search

epi2me-labs / wf-pore-c

Other
34 stars 9 forks source link

离线使用wf-pore-c #74

Open Blosers opened 2 months ago

Blosers commented 2 months ago

Ask away!

作者您好，在我已经下载了wf-pore-c.sif情况下，我想使用singularity去运行wf-pore-c.sif的时候依旧会出现报错，申请需要拉去网络需求，然后就会终止我的任务。但是我已经在.bashrc的环境中设置了： export NXF_SINGULARITY_CACHEDIR=/home/dingyuanhao/zxl_software/wf-pore-c export NXF_OFFLINE='true'

以及我运行的命令中也设置了使用后singularity，以下是我的命令：

!/bin/bash

SBATCH --job-name=pore-c

SBATCH --partition=Par-2

SBATCH --nodes=1

SBATCH --ntasks-per-node=20

SBATCH --error=/home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/pore-c.err

SBATCH --output=/home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/pore-c.out

激活 Conda 环境（如果使用 Conda 管理 Nextflow 环境）

source ~/.bashrc conda activate pore-c

nextflow run /home/dingyuanhao/zxl_software/wf-pore-c \ --fastq /home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/hic_data \ --chunk_size 100 \ --cutter DpnII \ --hi_c \ --mcool \ --mcool_resolutions '1000,5000,10000,50000,100000,1000000' \ --paired_end_maximum_distance 200 \ --paired_end_minimum_distance 100 \ --ref /home/dingyuanhao/zxl_work/red_dwarf/HA-T2T.fasta \ -profile singularity \ -with-singularity /home/dingyuanhao/zxl_software/wf-pore-c/wf-pore-c.sif

以下是我的日志文件 .nextflow.log

Aug-30 10:58:49.185 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /home/dingyuanhao/zxl_software/wf-pore-c --fastq /home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/hic_data --chunk_size 100 --cutter DpnII --hi_c --mcool --mcool_resolutions 1000,5000,10000,50000,100000,1000000 --paired_end_maximum_distance 200 --paired_end_minimum_distance 100 --ref /home/dingyuanhao/zxl_work/red_dwarf/HA-T2T.fasta -profile singularity -with-singularity /home/dingyuanhao/zxl_software/wf-pore-c/wf-pore-c.sif Aug-30 10:58:49.355 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.4 Aug-30 10:58:49.402 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/dingyuanhao/.nextflow/plugins; core-plugins: nf-amazon@2.5.3,nf-azure@1.6.1,nf-cloudcache@0.4.1,nf-codecommit@0.2.1,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2-patch1,nf-tower@1.9.1,nf-wave@1.4.2-patch1 Aug-30 10:58:49.525 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Aug-30 10:58:49.526 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Aug-30 10:58:49.531 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Aug-30 10:58:49.547 [main] INFO org.pf4j.AbstractPluginManager - No plugins Aug-30 10:58:50.465 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/dingyuanhao/zxl_software/wf-pore-c/nextflow.config Aug-30 10:58:50.468 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/dingyuanhao/zxl_software/wf-pore-c/nextflow.config Aug-30 10:58:50.486 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/dingyuanhao/.nextflow/secrets/store.json Aug-30 10:58:50.490 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@71f1cc02] - activable => nextflow.secret.LocalSecretsProvider@71f1cc02 Aug-30 10:58:50.505 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: singularity Aug-30 10:58:50.691 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, conda, singularity, awsbatch, local] Aug-30 10:58:50.722 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by command-line option -with-singularity null Aug-30 10:58:50.736 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration Aug-30 10:58:50.756 [main] DEBUG nextflow.cli.CmdRun - Launching /home/dingyuanhao/zxl_software/wf-pore-c/main.nf [jovial_poisson] DSL2 - revision: 8c2550bad6 Aug-30 10:58:50.757 [main] WARN nextflow.cli.CmdRun - Nextflow variables must be defined in the launching environment - The following variable set in the config file is going to be ignored: 'NXF_SINGULARITY_CACHEDIR' Aug-30 10:58:50.758 [main] WARN nextflow.cli.CmdRun - Nextflow variables must be defined in the launching environment - The following variable set in the config file is going to be ignored: 'NXF_OFFLINE' Aug-30 10:58:50.759 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Aug-30 10:58:50.760 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Aug-30 10:58:50.818 [main] DEBUG nextflow.Session - Session UUID: f2713be6-55f3-4444-8149-ba7dab6f6f30 Aug-30 10:58:50.819 [main] DEBUG nextflow.Session - Run name: jovial_poisson Aug-30 10:58:50.819 [main] DEBUG nextflow.Session - Executor pool size: 20 Aug-30 10:58:50.829 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Aug-30 10:58:50.860 [main] DEBUG nextflow.cli.CmdRun - Version: 24.04.4 build 5917 Created: 01-08-2024 07:05 UTC (15:05 CDT) System: Linux 3.10.0-862.el7.x86_64 Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 21-internal-adhoc.conda.src Encoding: UTF-8 (UTF-8) Process: 114300@fat02 [12.12.20.2] CPUs: 20 - Mem: 1.5 TB (1.7 GB) - Swap: 31.2 GB (29.1 GB) - Virtual threads ON Aug-30 10:58:51.085 [main] DEBUG nextflow.Session - Work-dir: /home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/work [nfs] Aug-30 10:58:51.120 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Aug-30 10:58:51.134 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Aug-30 10:58:51.189 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Aug-30 10:58:51.200 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool Aug-30 10:58:51.538 [main] DEBUG nextflow.Session - Session start Aug-30 10:58:51.541 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/output/execution/trace.txt Aug-30 10:58:51.617 [main] DEBUG nextflow.Session - Using default localLib path: /home/dingyuanhao/zxl_software/wf-pore-c/lib Aug-30 10:58:51.623 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/dingyuanhao/zxl_software/wf-pore-c/lib Aug-30 10:58:51.624 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/dingyuanhao/zxl_software/wf-pore-c/lib/nfcore_external_javadeps.jar Aug-30 10:58:53.448 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Aug-30 10:58:55.985 [main] INFO nextflow.Nextflow - |||||||||| ____ _ __ _ |||||||||| | _| _ | | \/ | __| | | | | ||||| | | | |) | | ) | |\/| | _| ___| |/ ` | ' \/ | ||||| | |_| /| | / /| | | | |_|| | (| | |) _ \ |||||||||| |____|_| |_|___|| ||| ||\,|._/|/ |||||||||| wf-pore-c v1.2.2

