Tag: bin

Bug#1055414: bedtools: FTBFS on i386: “intersect” tool failure

Source: bedtools Version: 2.31.0+dfsg-1 Severity: serious Tags: ftbfs Justification: ftbfs Dear Maintainer, While making a routine metadata update on a Debian patch against bedtools, Salsa CI caught a build failure on i386[1] which I could reproduce multiple times in sid and in testing with the unmodified version of the package. [1]: salsa.debian.org/med-team/bedtools/-/jobs/4891166 The…

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Braker – gc_content.stderr

Good day! I am new to genome annotation. I want to annotate my genome using the Braker tool. I assembled my sample using SOAPdenovo2 and got a genome size of 1.3Gb, now when I try to annotate my genome I get a GC content error (I have shared the error…

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What is the difference between CNV binning and aligning to gene?

What is the difference between CNV binning and aligning to gene? 0 Hi All, I have datasets of Whole Genome Seq of cancer and non-cancer cell. I would like to investigate the copy-number variation between the two conditions. After aligning read to reference genome, there would be two possible ways…

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‘NoneType’ object has no attribute ‘utcoffset’

Source: undertime Version: 3.2.0 Severity: serious Tags: sid trixie User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. The release team has announced…

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assignment 05.pdf – Homework 5 of STAT 3355 Introduction to Data Analysis Question 1 Let’s work on the dataset diamonds in the package ggplot2. You can

Homework 5 of STAT 3355 Introduction to Data Analysis Question 1 Let’s work on the datasetdiamondsin the packageggplot2. You can use the following code to load the data. Use necessary code to read the description of the dataset, which contains53940samples and10variables. #Installthepackageifyouneverdid install.packages(“ggplot2“) #Loadthepacakge library(ggplot2) #Loadthempgdataset data(“diamonds”) Useggplot2to visualize the…

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Creating an OpenAPI generator from scratch : From YAML to JetBrains HTTP Client – DEV Community

This is the online version of the article with the same name I wrote for the Dutch Java Magazine 😊. Creating your own code generator for the @jetbrains http client from an #openapi specification? It’s possible and you can read how in the latest edition of the Dutch #java magazine!…

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[genome-www] Where can we find Repeats Fasta for CAST_EiJ genome assembly?

Hi Matthew and Robert,   HNY!  I have a question for the UCSC Genome Browser Help Desk I was wondering if you could advise us how to do this.  I downloaded the table information for the Track NumtS Sequence from the Group Variations and Repeats from the Mouse mm9 Assembly…

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sequence alignment – I can’t make mafft run inside my program

This is easy because MAFFT is installed via Conda, but you have not activated that Conda environment, thus it will not give you access to the program. If you type … conda activate labinf mafft This will now work. To activate this inside a shell script you simply include the…

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Index of /~psgendb/birchhomedir/admin/launchers/biolegato.app/Contents/Resources/pkg/transrate/bin

Name Last modified Size Description Parent Directory   –   bam-read 2016-06-06 08:37 5.4M   libgcc_s.so.1 2019-03-08 21:07 89K   libgomp.so.1 2019-03-08 21:07 83K   liblzma.so.0 2019-03-08 21:07 132K   libm.so.6 2019-03-08 21:07 582K   libtbb.so 2019-03-08 21:07 20   libtbb.so.2 2019-03-08 21:07 4.5M   libtbbmalloc.so 2019-03-08 21:07 26  …

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Error message in Standalone BLAST

Error message in Standalone BLAST 1 I was trying to make a nucleotide database for standalone blast. but this message keeps coming. Any suggestion to overcome this problem? BLAST Database error: No alias or index file found for nucleotide database [C:\Program] in search path [C:\Program Files\NCBI\blast-BLAST_VERSION+\bin;;] windows commandprompt StandaloneBlast NCBI…

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Development of a separation platform comprising magnetic beads combined with the CRISPR/Cas12a system enabling ultrasensitive and rapid detection of miRNA-21

Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR (2005) MicroRNA expression profiles classify human cancers. Nature 4357043:834–838 Article  Google Scholar  Volinia S, Calin GA, Liu C-G, Ambs S, Cimmino A,…

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Container is gone after start – JupyterHub

Hi ! I try to mount a jupyterhub container. The server seems to run smoothly but cannot create a user notebook container (DockerSpawner). After a few seconds, the container disappears. Hereafter is my jupyterhub log (user: donzel): [D 2023-11-03 14:18:16.039 JupyterHub application:908] Looking for /srv/jupyterhub/jupyterhub_config in /srv/jupyterhub [D 2023-11-03 14:18:16.054…

