Blosers
commented
1 day ago I think I have already configured local running in the NextFlow.dentig file, but why is the network still being pulled? Is there any problem with my offline running configuration in the NextFlow.dentig file?
sarahjeeeze
Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
wf-pore-c.sif the latest
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
!/bin/bash
SBATCH --job-name=pore-c
SBATCH --partition=Par-1
SBATCH --nodes=1
SBATCH --ntasks-per-node=20
SBATCH --error=/home/dingyuanhao/zxl_work/red_dwarf/wf-pore-c/pore-c.err
SBATCH --output=/home/dingyuanhao/zxl_work/red_dwarf/wf-pore-c/pore-c.out
Execute your command
source ~/.bashrc
conda activate pore-c
nextflow run /home/dingyuanhao/zxl_software/wf-pore-c/ \ --bam '/home/dingyuanhao/zxl_software/wf-pore-c/test_data/porec_test.concatemers.bam' \ --chunk_size 100 \ --cutter 'NlaIII' \ --hi_c \ --mcool \ --paired_end \ --paired_end_maximum_distance 200 \ --paired_end_minimum_distance 100 \ --phased_vcf '/home/dingyuanhao/zxl_software/wf-pore-c/test_data/porec_test.phased_variants.vcf.gz' \ --ref '/home/dingyuanhao/zxl_software/wf-pore-c/test_data/porec_test.fasta' \ --vcf '/home/dingyuanhao/zxl_software/wf-pore-c/test_data/porec_test.phased_variants.vcf.gz' \ -profile singularity \ -c /home/dingyuanhao/zxl_software/wf-pore-c/nextflow.config
Workflow Execution - CLI Execution Profile
singularity
What happened?
cat nextflow.contig // // Notes to End Users. // // The workflow should run without editing this configuration file, // however there may be instances in which you wish to edit this // file for compute performance or other reasons. Please see: // // https://nextflow.io/docs/latest/config.html#configuration // // for further help editing this file.
params { help = false version = false bam = null fastq = null ref = null cutter = 'NlaIII' out_dir = 'output' chunk_size = 20000 sample = null vcf = null pairs = false mcool = false mcool_resolutions = '1000,2000,5000N' // 4DN tuple default coverage = false
}
manifest { name = 'epi2me-labs/wf-pore-c' author = 'Oxford Nanopore Technologies' homePage = 'https://github.com/epi2me-labs/wf-pore-c' description = 'workflow for analysing pore-c data.' mainScript = 'main.nf' nextflowVersion = '>=23.04.2' version = 'v1.2.2' }
epi2melabs { tags = "pore-c,contact,map,chromatin,conformation,capture" }
// used by default for "standard" (docker) and singularity profiles, // other profiles may override. process { withLabel:wfporec { container = "home/dingyuanhao/zxl_software/wf-pore-c/wf-pore-c.sif" } withLabel:pore_c_py { container = "/home/dingyuanhao/zxl_software/wf-pore-c/pore-c-py.sif" } withLabel:wf_common { container = "/home/dingyuanhao/zxl_software/wf-pore-c/wf-common.sif" } shell = ['/bin/bash', '-euo', 'pipefail'] withName: "merge_coordsorted_bams|merge_namesorted_bams" { publishDir = [ path: { "${params.out_dir}/bams/" }, mode: "copy", pattern: '.{bam,csi,bai}' ] } withName: "merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_stats_report" { publishDir = [ path: { "${params.out_dir}/pairs/" }, mode: "copy", pattern: '.{gz,stats.txt,bed,mcool,html}' ] } withName: "mosdepth_coverage" { publishDir = [ path: { "${params.out_dir}/coverage/" }, mode: "copy", pattern: '.' ] } withName: "merge_parquets_to_dataset" { publishDir = [ path: { "${params.out_dir}/chromunity/" }, mode: "copy", pattern: '.' ] } withName: "merge_paired_end_bams" { publishDir = [ path: { "${params.out_dir}/paired_end/" }, mode: "copy", pattern: '.{bam,csi,bai}' ] } withName: "makeReport" { publishDir = [ path: { "${params.out_dir}/" }, mode: "copy", pattern: '.{html}' ] } withName: "prepare_hic" { publishDir = [ path: { "${params.out_dir}/hi-c" }, mode: "copy", pattern: '.{hic}' ] } withName: "mergeBed" { publishDir = [ path: { "${params.out_dir}/bed" }, mode: "copy", pattern: '.{bed}' ] } withName: "get_filtered_out_bam" { publishDir = [ path: { "${params.out_dir}/filtered_out" }, mode: "copy", pattern: '*.{bam}' ] } }
profiles { // the "standard" profile is used implicitely by nextflow // if no other profile is given on the CLI standard { docker { enabled = true // this ensures container is run as host user and group, but // also adds host user to the within-container group runOptions = "--user \$(id -u):\$(id -g) --group-add 100" } }
}
timeline { enabled = true overwrite = true file = "${params.out_dir}/execution/timeline.html" } report { enabled = true overwrite = true file = "${params.out_dir}/execution/report.html" } trace { enabled = true overwrite = true file = "${params.out_dir}/execution/trace.txt" }
env { PYTHONNOUSERSITE = 1 JAVA_TOOL_OPTIONS = "-Xlog:disable -Xlog:all=warning:stderr" }
error
Plus 7 more processes waiting for tasks… ERROR ~ Error executing process > 'POREC:index_bam (1)'
Caused by: Failed to pull singularity image command: singularity pull --name home-dingyuanhao-zxl_software-wf-pore-c-wf-pore-c.sif.pulling.1729494354443 docker://home/dingyuanhao/zxl_software/wf-pore-c/wf-pore-c.sif > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: [31mFATAL: While making image from oci registry: failed to get checksum for docker://home/dingyuanhao/zxl_software/wf-pore-c/wf-pore-c.sif: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp 103.200.30.143:443: i/o timeout
-- Check '.nextflow.log' file for details
I think I have already configured local running in the NextFlow.dentig file, but why is the network still being pulled? Is there any problem with my offline running configuration in the NextFlow.dentig file?
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response