Core Nextflow options runName : jovial_poisson containerEngine : singularity container : [withLabel:wfporec:ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0, withLabel:pore_c_py:ontresearch/pore-c-py:sha50378db56ddafe19f5e1d313ddb52dc70bbcc2bd, withLabel:wf_common:ontresearch/wf-common:shad399cf22079b5b153920ac39ee40095a677933f1, default:/home/dingyuanhao/zxl_software/wf-pore-c/wf-pore-c.sif] launchDir : /home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c workDir : /home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/work projectDir : /home/dingyuanhao/zxl_software/wf-pore-c userName : dingyuanhao profile : singularity configFiles : /home/dingyuanhao/zxl_software/wf-pore-c/nextflow.config

Input Options fastq : /home/dingyuanhao/zxl_work/red_dwarf/DNPII/pore-c/hic_data ref : /home/dingyuanhao/zxl_work/red_dwarf/HA-T2T.fasta cutter : DpnII

Output Options hi_c : true

Advanced Options chunk_size : 100

4DN files Options mcool : true mcool_resolutions : 1000,5000,10000,50000,100000,1000000

Paired-end BAM Options paired_end_minimum_distance: 100 paired_end_maximum_distance: 200

!! Only displaying parameters that differ from the pipeline defaults !!

If you use epi2me-labs/wf-pore-c for your analysis please cite:

This is epi2me-labs/wf-pore-c v1.2.2.

