Tag: LZMA

ubuntu – Medaka: unrecognized command ‘tools’ and samtools not found

When trying to run medaka_consensus in ubuntu, I am getting the following error. I installed into a virtualenv to run on ubuntu. (medaka) ubuntu:~/medaka$ medaka_consensus -i combined.fastq -d curated.fasta -t -o ~/medaka 10 -m r941_sup_plant_g610 TF_CPP_MIN_LOG_LEVEL is set to ‘3’ [main] unrecognized command ‘tools’ Attempting to automatically select model version….

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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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Issue VEP installation MacOS

Issue VEP installation MacOS 0 Hi, I’m trying to install VEP on Mac. I’ve tried on the Anaconda Navigator, but I couldn’t install. I also tried through the terminal, but also in this way I can’t install. The last error that I’ve got is: User cram/cram_io.c:61:10: fatal error: ‘lzma.h’ file…

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Feature flags of Rust-Htslib crate // Lib.rs

Cargo Features [dependencies] rust-htslib = { version = “0.44.1”, default-features = false, features = [“bindgen”, “bzip2”, “curl”, “gcs”, “libdeflate”, “lzma”, “s3”, “serde_feature”, “static”] } default = bzip2, curl, lzma These default features are set whenever rust-htslib is added without default-features = false somewhere in the dependency tree. bindgen Enables bindgen…

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rust-htslib 0.44.1 – Docs.rs

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files. To clone this repository, issue $ git clone –recursive github.com/rust-bio/rust-htslib.git ensuring that the HTSlib submodule is fetched, too. If you only want to use the library, there is no need to clone the…

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Error with dada2 while running Parkinson’s Mouse Tutorial – Technical Support

Hi, everyone. I’m new to qiime2 and I have a technical issue. I have the same problem with forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-255/21016 when I ran Parkinson’s Mouse Tutorial, but I noticed the problem didn’t solved in the website above.That’s my error info: Plugin error from dada2: An error was encountered while running DADA2…

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LAMMPS produce memory error with ReaxFF and OpenMP – LAMMPS Development

jhill April 19, 2023, 2:00pm 1 When I try to run attached LAMMPS input with:lmp -sf omp -pk omp 12 -in input.datI get a segmentation fault (LAMMPS 28Mar2023). Without OpenMP or on a GPU the calculation runs. There is nothing attached to your message. Please try the KOKKOS package instead…

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Processing samples… error during StrainPhlAn 4 run – StrainPhlAn

Hi, @aitor.blancomiguez ,Question: I am getting the following error when running StrainPhlAn 4. I had some problems in step 5 “build the multiple sequence alignment and the phylogenetic tree”,Where could be a problem? What I should search for? Database: I’m using sample data(cmprod1.cibio.unitn.it/biobakery4/github_strainphlan4/) Command: strainphlan -s consensus_markers/*.pkl -m db_markers/t__SGB1877.fna -r…

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Universal LAMMPS binaries for Linux – LAMMPS Installation

Dear LAMMPS Users, Today I would like to draw your attention to an experiment that may help people to get started with LAMMPS faster and lower the barrier to test your inputs with the latest LAMMPS versions before reporting a bug. Most people will need to compile LAMMPS themselves from…

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query regarding error in installation of “goseq” R bioconductor package

query regarding error in installation of “goseq” R bioconductor package 0 @6d5973d2 Last seen 19 hours ago India I am trying to install “goseq” Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are…

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bioconductor – Trouble installing Rhtslib in R/R studio

I’m using RStudio on Ubuntu 18 and I’m trying to install the htslib package from the Bioconductor repo, but I’m stuck now. This is what I get: * installing *source* package ‘Rhtslib’ … ** using non-staged installation via StagedInstall field ** libs cd “htslib-1.7” && make -f “/usr/lib/R/etc/Makeconf” -f “Makefile.Rhtslib”…

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Running samtools view on bam affects the number of variants called by both haplotypecaller and deepvariant – C samtools

Thanks for getting back to me Valeriu. As you suggested, I used the latest commit from the develop branch in my pipeline, and the results look good. I was able to replicate the numbers from samtools v1.10.2 and v1.11 for both variant callers. FYI $ docker run scilifelabram/htslib:dev_proper /opt/samtools/samtools version…

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install GenomicFeatures fail

install GenomicFeatures fail 1 @5b9023e7 Last seen 19 hours ago China BiocManager::install(‘GenomicFeatures’) results show ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) ‘GenomicFeatures’ also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’ Packages which are only…

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The Biostar Herald for Tuesday, August 17, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by lakhujanivijay,…

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