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Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls [PeerJ]

Introduction The microbiomes of different host organisms are currently described by using culture-independent sequencing methods (Harvey & Holmes, 2022). Shotgun metagenomic and 16S rDNA sequencing methods are commonly used to identify the taxonomic composition of microbial communities in several studies (de Melo et al., 2020; Mackelprang et al., 2011; Monaco…

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dplyr – installation error package/DESCRIPTION after upgrading R and R studio

Recently I updated R and R studio R version 4.3.2 (2023-10-31 ucrt) — “Eye Holes” Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) RStudio 2023.09.1+494 “Desert Sunflower” Release (cd7011dce393115d3a7c3db799dda4b1c7e88711, 2023-10-16) for windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.09.1+494 Chrome/116.0.5845.190 Electron/26.2.4 Safari/537.36…

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Q3 2023 Grid Dynamics Holdings Inc Earnings Call

Participants Anil Kumar Doradla; CFO & Secretary; Grid Dynamics Holdings, Inc. Leonard Livschitz; CEO & Director; Grid Dynamics Holdings, Inc. Bryan C. Bergin; MD of TMT – Services, HCM & Automation Software and Analyst; Cowen Inc. Joshua Michael Siegler; Research Analyst; Cantor Fitzgerald & Co., Research Division Maggie Nolan Mayank…

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ANGSD beagle generation returning empty file

ANGSD beagle generation returning empty file 0 Hello Biostars community, I am struggling quite a bit with ANGSD these days as it seems that no code I provide to the machine is working as intended. I want now to produce a beagle file but the following script is returning me…

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How to install or uninstall “gromacs-openmpi” on Ubuntu 21.10 (Impish Indri) ?

1. Install gromacs-openmpi package Here is a brief guide to show you how to install gromacs-openmpi package: sudo apt install gromacs-openmpi Copy 2. Uninstall / Remove gromacs-openmpi package Please follow the guidelines below to uninstall gromacs-openmpi package: sudo apt remove gromacs-openmpi Copy sudo apt autoclean && sudo apt autoremove Copy…

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Optimizing LAMMPS for my purposes – LAMMPS Beginners

Nope, still can’t post.pastebin.com/uXpAuPnySidenote, Pastebin flagged it as potentially harmful…Edit: I could only post it as private, I’m linking here instead. LAMMPS (2 Aug 2023 – Development – patch_2Aug2023-427-g75682ffbca) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task package gpu 0 echo…

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Got an error when using chilin

Got an error when using chilin 0 I installed chilin and all the dependencies following the guidance, but when I run bash foxa1 and my own data, I got an error as below: Traceback (most recent call last): File “/chipseq/3.fastqc/chilin/software/mdseqpos/bin/MDSeqPos.py”, line 421, in <module> main() File “/chipseq/3.fastqc/chilin/software/mdseqpos/bin/MDSeqPos.py”, line 385, in…

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140releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere3/data/140releng-armv7-default/08943441f26e/logs/py39-pytorch-2.0.1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=140releng-armv7-default&build=08943441f26e Log: =>> Building misc/py-pytorch build started at Thu Nov 2…

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8 Tips for Documenting API Specification

Previously, you might have been using Swagger 2.0 (also known as OAS 2), but now, it’s time to upgrade to the OpenAPI Specification (OAS) 3. In this article, we will outline the key points of the upgrade process and the essentials of documenting APIs using OAS 3. Some of these…

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RStudio Guide | The GitLab Handbook

RStudio Guide {:toc .toc-list-icons .hidden-md .hidden-lg} {::options parse_block_html=“true” /} What is R? Similar to Python, R is an open-source statistical software that is used to clean and analyze data. It is popular within the data science community and has many packages that make statistical modeling easier for statisticians and data…

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Snakemake issue with wrappers

I have issues when running a wrapper of BWA mem with Snakemake. The error message “No module named ‘snakemake_wrapper_utils’” appear (see below). However, when checking if the package is installed in Python, I found the following: import snakemake_wrapper_utils print(snakemake_wrapper_utils.__version__) 0.1.0 Did anyone have this problem? Would you know why there…

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Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations

Ethical statement Our research complies with all relevant ethical regulations, including the Declaration of Helsinki and has been approved by the Institutional Review Boards of University of Chicago, Duke University and the Alliance to Cure Cavernous Malformations. Cerebral cavernous malformation lesions All human CCM tissue specimens have been previously reported18,19…

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Wrong with code_coverage – C++

