Tag: Ubuntu

How to fix deeptoolsintervals fatal error: python.h? ( Python, Python 3.X )

Problem : ( Scroll to solution ) I tried installing pip3 install deeptoolsintervals the error is: deeptoolsintervals/tree/tree.c:1:20: fatal error: Python.h: No such file or directory compilation terminated. error: command ‘/usr/bin/x86_64-linux-gnu-gcc’ failed with exit code 1 I have Ubuntu 16.04.7 and Python versions installed: ls /usr/bin | grep python dh_python2 dh_python3…

Continue Reading How to fix deeptoolsintervals fatal error: python.h? ( Python, Python 3.X )

[Bug 1786013] Autopkgtest regression report (linux-meta-hwe-5.13/5.13.0.28.31~20.04.15)

All autopkgtests for the newly accepted linux-meta-hwe-5.13 (5.13.0.28.31~20.04.15) for focal have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-340/340.108-0ubuntu5.20.04.2 (amd64) systemd/245.4-4ubuntu3.15 (amd64, s390x, ppc64el) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding…

Continue Reading [Bug 1786013] Autopkgtest regression report (linux-meta-hwe-5.13/5.13.0.28.31~20.04.15)

[Bug 1786013] Autopkgtest regression report (linux-meta-oem-5.14/5.14.0.1021.18)

All autopkgtests for the newly accepted linux-meta-oem-5.14 (5.14.0.1021.18) for focal have finished running. The following regressions have been reported in tests triggered by the package: virtualbox-hwe/6.1.26-dfsg-3~ubuntu1.20.04.2 (amd64) virtualbox/6.1.26-dfsg-3~ubuntu1.20.04.2 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…

Continue Reading [Bug 1786013] Autopkgtest regression report (linux-meta-oem-5.14/5.14.0.1021.18)

Ubuntu Manpage: samtools reheader – replaces the header in the input file

Provided by: samtools_1.13-2_amd64 NAME samtools reheader – replaces the header in the input file SYNOPSIS samtools reheader [-iP] [-c CMD | in.header.sam ] in.bam DESCRIPTION Replace the header in in.bam with the header in in.header.sam. This command is much faster than replacing the header with a BAM→SAM→BAM conversion. By default…

Continue Reading Ubuntu Manpage: samtools reheader – replaces the header in the input file

[slurm-users] Strange sbatch error with 21.08.2&5

Running test job with srun works: wayneh@login:~$ srun -G16 -p v100 /home/wayne.hendricks/job.sh 179851 Linux dgx1-1 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 179851 Linux dgx1-2 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Submitting the same with sbatch does…

Continue Reading [slurm-users] Strange sbatch error with 21.08.2&5

Fail to install Ensembl VEP

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

Continue Reading Fail to install Ensembl VEP

python – Where to upload the image files to JupyterHub server (ltjh)

I would like to create a jupyter notebook that displays some images like this. In the case of my computer, the image files are stored in the local device. So I wrote one-line tag to show the image. <img src=”images/python_with_Birds.gif” width=”400″/> But if I want to share my created jupyter…

Continue Reading python – Where to upload the image files to JupyterHub server (ltjh)

Lammps in wsl – LAMMPS Installation

after making ubuntu in windows and installing the prerequisite commands ( sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tool)I downloadedLAMMPS Patch Release 14 Dec 2021 From www.lammps.org/download.htmland after extracting, I put it on the desktop. Next I entered…

Continue Reading Lammps in wsl – LAMMPS Installation

VEP issue: ERROR: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match

Describe the issue VEP give errors even my query and reference has same assembly version Command :$: ./vep -i examples/homo_sapiens_GRCh37.vcf –cache –refseq cache reference details while running install.pl ? 458 NB: Remember to use –refseq when running the VEP with this cache! downloading ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_refseq_vep_104_GRCh37.tar.gz unpacking homo_sapiens_refseq_vep_104_GRCh37.tar.gz converting cache, this may…

Continue Reading VEP issue: ERROR: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match

Installing Bio::DB::Big::File on Ubuntu (Building and testing…)

Installing Bio::DB::Big::File on Ubuntu (Building and testing…) 0 Hi everyone, I’m trying to install VEP, I already downloaded all the recommended PERL libraries/dependencies/modules But I still have a problem with Bio::DB::Big::File and Bio::DB::Big::AutoSQL They asked for lib big wig. I’ve found three ways to install this (in my understanding): sudo…

Continue Reading Installing Bio::DB::Big::File on Ubuntu (Building and testing…)

Issues installing Pindel from git

Issues installing Pindel from git 1 I’m currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with git clone github.com/samtools/htslib

Continue Reading Issues installing Pindel from git

Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

Continue Reading Gromacs Contact Map | Contact Information Finder

Install alphafold on the local machine, get out of docker.