Aug-30 10:58:56.191 [main] INFO nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files. Aug-30 10:58:56.429 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_common matches labels ingress,wf_common for process with name POREC:fastcat Aug-30 10:58:56.442 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.443 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.450 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Aug-30 10:58:56.458 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=20; memory=1.5 TB; capacity=20; pollInterval=100ms; dumpInterval=5m Aug-30 10:58:56.461 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Aug-30 10:58:56.543 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:index_bam Aug-30 10:58:56.546 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.546 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.578 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:prepare_genome:index_ref_mmi Aug-30 10:58:56.580 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.580 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.628 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:pore_c_py matches labels pore_c_py for process with name POREC:digest_align_annotate Aug-30 10:58:56.631 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.631 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.653 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:haplotag_alignments Aug-30 10:58:56.656 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.656 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.673 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:merge_coordsorted_bams Aug-30 10:58:56.674 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:merge_coordsorted_bams|merge_namesorted_bams matches process POREC:merge_coordsorted_bams Aug-30 10:58:56.677 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.677 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.686 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:merge_namesorted_bams Aug-30 10:58:56.686 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:merge_coordsorted_bams|merge_namesorted_bams matches process POREC:merge_namesorted_bams Aug-30 10:58:56.690 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.690 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.712 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:create_restriction_bed Aug-30 10:58:56.713 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_stats_report matches process POREC:create_restriction_bed Aug-30 10:58:56.715 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.715 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:to_pairs_file Aug-30 10:58:56.734 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.734 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.744 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:pairsToCooler Aug-30 10:58:56.748 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.748 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.759 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:merge_mcools Aug-30 10:58:56.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_stats_report matches process POREC:merge_mcools Aug-30 10:58:56.762 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.762 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.771 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:merge_pairs Aug-30 10:58:56.771 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_stats_report matches process POREC:merge_pairs Aug-30 10:58:56.773 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.773 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.780 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:merge_pairs_stats Aug-30 10:58:56.781 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_stats_report matches process POREC:merge_pairs_stats Aug-30 10:58:56.782 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.782 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.788 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:pair_stats_report Aug-30 10:58:56.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_stats_report matches process POREC:pair_stats_report Aug-30 10:58:56.790 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.790 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.795 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:getVersions Aug-30 10:58:56.796 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.797 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.800 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:getParams Aug-30 10:58:56.802 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.802 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.821 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_common matches labels wf_common for process with name POREC:makeReport Aug-30 10:58:56.821 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:makeReport matches process POREC:makeReport Aug-30 10:58:56.823 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.823 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.833 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:prepare_hic Aug-30 10:58:56.833 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:prepare_hic matches process POREC:prepare_hic Aug-30 10:58:56.835 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.835 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.842 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_common matches labels wf_common for process with name POREC:collectIngressResultsInDir Aug-30 10:58:56.843 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.844 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.859 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name POREC:get_filtered_out_bam Aug-30 10:58:56.860 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:get_filtered_out_bam matches process POREC:get_filtered_out_bam Aug-30 10:58:56.861 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.861 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.867 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfporec matches labels wfporec for process with name publish Aug-30 10:58:56.868 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Aug-30 10:58:56.868 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Aug-30 10:58:56.872 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: collectIngressResultsInDir, move_or_compress_fq_file, haplotag_alignments, pair_stats_report, haplotagReads, POREC:pairsToCooler, POREC:makeReport, POREC:prepare_genome:index_ref_mmi, POREC:merge_coordsorted_bams, prepare_hic, checkBamHeaders, merge_pairs_stats, POREC:merge_mcools, mergeBams, POREC:getVersions, makeReport, merge_coordsorted_bams, POREC:prepare_hic, getVersions, POREC:fastcat, validateIndex, POREC:get_filtered_out_bam, index_ref_mmi, POREC:merge_namesorted_bams, mosdepth_coverage, merge_pairs, bamstats, merge_namesorted_bams, mergeBed, fastcat, pairsToCooler, POREC:to_pairs_file, to_pairs_file, merge_paired_end_bams, samtools_index,getParams, POREC:merge_pairs, index_bam, sortBam, merge_parquets_to_dataset, validate_sample_sheet, POREC:index_bam, POREC:merge_pairs_stats, createBed, POREC:getParams, POREC:pair_stats_report, POREC:collectIngressResultsInDir, index_ref_fai, digest_align_annotate, create_restriction_bed, publish_artifact, POREC:create_restriction_bed, POREC:haplotag_alignments, merge_mcools, split_fq_file, POREC:digest_align_annotate, publish, decompress_ref, get_filtered_out_bam, catSortBams Aug-30 10:58:56.877 [main] DEBUG nextflow.Session - Igniting dataflow network (27) Aug-30 10:58:56.878 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:fastcat Aug-30 10:58:56.879 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:index_bam Aug-30 10:58:56.886 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:prepare_genome:index_ref_mmi Aug-30 10:58:56.887 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:digest_align_annotate Aug-30 10:58:56.887 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:haplotag_alignments Aug-30 10:58:56.887 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_coordsorted_bams Aug-30 10:58:56.887 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_namesorted_bams Aug-30 10:58:56.887 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:create_restriction_bed Aug-30 10:58:56.888 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:to_pairs_file Aug-30 10:58:56.888 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:pairsToCooler Aug-30 10:58:56.888 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_mcools Aug-30 10:58:56.889 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_pairs Aug-30 10:58:56.889 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_pairs_stats Aug-30 10:58:56.889 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:pair_stats_report Aug-30 10:58:56.890 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:getVersions Aug-30 10:58:56.890 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:getParams Aug-30 10:58:56.890 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:makeReport Aug-30 10:58:56.890 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:prepare_hic Aug-30 10:58:56.890 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:collectIngressResultsInDir Aug-30 10:58:56.890 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:get_filtered_out_bam Aug-30 10:58:56.890 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > publish Aug-30 10:58:56.891 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_abbb0bad601915d5: /home/dingyuanhao/zxl_software/wf-pore-c/./subworkflows/local/../../modules/local/common.nf Script_dc8ae76559e7dced: /home/dingyuanhao/zxl_software/wf-pore-c/./modules/local/4dn.nf Script_e31f33af809aed36: /home/dingyuanhao/zxl_software/wf-pore-c/./modules/local/pore-c.nf Script_2f0b9f806b07aaca: /home/dingyuanhao/zxl_software/wf-pore-c/main.nf Script_6f2dfe738e879fd7: /home/dingyuanhao/zxl_software/wf-pore-c/./subworkflows/local/prepare_genome.nf Script_b6fd3c4ddd1b8546: /home/dingyuanhao/zxl_software/wf-pore-c/./lib/ingress.nf Aug-30 10:58:56.891 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Aug-30 10:58:56.891 [main] DEBUG nextflow.Session - Session await Aug-30 10:58:56.963 [Actor Thread 123] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 [cache /home/dingyuanhao/zxl_software/wf-pore-c/ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img] Aug-30 10:58:56.965 [Actor Thread 124] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://ontresearch/wf-common:shad399cf22079b5b153920ac39ee40095a677933f1 [cache /home/dingyuanhao/zxl_software/wf-pore-c/ontresearch-wf-common-shad399cf22079b5b153920ac39ee40095a677933f1.img] Aug-30 10:58:57.011 [Actor Thread 117] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=POREC:getParams; work-dir=null error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to pull singularity image command: singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1724986736964 docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: time="2024-08-30T10:58:57+08:00" level=warning msg="\"/run/user/32039\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/32039: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp: lookup registry-1.docker.io on 210.37.40.4:53: dial udp 210.37.40.4:53: connect: network is unreachable

