Tag: EOF

Is seems the container fails to boot. From a bad run: 9109s autopkgtest [10:39:17]: test tests-in-lxd: [———————– 9145s 2023-11-28T10:39:50Z INFO Waiting for automatic snapd restart… 9259s lxd 5.19-8635f82 from Canonical** installed 9288s Creating autopkgtest-prepare-jhI 9475s Retrieving image: metadata: 100% (323.81MB/s) Retrieving image: rootfs: 1% (3.53MB/s) <SNIP> Retrieving image: rootfs: 100%…

Device layout and graphical outline of experimental flow. Small extracellular vesicles (sEVs) were simultaneously extracted from human biofluids using the insulator-based dielectrophoretic (iDEP) device, wherein a trapping zone was created at the tip region of micropipettes by balancing the dielectrophoretic (DEP) force with two electrokinetic forces, including electroosmosis (EOF) and…

time series – DATA PREPERATION FOR EOF Analysis in R Studio – Cross Validated …

tests-in-lxd seems to fail to download the lxd image used for the test (or something similar), looking at the log:…Publishing instance: Image pack: 85% (5.51MB/s) Instance published with fingerprint: 83b511be44395f2afc7d4d1ee0708cb18834c8b15cb208c9d218964ed84791146845s autopkgtest [09:11:14]: starting date and time: 2023-10-03 09:11:14+00006845s autopkgtest [09:11:14]: version 5.28ubuntu16845s autopkgtest [09:11:14]: host autopkgtest; command line: /usr/bin/autopkgtest -U…

In this tutorial, we will show you how to install R and Rstudio on Debian 12. RStudio is a pivotal tool for data scientists and analysts, offering an integrated development environment (IDE) that streamlines the process of working with R, a powerful language for statistical computing and data analysis. While…

I am trying to automate extracting data from an indexed BAM file and I am getting read errors: [E::bgzf_read_block] Invalid BGZF header at offset 51686517456 [E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes This failure happens after about 12 hours of analysis, near the end…

import of HDF5 file into R 1 Hello, I have GSE183206_aggr_filtered_counts_matrix.h5 file downloaded from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE183206. I try to import of HDF5 file into R. Thank you in advance for great help! Best regards, Yue > library(Seurat) > library(rhdf5) > setwd(“~/gse183206_lj”) > seurat_data <- Read10X_h5(“GSE183206_aggr_filtered_counts_matrix.h5”) Error in H5File.open(filename, mode, file_create_pl, file_access_pl)…

When you think about making your microservice architecture more secure, would you know where to start? There are so many ways to begin securing a system that it quickly becomes overwhelming. This blog post introduces you to two approaches to minimize security exposure. It starts with documentation What does documentation…

In my previous blog post, OpenFOAM Supports Apptainer v1.2.0 Template Definition File Feature, I showed you how to use OpenFOAM (R) (OpenCFD Ltd.) with Apptainer; and in A New Approach to MPI in Apptainer, I demonstrated how to build and run a a portable MPI container with Apptainer’s “Fully Containerized…

Hi all! We had our deployment running on EKS for a few months without issues. For the issues we did have deleting and triggering the pods would cut it and solve the issue. Been using this binderhub image: jupyterhub/k8s-binderhub:0.2.0-n956.h64a6ec4 with EKS 1.21 Now a few weeks ago, we’ve started seeing…

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/ampere2/data/main-arm64-default/p8fb94260154e_s510fd83138/logs/mothur-1.48.0.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p8fb94260154e_s510fd83138 Log: =>> Building biology/mothur build started at Mon Jul 17…

Hi guys, I’m running velocyto on bam files via ssh. One sample was succeeded, but when I started running the other two samples, I saw this error showed up over and over again, at the beginning, I thought something was wrong with my bam files, so I re-transferred them to…

Description: Unable to add External process Monitor Steps to Reproduce: Install pmm and standard YUM process that works properly as well as mysql monitor All agents and items are being monitored properly. Install of process-exporter Reason: I want to be able to monitor the amount of items like httpd processes…

Dear maintainer(s), I saw the autoremoval notice for 11th July on the Debian Package Tracker. Hope this is the right place to respond. I use `at` regularly and would be sad to see it being removed from the Debian repositories. Unfortunately I have not been able to reproduce this issue…

I execute the below line in RStudio to append a text to myfile.rds, which contains only one column named X write(“mytext”, file = “myfile.rds”, append = TRUE) It executes without throwing any error or warning as shown below > write(“mytext”, file = “myfile.rds”, append = TRUE) > However, when I…

swong June 14, 2023, 11:52am 1 GROMACS version: 2023.1GROMACS modification: Yes/NoHere post your question: I successfully compiled on a AMD/GPU node cluster. Each node has 8 gpus. So I’m running 8 simultaneous simulations on each node. As the simulations proceed the memory usage keeps increasing until some of the jobs…

I would like to read iteratively the same BAM file twice using htslib. My option is to use hts_open, sam_hdr_read, then sam_read1 as much as needed to read the file until EOF. Is there a possibility to “rewind”, and use sam_read1 again from the beginning of the file, without closing…