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

Continue Reading Install alphafold on the local machine, get out of docker.

glmcdona/LuxPythonEnvGym: Matching python environment code for Lux AI 2021 Kaggle competition, and a gym interface for RL models.

Matching python environment code for Lux AI 2021 Kaggle competition, and a gym interface for RL models. This is still in-progress and not ready for use yet. I’ll post official docs and usage guide here once a simple example converges, and can be transformed to a kaggle-submission format. Features LuxAi2021…

Continue Reading glmcdona/LuxPythonEnvGym: Matching python environment code for Lux AI 2021 Kaggle competition, and a gym interface for RL models.

R package error messages have missing package names

R package error messages have missing package names 0 Hi, I have R running with this sessionInfo -> R version 4.0.4 (2021-02-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 21.04 I am running into a problem with trying to install packages. Usually you get error messages that tell you which dependencies…

Continue Reading R package error messages have missing package names

‘Can’t connect to eutils.ncbi.nlm.nih.gov:443’

‘Can’t connect to eutils.ncbi.nlm.nih.gov:443′ 0 Using an AWS AMI to predict small RNA targets. Getting following error. =========Prepping RefSeq Files==================== [Wed Sep 8 08:34:12 UTC 2021] 500 Can’t connect to eutils.ncbi.nlm.nih.gov:443 No do_post output returned from ‘https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NZ_CP039025&rettype=native&retmode=text&edirect=6.00&tool=edirect&email=ubuntu@ip-172-31-26-35.ec2.internal‘ Result of do_post http request is $VAR1 = bless( { ‘_msg’ => ‘Can’t…

Continue Reading ‘Can’t connect to eutils.ncbi.nlm.nih.gov:443’

error:Support for writing images in JPEG format not included – LAMMPS Beginners

If you are not very familiar with building software from source and using/editing makefiles (as it seems to be the case here), then we recommend to use the CMake based build procedure instead. It will autodetect and configure available features like JPEG or PNG libraries and MPI etc. That said,…

Continue Reading error:Support for writing images in JPEG format not included – LAMMPS Beginners

How to remove the header in fasta file and keep only the desirable part on ubuntu?

How to remove the header in fasta file and keep only the desirable part on ubuntu? 2 Hi all, I have a fasta file with this header >10005_M12.fastq Otu0001|242290|M1.fastq-M12.fastq-M5.fastq-URTM6.fastq-M7.fastq-M9.fastq I want to remove all the header parts except the OTU (with its number), I used the this command “sed ‘s/>M.Otu/>Otu/g’…

Continue Reading How to remove the header in fasta file and keep only the desirable part on ubuntu?

Kmergenie module readfq not found

Forum:Kmergenie module readfq not found 0 I have been trying to run kmergenie for my data on ubuntu and every time I enter the code it gives an import error: no module named readfq. I have tried downloading the module from bioconda and when checking the directory it showed that…

Continue Reading Kmergenie module readfq not found

Segmentation fault (core dumped) error when running MUSCLE

Segmentation fault (core dumped) error when running MUSCLE 0 I come across a question when running the multiple sequence alignment program MUSCLE. My operation system is win10, with a WSL, ubuntu LTS 18. I download the MUSCLE program , and run the command. tar -zxvf muscle3.8.31_i86linux64.tar.gz mv muscle3.8.31_i86linux64 muscle chmod…

Continue Reading Segmentation fault (core dumped) error when running MUSCLE

Gromacs 4.5.4 manual

Gromacs 4.5.4 manual OntheStabilityofNegativelyChargedPlatelets inCalcium g_energy(1) [debian man page] Gromacs User Manual Version 4.6The defence of Königsberg had cost the lives of 42,000 German soldiers and 25,000 civilians. He yanked the seaman out and shouted at him to report straight to…

Continue Reading Gromacs 4.5.4 manual

Can’t run java in bash script : bioinformatics

I was trying to re-use one of my old scripts for trimmomatic but I was getting error “java: command not found”. I realised that it will work if the java command is first. It stops if there is anything above it, e.g This works: #!/bin/bash java –version PATH=/media/msz/Arabidopsis_project/scripts $ ./test.sh…

Continue Reading Can’t run java in bash script : bioinformatics

Failed to open required defaults file mysql.cnf

Failed to open required defaults file mysql.cnf 0 Hi everyone. I know this may be a more general problem but I don’t know where to ask. I’m trying to run Stacks but this error keeps appearing: Failed to open required defaults file: usr/miniconda3/envs/genomevol/share/stacks/sql/mysql.cnf I’ve tried updating mysql, installing mysql-server instead…

Continue Reading Failed to open required defaults file mysql.cnf

how to install packages in r

In classic R you will have to press the tab button to show the functions on the screen, although it should be noted that if the package contains many functions not all will be shown, as is the case with the ggplot2 package: Sometimes it can be interesting to inspect…