Aug-30 10:58:57.011 [Actor Thread 118] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=POREC:fastcat (1); work-dir=null error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to pull singularity image command: singularity pull --name ontresearch-wf-common-shad399cf22079b5b153920ac39ee40095a677933f1.img.pulling.1724986736966 docker://ontresearch/wf-common:shad399cf22079b5b153920ac39ee40095a677933f1 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: time="2024-08-30T10:58:57+08:00" level=warning msg="\"/run/user/32039\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/32039: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://ontresearch/wf-common:shad399cf22079b5b153920ac39ee40095a677933f1: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp: lookup registry-1.docker.io on 210.37.40.4:53: dial udp 210.37.40.4:53: connect: network is unreachable

Aug-30 10:58:57.011 [Actor Thread 116] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=POREC:getVersions; work-dir=null error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to pull singularity image command: singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1724986736964 docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: time="2024-08-30T10:58:57+08:00" level=warning msg="\"/run/user/32039\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/32039: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp: lookup registry-1.docker.io on 210.37.40.4:53: dial udp 210.37.40.4:53: connect: network is unreachable

Aug-30 10:58:57.011 [Actor Thread 115] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=POREC:prepare_genome:index_ref_mmi (1); work-dir=null error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to pull singularity image command: singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1724986736964 docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: time="2024-08-30T10:58:57+08:00" level=warning msg="\"/run/user/32039\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/32039: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp: lookup registry-1.docker.io on 210.37.40.4:53: dial udp 210.37.40.4:53: connect: network is unreachable

Aug-30 10:58:57.015 [Actor Thread 74] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=POREC:fastcat; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-30 10:58:57.015 [Actor Thread 106] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=POREC:getVersions; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-30 10:58:57.015 [Actor Thread 107] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=POREC:getParams; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-30 10:58:57.025 [Actor Thread 115] ERROR nextflow.processor.TaskProcessor - Error executing process > 'POREC:prepare_genome:index_ref_mmi (1)'