When I run python oss_coverage.py –run-only=test_complex.py, I get a Warning pytorch/tools/code_coverage/package/util/../../profile/raw/test_complex.py.profraw: unsupported instrumentation profile format version and a Error error: no profile can be merged The results as follows: (pytorchcov) myconda@.. code_coverage % python oss_coverage.py –run-only=test_complex.py …. ———————————————————————- Ran 4 tests in 0.002s OK …. ———————————————————————- Ran 4 tests in…

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CombineGVCFs skips a chromosome

Hi! I am having issues for the first time with CombineGVCFs. Specifically, it outputs a combined gvcf without chromosome 8 (SUPER_8) even though this is present in the individual gvcfs that I input in the command. There is no error in the log file, the engine just shuts down after…

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An extremely fast Non-Overlapping Exon Length calculator written in Rust

Hi all! Introducing the Non-Overlapping Exon Length calculator (NOEL), an extremely fast GTF/GFF per gene exon length extractor written in Rust. See the code and latest updates here: github/alejandrogzi/noel In case you do not want to read the whole text: NOEL outperforms all open-sourced scripts/tools for this task. It can…

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run-bwamem from BWAKIT does not work

run-bwamem from BWAKIT does not work 1 Hi, everyone! I am currently performing HLA typing analysis using the bwakit-0.7.17 for Linux Mint 20. The problem comes when running the “run-bwamem” file, when we obtain empty output files. We have even tried to perform it through Miniconda by typing the next:…

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Quickstart to Lightning Fabric – Lightning AI

Takeaways Readers will learn how to convert and scale PyTorch models and training loops with Lightning Fabric. Introduction Some engineers may prefer the greatest amount of control as possible over their PyTorch training loop. Yet, those same engineers also know the benefits of a lightweight, production ready framework that handles…

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Index of /~psgendb/birchhomedir/FTP/doc/local/bin-linux-x86_64

Name Last modified Size Description Parent Directory   –   Translate 2003-02-20 12:39 111K   caf2caf 2010-11-27 18:22 4.6M   caf2fasta 2010-11-27 18:22 4.6M   caf2gbf 2010-11-27 18:22 4.6M   caf2html 2010-11-27 18:22 4.6M   caf2tcs 2010-11-27 18:22 4.6M   caf2text 2010-11-27 18:22 4.6M   convert_project 2010-11-27 18:22 4.6M  …

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Epigenetic regulation during cancer transitions across 11 tumour types

Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…

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How to extract specific region from multiple bam files and merge the outputs into single bam?

How to extract specific region from multiple bam files and merge the outputs into single bam? 0 I have more than 50 bam files and wanted to extract the reads from a region from all those bam files and merge the outputs into a single bam. I’m using samtools for…

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Pacific Biosciences of California, Inc. (NASDAQ:PACB) Q3 2023 Earnings Call Transcript

Pacific Biosciences of California, Inc. (NASDAQ:PACB) Q3 2023 Earnings Call Transcript October 30, 2023 Pacific Biosciences of California, Inc. beats earnings expectations. Reported EPS is $-0.26, expectations were $-0.3. Operator: Good afternoon, everyone, and welcome to the PacBio Third Quarter 2023 Earnings Conference Call. All participants will be in a…

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No –bgen REF/ALT mode specified

runPLINK <- function(PLINKoptions = “”) system(paste(“/opt/apps/plink/2.0/bin/plink2”, PLINKoptions))runPLINK() runPLINK(“–bgen /DATA/shared/bcac/genotypes/v10/bgen/icogs_euro/iCOGS_european_chr21.bgen –out /DATA/users/m.shokouhi/plink/plink2”) The mentioned code makes PGEN/PVAR/PSAM files but there is a warning in the procedure: No –bgen REF/ALT mode specified. In plink2 website it is written that it considers the first allele as a reference allele if you do not specify…

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Q3 2023 Pacific Biosciences of California Inc Earnings Call

Participants Christian O. Henry; President, CEO & Director; Pacific Biosciences of California, Inc. Susan G. Kim; CFO; Pacific Biosciences of California, Inc. Todd Friedman; Former Director of IR; Pacific Biosciences of California, Inc. Daniel Gregory Brennan; MD and Senior Tools & Diagnostics Analyst; TD Cowen, Research Division Eve Burstein Jack…

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[slurm-users] multiple srun commands in the same SLURM script

Here is my SLURM script: #!/bin/bash #SBATCH –job-name=”gpu_test” #SBATCH –output=gpu_test_%j.log # Standard output and error log #SBATCH –account=berceanu_a+ #SBATCH –partition=gpu #SBATCH –cpus-per-task=1 #SBATCH –mem-per-cpu=31200m # Reserve 32 GB of RAM per core #SBATCH –time=12:00:00 # Max allowed job runtime #SBATCH –gres=gpu:16 # Allocate four GPUs export SLURM_EXACT=1 srun –mpi=pmi2 -n 1 –gpus-per-node 1 python gpu_test.py & srun…

