka $HOME/prokka/bin/prokka –setupdb All the steps worked pretty well except the last line for database indexing $HOME/prokka/bin/prokka –setupdb I…

fastq-dump – connection failed 1 Hi, I need to install a specific RNA sequence data using sra toolkit. I installed the toolkit using this command: sudo apt install sra-toolkit Then confirmed installation by which fastq-dump and got this /usr/bin/fastq-dump But when downloaded SRR21627290 fastq-dump –stdout -X 2 SRR21627290 I got…

Endless Updating service celery-beat message with galaxy 0 Hello, I am trying to run galaxy and upon running sh run.sh (after successfully running it the first time and installing venv and all required galaxy packages, my galaxy script is stuck at Updating service celery-beat Activating virtualenv at .venv Requirement already…

hi, I use aishell recipe and running asr_train.py. When I use single GPU, it work well. However, when I use 2GPU, it finish training at the end of first epoch and throw the error: KeyError: ‘validation/main/loss’ error. [J/home/lcf/anaconda3/envs/python36/lib/python3.6/site-packages/torch/nn/parallel/_functions.py:61: UserWarning: Was asked to gather along dimension 0, but all input tensors…

You can use scale_x_continuous to modify how the x axis scale looks. You can change the number of breaks using n.breaks or adjust using breaks or labels. The documentation gives great detail, and this book is an awesome resource for understanding scales a bit better (and ggplot2 as a whole)….

Tell me if I’m in the way. I have the CRAM file and the respective CRAI (index). So I just ran the SAM like this, clipping my area of interest: > $ samtools view -b NG1PSZ7BE9.mm2.sortdup.bqsr.cram “chrX:147912050-147912110” > result.bam Then I indexed the .bam file: > $ samtools index result.bam…

I’m working on using Bazel to compile the C++ distribution of pytorch as an external library. I used the process provided in the solution here and was able to setup libtorch as a external library/remote repository. My file directory follows that of the one shown in the article. I verified…

gspazmino (GiulianaPazmino) May 15, 2023, 3:21pm 1 Hi!I need some help. I am currently trying to export a biom table from a .tsv format.I run the following command:biom add-metadata -i exported/feature-table.biom -o table-with-taxonomy.biom –observation-metadata-fp biom-taxonomy.tsv –sc-separated taxonomy But the following error appeared:Traceback (most recent call last):File “/Users/giulianapazmino/miniconda3/envs/qiime2-2023.2/bin/biom”, line 11, in…

I am trying to use wrappers in my pipeline on a SLURM cluster, where the compute nodes do not have internet access. I have run the pipeline with –conda-create-envs-only first, and then changed the wrapper: directives to point to local folders containing environment.yaml files. Jobs fail without specific error. Test…

GROMACS version: 2023GROMACS modification: No My desktop has Intel(R) Core™ i9-10900K CPU @ 3.70GHz processor and Nvidia RTX 4090 GPU. This is gromacs version installed on my systemgmx –version GROMACS version: 2023Precision: mixedMemory model: 64 bitMPI library: thread_mpiOpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)GPU support: CUDANB cluster size: 8SIMD instructions: AVX2_256CPU…

The pytorch DEBUG build crashes cicc nvcc error : ‘cicc’ died due to signal 11 (Invalid memory reference) nvcc error : ‘cicc’ core dumped Here’s a sample (generated) command that causes a crash /opt/cuda/bin/nvcc -forward-unknown-to-host-compiler -DAT_PER_OPERATOR_HEADERS -DHAVE_MALLOC_USABLE_SIZE=1 -DHAVE_MMAP=1 -DHAVE_SHM_OPEN=1 -DHAVE_SHM_UNLINK=1 -DIDEEP_USE_MKL -DMINIZ_DISABLE_ZIP_READER_CRC32_CHECKS -DONNXIFI_ENABLE_EXT=1 -DONNX_ML=1 -DONNX_NAMESPACE=onnx_torch -DTORCH_CUDA_BUILD_MAIN_LIB -DUSE_C10D_GLOO -DUSE_C10D_MPI -DUSE_C10D_NCCL -DUSE_CUDA…

Non-Coding RNA 2023, 9(3), 31; doi.org/10.3390/ncrna9030031 (registering DOI) Non-Coding RNA 2023, 9(3), 31; doi.org/10.3390/ncrna9030031 (registering DOI) Received: 26 March 2023 / Revised: 8 May 2023 / Accepted: 9 May 2023 / Published: 15 May 2023 Round 1 Reviewer 1 Report Dear authors, I have read with interest your paper. I find it…

After deploying the pytorch environment on jetson nano, an error is reported when using pytorch efficiency analysis make sure PyTorch is built with USE_KINETO=1″“”AssertionError: Requested Kineto profiling but Kineto is not available,make sure PyTorch is built with USE_KINETO=1 code show as belowtime_test.py (1.6 KB) Hi @18981275647, which PyTorch wheel did…

Cerejeira, J., Lagarto, L. & Mukaetova-Ladinska, E. B. Behavioral and psychological symptoms of dementia. Front. Neurol. 3, 73 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Murphy, M. P. & LeVine, H. III Alzheimer’s disease and the amyloid-beta peptide. J. Alzheimers Dis. 19, 311–323 (2010). Article  PubMed  PubMed Central  Google…

GROMACS version: gromacs/2021.4_cuda-11.4.3 [supercomputer]GROMACS modification: No Hello everyone! I am currently trying to the prepare protein-ligand complex. As I tried to do the grompp command, I’ve encountered 24 errors. [See below] I am using the latest CHARMM folder (jul2021) and have used the CGenFF in generating the .str file. I’d…

Hello all, I’m looking for guidance on how to write a non-interactive job script for qiime2. The HPC I have access to uses LSF and docker images, which are both new to me. So far, I have been creating an interactive shell to use qiime2 (I created a .sh file…

Error when converting hmmsearch output to gff file 0 Hello, I’m trying to convert a hmmsearch output to gff format. For this, I ran the following: hmmsearch –domtblout dom_results.txt –cpu 10 hydrocarbon.hmm orfs_file.faai > demo.log After getting the dom_Results.txt table, I ran the hmmer2gff program from the mgkit program: hmmer2gff…

Hi Jessica, On Sun, 2 Apr 2023 15:22:49 +0200 Paul Gevers <elb…@debian.org> wrote: Source: polyml Version: 5.7.1-5 Control: found -1 5.7.1-4 Severity: serious Your package has an autopkgtest, great. However, it fails since July 2020. Can you please investigate the situation and fix it? I copied some Looks like polyml…