Caused by: Failed to pull singularity image command: singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1724986736964 docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: time="2024-08-30T10:58:57+08:00" level=warning msg="\"/run/user/32039\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/32039: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp: lookup registry-1.docker.io on 210.37.40.4:53: dial udp 210.37.40.4:53: connect: network is unreachable

java.lang.IllegalStateException: java.lang.IllegalStateException: Failed to pull singularity image command: singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1724986736964 docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: time="2024-08-30T10:58:57+08:00" level=warning msg="\"/run/user/32039\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/32039: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp: lookup registry-1.docker.io on 210.37.40.4:53: dial udp 210.37.40.4:53: connect: network is unreachable

at nextflow.container.SingularityCache.getCachePathFor(SingularityCache.groovy:356)
at nextflow.container.ContainerHandler.createSingularityCache(ContainerHandler.groovy:108)
at nextflow.container.ContainerHandler.normalizeImageName(ContainerHandler.groovy:75)
at nextflow.container.resolver.DefaultContainerResolver.resolveImage0(DefaultContainerResolver.groovy:49)
at nextflow.container.resolver.DefaultContainerResolver.resolveImage(DefaultContainerResolver.groovy:42)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskRun.containerInfo0(TaskRun.groovy:685)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrentN(ScriptBytecodeAdapter.java:96)
at nextflow.processor.TaskRun.this$dist$invoke$1(TaskRun.groovy)
at nextflow.processor.TaskRun$4.methodMissing(TaskRun.groovy)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaClassImpl.invokeMissingMethod(MetaClassImpl.java:924)
at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1413)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1335)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskRun$4.apply(TaskRun.groovy:670)
at nextflow.processor.TaskRun$4.apply(TaskRun.groovy)
at java.base/java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1708)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskRun.containerInfo(TaskRun.groovy:667)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskRun.getContainer(TaskRun.groovy:693)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskRun.isContainerEnabled(TaskRun.groovy:738)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.createTaskHashKey(TaskProcessor.groovy:2193)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.invokeTask(TaskProcessor.groovy:659)
at nextflow.processor.InvokeTaskAdapter.call(InvokeTaskAdapter.groovy:52)
at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.access$001(ForkingDataflowOperatorActor.java:35)
at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor$1.run(ForkingDataflowOperatorActor.java:58)
at java.base/java.util.concurrent.ThreadPerTaskExecutor$TaskRunner.run(ThreadPerTaskExecutor.java:314)
at java.base/java.lang.Thread.run(Thread.java:1583)

Caused by: java.lang.IllegalStateException: Failed to pull singularity image command: singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1724986736964 docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: time="2024-08-30T10:58:57+08:00" level=warning msg="\"/run/user/32039\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/32039: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp: lookup registry-1.docker.io on 210.37.40.4:53: dial udp 210.37.40.4:53: connect: network is unreachable

at nextflow.container.SingularityCache.runCommand(SingularityCache.groovy:308)
at nextflow.container.SingularityCache.downloadContainerImage0(SingularityCache.groovy:275)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.container.SingularityCache$_downloadContainerImage_closure1.doCall(SingularityCache.groovy:243)
at nextflow.container.SingularityCache$_downloadContainerImage_closure1.call(SingularityCache.groovy)
at nextflow.file.FileMutex.lock(FileMutex.groovy:106)
at nextflow.container.SingularityCache.downloadContainerImage(SingularityCache.groovy:243)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.container.SingularityCache$_getLazyImagePath_closure2.doCall(SingularityCache.groovy:333)
at nextflow.container.SingularityCache$_getLazyImagePath_closure2.call(SingularityCache.groovy)
at groovyx.gpars.dataflow.LazyDataflowVariable$1.run(LazyDataflowVariable.java:70)
... 2 common frames omitted

Aug-30 10:58:57.030 [Actor Thread 115] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.IllegalStateException: Failed to pull singularity image command: singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1724986736964 docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: time="2024-08-30T10:58:57+08:00" level=warning msg="\"/run/user/32039\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/32039: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0: pinging docker registry returned: Get "https://registry-1.docker.io/v2/": dial tcp: lookup registry-1.docker.io on 210.37.40.4:53: dial udp 210.37.40.4:53: connect: network is unreachable

Aug-30 10:58:57.050 [Actor Thread 115] DEBUG nextflow.Session - The following nodes are still active: [process] POREC:index_bam status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: chunk_size port 2: (cntrl) - ; channel: $

[process] POREC:prepare_genome:index_ref_mmi status=ACTIVE port 0: (queue) closed; channel: reference.fasta port 1: (value) bound ; channel: minimap_settings port 2: (cntrl) - ; channel: $