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samtools sort- no output file generated

samtools sort- no output file generated 3 Hi, I am doing variant calling and am using samtools sort o sort my .bam files. I have 40 threads in my workstation [Thread(s) per core:2; Core(s) per socket:10; Socket(s):2]. So, I used the following command $ samtools sort brs11b.bam -o brs11_sorted.bam -@…

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BDQ resistance and molecular characterization of RR-TB

Enyu Tong,1,&ast; Ying Zhou,1,&ast; Zhengwei Liu,2 Yelei Zhu,2 Mingwu Zhang,2 Kunyang Wu,2 Junhang Pan,2 Jianmin Jiang1– 3 1School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China; 2Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China; 3Key Laboratory of…

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Restart a simulation in LAMMP – LAMMPS General Discussion

Dear LAMMPS users,I want to restart a simulation in LAMMPS. I followed instroduction in LAMMPS document at this link: 8.1.1. Restart a simulation — LAMMPS documentationWhen I check atomic positions followed by the instroduction, I see the results are not the same.Could anyone explain to me, please?Thank you very much….

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How to Install DataSpell on Linux: A Comprehensive Guide

With the boom of AI and data science, there’s a rise in the need for data scientists and machine learning engineers as well. Those engineers and developers need tools like an IDE to write their code and train models. A specialized IDE can enhance their workflow and improve their efficiency….

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CIMB | Free Full-Text | mtDNA Single-Nucleotide Variants Associated with Type 2 Diabetes

1. Introduction Type 2 diabetes (T2D) is the most prevalent metabolic disease and a significant public health concern [1,2], leading to early-onset disability and elevated mortality due to various related complications [3]. Between 1990 and 2017, the global trend in the age-standardized rates of T2D, as measured by the number…

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Deep Q Learnig with PyTorch

Introduction This blog is going to be my second one on Reinforcement Learning. You can check out the first one here. This blog will show how to use Deep Q Learning (DQN) to solve a reinforcement learning task. As an example, we will deploy DQN to solve the classic CartPole…

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Pytorch torch.distributed.launch v. torchrun | Wyzant Ask An Expert

I found this GitHub Repo, github.com/hbzju/pico, which trains a pytorch model to identify mislabeled data in a dataset. I don’t have much experience with torch and am trying to modify the repo’s code to train the model on my dataset. Running this command: python3 -m torch.distributed.launch –nproc_per_node 2 train.py \…

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Bug#1054792: lammps: FTBFS: dh_install: error: missing files, aborting

Source: lammps Version: 20220106.git7586adbb6a+ds1-2 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu…@debian.org Usertags: ftbfs-20231027 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[2]: Entering directory ‘/<<PKGBUILDDIR>>/debian/build’ > make[2]: Nothing to be done for ‘preinstall’. >…

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Clustering while deforming stulls the run – LAMMPS Development

I have a script where I first create a system in a grid, then deform it under NVE+langevin to the desired dimensions, then relax it under NPH+langevin. I want to track certain cluster sizes so it is implemented in LAMMPS. The issue is the following. The run stulls at a…

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How to run multiple jobs, one per GPU, with SLURM?

Apologies if this has be asked/answered before, but even after reading everything I can find, I am struggling to get SLURM to do what I want. Let’s say I have a machine with 4 GPUs. I want to train 4 models in parallel, each job running on a single GPU….

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Keywords in command line for getting good performance in gromacs – User discussions

I am trying to run gromacs 2023.2 gpu on HPC. I am getting super slow performance in HPC. I run the calculation for the test purpose on 8 cores for 10 mins only. The projected steps of calculation is about 15,000 in 10 minuites, unfortunately couldn’t get performance upto mark….