I am working on setting up a USB based secure communication between PC as client and STM32H753 microcontroller running a SSL Server. The network stack used is LwIP and Mbed TLS (TLS v1.2) is used for the secure communication layer. I adapted this using the SSL_Server example available and used…

#!/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…

seven April 7, 2023, 1:36am 1 jupyterhub:2.2.2system: centos 8the notebook page show nothing when i click new terminal in top menu.the server console: Traceback (most recent call last):File “/usr/local/lib/python3.6/site-packages/ptyprocess/ptyprocess.py”, line 522, in reads = self.fileobj.read1(size)OSError: [Errno 5] Input/output error During handling of the above exception, another exception occurred: Traceback (most…

Hi, running Rsubread 2.8.2/2.12.0 or featureCounts 2.0.3/2.0.1, I stumbled over two issues when allowing ambiguous read assignment (-O/allowMultiOverlap) 1) regarding assignment via minimum fractional overlap (–fracOverlap) using featureCounts stand-alone binary. 2) when combined with –/largestOverlap and –/fraction using Rsubread featureCounts function or the stand-alone binary. to 1) Assume a read…

Hello everyone, I have issues importing the filtered matrix files of STARsolo output to use with Seurat. I have tried multiple ways like: Drosophila.data <- ReadMtx(mtx =”~/genome/matrix/matrix.mtx”, cells=”~/genome/matrix/barcodes.tsv”, features=”~/genome/matrix/features.tsv”) and Drosophila.data <- ReadSTARsolo(data.dir =”~/genome/matrix/) But both give me the following error: Error: Matrix has 13968 rows but found 12507 features….

Context: I’m trying to call variants on a sequencing project using pooled genotyping-by-sequencing. Pools consist of 94 samples each, alongside a number of individuals. Sequence data was demultiplexed and then aligned to a reference genome using hisat2, and the resultant bams were merged with samtools merge. The problem bam is…

Issue Title State Comments Created Date Updated Date How to get a specific chromosome open 1 2022-07-14 2022-07-18 tabix returns row from VCF file multiple times open 4 2022-07-11 2022-07-18 Modified base parsing failure failure closed 0 2022-07-01 2022-07-18 extract genotype information open 1 2022-06-24 2022-07-18 sam_hdr_remove_lines is inefficient if…

BBMap/BBTools reformat.sh : real error or spurious message? [W::bgzf_read_block] EOF marker is absent reformat.sh 1 When subsampling paired-end .fastq.gz files using reformat.sh from BBMap/BBTools, I get this error message: [W::bgzf_read_block] EOF marker is absent reformat.sh I’ve checked the input files with gunzip -t, no error. The input files are a…

[W::bgzf_read_block] EOF marker is absent in BBMAP 0 Hello, I’m asking an issue encountered in bbmap. I was using bbmap to remove host contaminants from my microbiome data. The commands are simple as below (ref folder already generated in the last step) bbmap.sh -Xmx42g in=R1.fastq.gz in2=R2.fastq.gz outu=cleaned.interleaved.fastq.gz threads=12 overwrite=t unpigz=t…

I’m running bowtie2 to align multiple samples to one reference genome, and then run samtools flagstats to output the results. All but two samples have aligned and I’ve managed to run flagstat on them. For those two samples, when I run flagstat, I first get: [W::bam_hdr_read] EOF marker is absent….

Alternative to samtools quickcheck with bash scripting 1 Is there an alternative to samtools quickcheck? I need to perform a check some bam files in order to verify that they’re not truncated. Nevertheless, I can’t use samtools since in the linux machine where I have the data I can’t install…

bamdst gives error “EOF marker is absent. The input is probably truncated.” 0 I created a set of bam files from Poolseq data using bwa -aln, and all of the output files gave the following error when I ran bamdst to get summary statistics on read depth: “EOF marker is…

samtools mpileup fail to create bcf 1 I have indexed my reference.fasta using bowtie2: bowtie2-build reference.fasta reference.fasta created the bam file form the sam file using samtools, sorted and indexed the bam file: samtools view -S -b Sample1_mapped.sam > Sample1_mapped.bam samtools sort Sample1_mapped.bam -o Sample1_sorted > Sample1_sorted.bam samtools index Sample1_sorted.bam…

split pdb into submodels 1 There is a program called pdbsplitchains in this repository: github.com/ACRMGroup/bioptools pdbset from the CCP4 package can do all kinds of manipulations on PDB files – including splitting by chain – but it requires a bit of scripting. For example, these several lines would extract chain…

EOF marker absent in VCF – can this be safely ignored? 0 Hi, I generated a VCF file using a bcftools mpileup | bcftools call pipeline. I have done this before, and the file produced then looks fine. However, the log for this one had [W::bgzf_read_block] EOF marker is absent….

Error while subsetting VCF – error doesn’t check out with (z)grep 0 I’m using bcftools view -s to subset a VCF.gz file. I ran into an error: [E::vcf_parse_format] Number of columns at chr9:44897051 does not match the number of samples (90 vs 99) To look at this site, I ran…