Continue Reading how to install packages in r

bcl2fastq ERROR

bcl2fastq ERROR 1 Hi all, I have a problem. I’m running bcl2fastq software on Ubuntu, but I can’t demultiplex anything as the software gives me this error: *ERROR: bcl2fastq::common::Exception: 2021-Sep-02 12:12:34: Success (0): /home/Software/bcl2fastq/src/cxx/lib/layout/Layout.cpp(693): Throw in function void bcl2fastq::layout::handleDefaultSample(bool, bool, size_t, bcl2fastq::layout::LaneInfo&, bool&) Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError> std::exception::what: Missing a…

Continue Reading bcl2fastq ERROR

Sambamba

Sambamba 1 Hi can anyone guide me how to install sambamba package in ubuntu 20.04 install sambamba ubuntu • 22 views The documentation for getting binary (64bit linux) packages and compiling this software from source is found on the home page of the package: lomereiter.github.io/sambamba/ If you need more help…

Continue Reading Sambamba

remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch

Hello, I am trying to perform a remote blastn search through blast+ from the command line (on Linux Ubuntu). This results in an XML file with the following error message: internal_error: (Severe Error) Blast search error: Details: search failed. # Informational Message: [blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting…

Continue Reading remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch

samtools server vs cluster error

Using inspiration from this thread HISAT2 output direct to bam, I’m attempting to run this command. The shell variables in this case represent paths to files/locations that make sense and in fact this command runs fine on my Ubuntu 18.04 LTS server using hisat 2.1 and samtools 1.10 (this seems…

Continue Reading samtools server vs cluster error

Ubuntu Manpage: Bio::Procedural – Simple low-dependency procedural interfaces to BioPerl

Provided by: libbio-procedural-perl_1.7.4-2_all NAME Bio::Procedural – Simple low-dependency procedural interfaces to BioPerl VERSION version 1.7.4 SYNOPSIS See Bio::Perl for examples. DESCRIPTION The code in this distribution focuses on simple low-dependency procedural interfaces to BioPerl that don’t require knowledge of BioPerl classes and methods. FEEDBACK Mailing lists User feedback is an…

Continue Reading Ubuntu Manpage: Bio::Procedural – Simple low-dependency procedural interfaces to BioPerl

I want to change the color of text by file type in PuTTY

I want to change the color of text by file type in PuTTY 1 Hello To use ubuntu terminal in my laptop, I use application PuTTY. Unlike ubuntu terminal, the PuTTY always shows only white text regardless of the file format. But on the screens of other users show different…

Continue Reading I want to change the color of text by file type in PuTTY

Failed to open filename / unable to read

Failed to open filename / unable to read – Ubuntu 1 Hii, i’ve been trying using primersearch from emboss on ubuntu but this keeps getting me the same error primersearch -seqall filename.fna -infile filename.txt -mismatchpercent 10 -outfile filename.primersearch Error: Failed to open filename ‘filename’ Error: Unable to read sequence ‘filename’…

Continue Reading Failed to open filename / unable to read

SRA/ENA library layout is inconsistent with the data source

project number: PRJNA505380 An example of Run accession: SRR8244780 Issue: Inconsistency between the library layout of Run and data source. As the library layout both in ENA and SRA labeled, Runs in Bioproject PRJNA505380 should be pair-end reads data. But some of them only have a single fastq and without…

Continue Reading SRA/ENA library layout is inconsistent with the data source

Gmod linux error splicing

  20-08-2021   The Generic Model Organism System Database Project (GMOD) seeks to runs well on a variety of platforms including such Unix-based systems as Linux, Solaris, a polished user interface for user support, feature requests, and bug reports. Integrated Genome Browser reveals stress-induced alternative splicing of the. Splicing is…

Continue Reading Gmod linux error splicing

Kaggle Lyft Motion Prediction for Autonomous Vehicles 4th place solution

Lyft Motion Prediction for Autonomous Vehicles Code for the 4th place solution of Lyft Motion Prediction for Autonomous Vehicles on Kaggle. Directory structure input — Please locate data here src |-ensemble — For 4. Ensemble scripts |-lib — Library codes |-modeling — For 1. training, 2. prediction and 3. evaluation…

Continue Reading Kaggle Lyft Motion Prediction for Autonomous Vehicles 4th place solution

Ubuntu on Windows 10 – using Command line

Ubuntu on Windows 10 – using Command line 1 I am from a Biology background. To learn command line, GitHub, and Linux I have installed Ubuntu on Windows 10 laptop. When I run the app message pop-up To run a command as administrator (user “root”), use “sudo <command>”. See “man…

Continue Reading Ubuntu on Windows 10 – using Command line

Ubuntu Manpage: macs2_bdgdiff – Ddp 1313.com

Compare bedgraphs of two treatments after MACS2 callpeak . Output Files of MACS2 bdgdiff . Hello everyone, I have some bedgraph files from a ChIP- … Source link

Continue Reading Ubuntu Manpage: macs2_bdgdiff – Ddp 1313.com