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[ccp4bb] AlphaFold Database introduces sequence-based search and structure cluster members

Dear all, We are excited to announce two significant functionalities added to the AlphaFold Protein Structure Database (AlphaFold DB). The database has expanded since its inception in 2021 to cover over 214 million predicted structures from Google Deepmind’s AlphaFold 2 system. We now introduce sequence similarity-based search and enhanced prediction…

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BrdU analysis of yeast replication

BrdU analysis of yeast replication 0 Hi all, I would like to ask how people normalise their data of BrdU-IP sequencing? This is a plot of BrdU-IP-seq across a region in chromosome V in yeast. BrdU labels nascent DNA so here I am basically seeing newly replicated DNA as the…

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Fedora 37 : mbedtls (2023-e0ab860391) – vulnerability database

Fedora 37 : mbedtls (2023-e0ab860391) – vulnerability database | Vulners.com {“id”: “FEDORA_2023-E0AB860391.NASL”, “vendorId”: null, “type”: “nessus”, “bulletinFamily”: “scanner”, “title”: “Fedora 37 : mbedtls (2023-e0ab860391)”, “description”: “The remote Fedora 37 host has a package installed that is affected by a vulnerability as referenced in the FEDORA-2023-e0ab860391 advisory.\n\n – Mbed TLS 2.x…

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TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells

Animal models Animal studies were approved by the Institutional Animal Care Use Committee of the Institute of Biosciences and Technology, Texas A&M University (AUP 2020-0195). Most mouse strains bear a C57BL/6 genetic background unless otherwise noted. All the animals were housed in a certified animal facility with a standard dark/light…

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Gromacs 2023 installation issue, slower run with gmx_mpi on multiple nodes – User discussions

GROMACS version: 2023GROMACS modification: NoHere post your question I am trying to install Gromacs 2023 on an HPC and hoping to do it correctly to get highest performance possible. HPC has Dual Intel Xeon Gold Skylake 6154 (3.0 GHz, 18-core) processors and Dual NVIDIA Tesla V100 PCIe 16 GB Computational…

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python – Error in snakemake when running conda envs in container

I am facing an issue when running snakemake with a container and conda. Let me explain better. I am developing a workflow (locally) in snakemake, where some rules use a conda env (defined in /envs/env.yaml) and other rules use wrappers (so they also are based on conda envs). An example…

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Bioconductor – Bioconductor 3.18 Released

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

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DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages

Parasite culture, maintenance, synchronization and transfection The DiCre-expressing P. falciparum clone II3 (ref. 10) was maintained in human A+ erythrocytes at 37 °C in Roswell Park Memorial Institute 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM l-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using…

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Rstudio does not found R, but R is install – RStudio IDE

Hi,Here is my PC configuration : Ubuntu 22.04.3 I am trying to install Rstudio on my computer (version rstudio-2023.09.1-494-amd64)The install goes at the end but when i am trying to open Rstudio , there is a prompt with the messqge : R dos not appear to be installed.please install R…

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Could connect to the R session on RStudio Server – R Admins

I ran a RStudio Server on a cent-os7 server and it used to work fine for a long time.Recently I got the error when login remotely from the web browser,Could connect to the R session on RStudio Server. Error occurred during transmission (6).I have tried several solutions such as 1)…

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Precompiling IJulia times out – Kernels

I’m having an issue starting Julia kernels and the Pluto interface when using the jupyter/datascience-notebook image as a base to build my own image. The issues occur when running locally on my Macbook (M1) and when used on a JupyterHub hosted on GCP. When using the jupyter/datascience-notebook image “as is”,…

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python – Error “Microsoft Visual C++ 14.0 is required (Unable to find vcvarsall.bat)”

TLDR run vcvars64.bat After endlessly searching through similar questions with none of the solutions working. -Adding endless folders to my path and removing them. uninstalling and reinstalling visual studio commmunity and build tools. and step by step attempting to debug I finally found a solution that worked for me. (background…

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STARsolo seg fault without readMapNumber flag

STARsolo seg fault without readMapNumber flag 0 Hi, So I’m trying to use STARsolo on a couple of datasets and having strange issue, when running the following command via slurm and NOT using the –readMapNumber flag I always get a segmentation fault when the counting begins irrespective of different thread…

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Solved Now write an R script with the contents shown below

Now write an R script with the contents shown below to import the Salmon alignments into `DESeq2` and perform differential expression analysis. As with the previous script, since I provide the complete script, look up each of the functions used and make sure you understand how they are used here….

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gnu parallel – How to get reliable results on SLURM for performance tests?