[process] POREC:digest_align_annotate status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:haplotag_alignments status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:merge_coordsorted_bams status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:merge_namesorted_bams status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:create_restriction_bed status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:to_pairs_file status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:pairsToCooler status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:merge_mcools status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:merge_pairs status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:merge_pairs_stats status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:pair_stats_report status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:makeReport status=ACTIVE port 0: (value) OPEN ; channel: metadata port 1: (value) OPEN ; channel: stats port 2: (value) OPEN ; channel: versions/* port 3: (value) OPEN ; channel: params.json port 4: (value) bound ; channel: wf_version port 5: (cntrl) - ; channel: $

[process] POREC:prepare_hic status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:collectIngressResultsInDir status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] POREC:get_filtered_out_bam status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] publish status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

Aug-30 10:58:57.058 [main] DEBUG nextflow.Session - Session await > all processes finished Aug-30 10:58:57.058 [main] DEBUG nextflow.Session - Session await > all barriers passed Aug-30 10:58:57.059 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Aug-30 10:58:57.099 [Actor Thread 88] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=POREC:prepare_genome:index_ref_mmi; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Aug-30 10:58:57.105 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] Aug-30 10:58:57.105 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Aug-30 10:58:57.107 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Aug-30 10:58:57.893 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Aug-30 10:58:57.985 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Aug-30 10:58:58.012 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

很抱歉又打扰您了，非常希望您可以在百忙之中抽空解答一下我的问题，谢谢您。

sarahjeeeze commented 2 months ago

Hi, i think its trying to pull the container even though you are providing it. Try running it in offline mode with export NXF_OFFLINE='true'

Blosers commented 1 month ago

Hello author, may I ask where the command 'export NXF_OFFLINE='true' should be written? I found that writing this command in my. bashrc file still cannot run offline.

JWJ13164328557 commented 1 month ago

Hello, I have also encountered the same problem. Have you solved it?

Blosers commented 1 month ago

抱歉，我到现在也没有解决这个问题，我也不知道该怎么处理这个问题。已经卡了好久了。  

印痕 @.***

 

------------------ 原始邮件 ------------------ 发件人: @.>; 发送时间: 2024年10月16日(星期三) 下午4:47 收件人: @.>; 抄送: @.>; @.>; 主题: Re: [epi2me-labs/wf-pore-c] 离线使用wf-pore-c (Issue #74)

你好，我也遇到了同样的问题。你解决了吗

- 直接回复这封邮件，在GitHub上查看，或取消订阅. @.*** >

JWJ13164328557 commented 1 month ago

Hello, I may have solved this problem. You need to run this command with root privileges to run it smoothly. You can give it a try

Blosers commented 1 month ago

Do you mean that as long as you download three. sif files and configure them in Nextflow.comntig with root privileges, you can run them? May I ask how you configure the Nextflow.comntig file? I found that there seem to be two areas that need to be modified for configuration issues. Can you please help me check my configuration file?

 

印痕 @.***

 

------------------ 原始邮件 ------------------ 发件人: @.>; 发送时间: 2024年10月22日(星期二) 中午11:54 收件人: @.>; 抄送: @.>; @.>; 主题: Re: [epi2me-labs/wf-pore-c] 离线使用wf-pore-c (Issue #74)

你好，这个问题我可能已经解决了。需要以root权限运行此命令才能顺利运行。你可以试试看

- 直接回复这封邮件，在GitHub上查看，或取消订阅. @.*** >

JWJ13164328557 commented 1 month ago

No, you need root privileges to run NextFlow in order to call Docker to run the process

JWJ13164328557 commented 1 month ago

If you run Nextflow with root privileges, you don't need to download the SIF file to configure it

Blosers commented 1 month ago

My current issue is that firstly, I do not have root privileges. Perhaps I can inquire with the administrator later to request this. Secondly, it seems that the backend of the task I submitted cannot pull the network, so I may need to configure the local files before I can run it offline. Thank you very much for taking the time to reply to your question amidst your busy schedule. Thank you very much.  

印痕 @.***

 

------------------ 原始邮件 ------------------ 发件人: @.>; 发送时间: 2024年10月22日(星期二) 下午3:41 收件人: @.>; 抄送: @.>; @.>; 主题: Re: [epi2me-labs/wf-pore-c] 离线使用wf-pore-c (Issue #74)

如果您以root权限运行 Nextflow ，则不需要下载SIF文件来配置它

- 直接回复这封邮件，在GitHub上查看，或取消订阅. @.*** >