I want to benchmark two algorithms ALG1 and ALG2 against each other using SLURM. Both binaries ALG1.o and ALG2.o contain serial implementations of the algorithms. In now, that ALG1.o is always faster than ALG2.o. Since I have thousands of experiments I want to use our cluster to run them. Each…

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Gmx rdf selection (selrpos and seltype) – User discussions

GROMACS version: 2021.5GROMACS modification: Yes/NoHere post your question Hello anyone, i want to ask about selection (selrpos and seltype) in rdf analysis Currently i am working on polymer and run MD simulation for pre-polymerization mixture I want to analyze rdf in 2 component in my system In molecule 1 i…

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main-powerpc64le-default][misc/pytorch] Failed for pytorch-1.13.1_1 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/main-powerpc64le-default/pbc0e38d0f08e_s0afcac3e37/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=pbc0e38d0f08e_s0afcac3e37 Log: =>> Building misc/pytorch build started at Tue Oct 24…

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R-Studio 9.3.191.251

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…

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vanengers/php-openapi-client-generator – Packagist

Generate a PHP client for an OPENAPI specification Installation composer require –dev vanengers/php-openapi-client-generator Usage OPENAPI=http://127.0.0.1:8000/docs.json NAMESPACE=VendorName\\PackageName\\Generated OUTPUT_DIR=src/Generated ./bin/api-client-generator generate Specify the openapi specifications JSON file OPENAPI=http://127.0.0.1:8000/docs.json Specify the namespace for the generated classes NAMESPACE=VendorName\\PackageName\\Generated Specify the output directory for the generated classes OUTPUT_DIR=src/Generated Run the generator ./bin/api-client-generator generate Example client…

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Error regarding fetching “hguid” cookie

Hello,  I am wondering if fetching data from UCSC is currently unavailable, because when I use the R/Bioconductor packages Gviz and rtracklayer, I receive the following same error.  1. library(Gviz) IdeogramTrack(genome=”hg38″,chromosome=”chr16″,fontsize=30,Gviz.ucscUrl=”genome.ucsc.edu/cgi-bin“)# Error in .local(.Object, …) : Failed to obtain ‘hguid’ cookie 2. library(Gviz) cpgIslands <- UcscTrack(genome = “hg38”, chromosome =…

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Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Abstract Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which…

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Custom Z2JH image creation using jupyter-repo2docker – Zero to JupyterHub on Kubernetes

Hello, members. 1. Goal I would like to create a custom image for Z2JH using jupyter-repo2docker command. jupyter-repo2docker github.com/norvig/pytudes works fine. 2. Question Does Z2JH use jupyter-repo2docker for creating a support images (ex. jupyter/pyspark-notebook) ? Is Z2JH base_image jupyter/base-notebook? Does anyone know how to avoid this error? (Maybe macOS docker…

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NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection

        NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…

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Re: How to create Postman collection for Apigee X?

As far as I know, Postman does not directly support creating an Open API Specification from the Apigee discovery document: ‘apigee.googleapis.com/$discovery/rest?version=v1‘ But, it can be done using: github.com/stackql/google-discovery-to-openapi Steps:   git clone github.com/stackql/google-discovery-to-openapi npm install chmod 755 bin/google-discovery-to-openapi.mjs bin/google-discovery-to-openapi.mjs   It will generate an OAS (3.1) for each of the services, Apigee…

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Body found inside Georgia dumpster 35 years ago identified

A body found wrapped in plastic inside a Georgia dumpster in 1988 has been identified, marking the first major breakthrough in the cold case in 35 years. Investigators used DNA analysis, paid for by donors from Project Justice, to determine the remains found in a garbage bin in rural Millen…

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r – How to increase size of the point of ggplot with new “hits” on that specific ordered pair?

I have a plot like this library(scattermore) library(ggplot2) gg <- ggplot() for (i in 1:6){ query <- exp_df[[i,1]] sup <- exp_df[[i,2]] query_path <- paste0(query,”.sscore.csv”) sup_path <- paste0(sup,”.sscore%0D.csv”) shell_command <- sprintf(“/bin/bash -c ‘paste -d, <(cut -d, -f4 %s) <(cut -d, -f4 %s)'”, query_path, sup_path) count_pairs <- system(shell_command, intern = TRUE) count_pairs_matrix…

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BLAST database error

BLAST database error 1 Hello, For my project I downloaded blast+ executables and also a database using this: perl ../ncbi-blast-2.14.1+/bin/update_blastdb.pl –passive –decompress nt_euk.01 Then I tried to extract fasta sequence from this nt_euk.01 database using this command: blastdbcmd -entry all -db nt_euk.01 -out nt_euk1.fasta But it gave me this error:…

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HOXC-AS3 as an Oncological Biomarker and Therapeutic Target

1Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, People’s Republic of China; 2Department of General Surgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, Jiangxi, 332007, People’s Republic of China; 3Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330038, People’s Republic of China Correspondence: Hongliang Luo,…

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parallel processing – Is it possible to run multiple Slurm job-steps which us a single GPU?

I have been trying to use Slurm to run multiple job steps on a single GPU. I know memory won’t be an issue if the jobs were able to run, however only the first job step will run in the below sequence. I have seen multiple places where the issues…

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r – Problems with Rprofile, dont load at startup

I have a R (4.2.2) and RStudio (2023.06.2) installed on a MacOS system, before I update Rstudio I have no problem, but with those version I don’t how to load .Rprofile at startup RStudio. The defaul working directory for RStudio is in ~/R and my ~/.Rprofile is at home file.path(Sys.getenv(“HOME”),…

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Install python lammps in a non-standard directory – LAMMPS Installation

izosgi October 23, 2023, 1:20pm 1 Dear all, I am trying to install LAMMPS v2Aug2023.update1 in a cluster.I am using EasyBuild to do this, but it does not succeed to install the python lammps/ directoy into non standard: $LAMMPS_DIR/lib64/python/python3.10/site-package I use cmake and enable python, but the system does not…

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R-Studio 7.3.191246 download free | macOS

R-Studio for Mac is specially designed for the Mac OS environment, including the Apple M1/M2 chip. It recovers files from APFS/HFS+/HFS (Macintosh), FAT/NTFS/ReFS (Windows), UFS1/UFS2 (FreeBSD/OpenBSD/NetBSD/Solaris) and XFS/Ext2/Ext3/Ext4 FS (Linux) partitions. In addition, raw file recovery (scan for known file types) can be used for heavily damaged or unknown file…

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OrthoMCL installation on Ubuntu Linux

About OrthoMCL OrthoMCL is a software used for assigning proteomes to ortholog groups. About this tutorial These are the steps I followed to install OrthoMCL on an Ubuntu 14.04 Linux server using MySQL as the database system. Requirements Ubuntu 14.04 (tested). Might work on other versions. All these steps are…

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Identification and Characterization of CtUGT3 as the Key Player of Astragalin Biosynthesis in Carthamus tinctorius L.

journal contribution posted on 2023-10-23, 12:35 authored by Chaoxiang Ren, Ziqing Xi, Bin Xian, Chao Chen, Xulong Huang, Huajuan Jiang, Jiang Chen, Cheng Peng, Jin Pei Safflower (Carthamus tinctorius L.) is a multipurpose economic crop that is distributed worldwide. Flavonoid glycosides are the main bioactive components in safflower, but only…

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Error Message from Diamond in humann v3.8 – HUMAnN

Hello,Iam trying to execute humann v3.8 for particular sample with input around 34 million. The sample has went through kneadata and Metaphlan4 separately. So the input for humann v3.8 is the fastq file from Kneaddata and taxonomy profile from metaphlan4. Tried this approach for various samples separately with resources as…

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Question on samtools view with –fast option

Question on samtools view with –fast option 0 Hi I had a question on samtools view with –fast option. I was trying to find any relevant docs and/or blogs detailing its usage and how best to use it. I could not find any and I thought I will ask the…

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Solved Using R-Studioa. Find the mean, median, variance, and

Using R-Studio a. Find the mean, median, variance, and standard deviation for stock_price. Interpret what the standard deviation tells you (be specific; don’t just give me the general definition of the standard deviation). b. For stock_price, how many companies fall within one standard deviation above the mean? c. Using ggplot,…

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[slurm-users] problem with slurm configuration and pmix

Hi I clone the slurm repository from github (version 23.11), and tried to configure it as follows: configure –config-cache –prefix=/usr/slurm_vm_23.11 –sysconfdir=/etc/slurm_vm_23 –with-http-parser=/usr/ –with-yaml=/usr/ –with-jwt=/usr/ –with-mysql_config=/usr/bin –enable-debug –with-pmix=/usr/lib/x86_64-linux-gnu/pmix2 But I receive the following error message: configure: error: unable to locate pmix installation I checked the pmix installation location, and it exists. I…

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Adversarial and variational autoencoders improve metagenomic binning

Overview of AAMB The AAMB workflow consists of the following main steps (Fig. 1a). First, Tetra Nucleotide Frequencies (TNF) and per sample co-abundances (Coab) are extracted from the contigs and BAM files of reads mapped to contigs, and input to the AAMB model as a concatenated vector. The AAMB model encodes…

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[ccp4bb] PDBe ligands API survey

Dear all, We are excited to inform you of some upcoming enhancements to PDBe’s ligand-related API endpoints and are seeking your valuable insights! *We are running this survey (forms.gle/agPUGCn59ffuayp57) *to collect information on two crucial points: – *Current Usage of PDBe’s Ligand-Related API Endpoints*: We want to understand which of…

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GMX_MPI running – User discussions

Hi everyone!I have some problems with running gmx_mpi on more then one nodes. I have 4 nodes to run with 64 threads, but when i use slurm script with “mpirun gmx_mpi …”, gromacs starts the process on 4 nodes with… 32 cores in total, when 4 nodes will be with…

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What are unbinned contigs ?

What are unbinned contigs ? 1 Hello community, by taking a look into the number of binned contigs from a binning refinement procedure I notice that the number of contigs employed to make bins or MAGs are less than half of the number of contigs produced by the assembly procedure….

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linux – SLURM able to send CPU, but not GPU jobs

I’ve built out a slurm “cluster” (just a job server and single compute server at the moment) and am trying to run jobs on it. I can run CPU jobs just fine, it sends them to the machine and runs them. However, when I try to run a GPU job,…

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error running gmx_MMPBSA HPC

Hello, I’m trying to run gmx_MMPBSA on the university cluster. The following error is occurring: [INFO ] Building AMBER topologies from GROMACS files… [INFO ] Get PDB files from GROMACS structures files… [INFO ] Making gmx_MMPBSA index for complex… [DEBUG ] Running command: echo -e “name 1 GMXMMPBSA_REC\n name 13…

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python – unable to install PyTorch

PyTorch is working in commandline but unable to run in Pycharm IDE.Got the error on following code. import torch print(torch.version) /Users/jamil/PycharmProjects/pythonProject/venv/bin/python /Users/jamil/PycharmProjects/pythonProject/main.py Traceback (most recent call last): File “/Users/jamil/PycharmProjects/pythonProject/main.py”, line 1, in import torch ModuleNotFoundError: No module named ‘torch’ want to use torch in pycharm Read more here: Source link

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Error on Chimera

I’m learning to use the chimera, but I encountered these two errors, how can I fix them? 1- Receptor and ligand cannot be the same model and 2- Traceback (most recent call last): File “C:\Program Files (x86)\MGLTools-1.5.6\Lib\site-packages\AutoDockTools\bin\runAdt.py”, line 16, in <module> AutoDockTools.runADT(sys.argv, ownInterpreter=ownInterpreter, AdtScriptPath=__file__) File “C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\__init__.py”, line 233,…

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Changed from an Icarus to a Icarus_SoM gaves error compiling – Nordic Q&A – Nordic DevZone

Hi, I’m trying to use the code of a board from Actinius in another board from Actinius but a SoM. When compiling I’ve got one error that I can’t understand. This is probably because of the configurations. [133/311] Building C object CMakeFiles/app.dir/src/modules/gpios/gpios.c.objFAILED: CMakeFiles/app.dir/src/modules/gpios/gpios.c.obj C:\ncs\toolchains\v2.3.0\opt\zephyr-sdk\arm-zephyr-eabi\bin\arm-zephyr-eabi-gcc.exe -DKERNEL -DLFS_CONFIG=zephyr_lfs_config.h -DMBEDTLS_CONFIG_FILE=\”nrf-config.h\” -DMBEDTLS_USER_CONFIG_FILE=\”nrf-config-user.h\” -DNRF9160_XXAA -DNRF_SKIP_FICR_NS_COPY_TO_RAM…

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Merge fastq files across different lanes in Nextflow

Hello, I’m trying to concatenate fastq files using Nextflow but I noticed that it doesn’t seem to work the way I wanted it to be. I saw this post (Merge fastq files ) and basically copied it off. nextflow.enable.dsl=2 def getLibraryId( prefix ){ // fastqfile = ABC-S16_L001_R1_001.fastq.gz, ABC-S16_L002_R1_001.fastq.gz prefix.split(“_”)[0] }…

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Chromatin compartmentalization regulates the response to DNA damage

Cell culture and treatments DIvA (AsiSI-ER-U2OS)19, AID-DIvA (AID-AsiSI-ER-U2OS)23 and 53BP1-GFP DIvA20 cells were developed in U2OS (ATCC HTB-96) cells and were previously described. Authentication of the U2OS cell line was performed by the provider ATCC, which uses morphology and short tandem repeat profiling to confirm the identity of human cell…

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Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice

Mouse strains All mouse procedures were approved by the Institutional Animal Care and Use Committees at Binghamton or Stanford University; and were conducted in accordance with the National Institute of Health Guide for Care and Use of Laboratory Animals, Eighth Edition. All mice were originally obtained from Jackson Laboratories, and…

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Different Output from lammps cpu vs gpu

Why energy/pressure are slighly off, what is possible solution for making them equal. Any suggestion/comment? clear package gpu 1 neigh no binsize 5.0 newton off units metal boundary p p p atom_style atomic variable lp equal “2.86” lattice bcc ${lp} orient x 1 0 0 orient y 0 1 0…

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