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Failed to pull singularity image #64

Closed wangguiqian closed 4 months ago

wangguiqian commented 5 months ago

Operating System

CentOS 7

Other Linux

CentOS 7

Workflow Version

v.23.10.1

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

bsub -J Pore_C -n 25 -o Pore_C1.out -e Pore_C1.err -q normal "nextflow run ~/Software/wf-pore-c-1.1.0 --fastq ../raw_data/Pore-C_part1.fq.gz --ref ../Gh_genome.fa --cutter DpnII -c increase_memory.config --threads 60 --paired_end_minimum_distance 100 --paired_end_maximum_distance 200 --chunk_size 10000 --filter_pairs --paired_end --hi_c --out_dir PoreC_part1 -profile singularity"

Workflow Execution - CLI Execution Profile

None

What happened?

Sender: LSF System lsfadmin@c05n06 Subject: Job 26222294: in cluster Exited

Job was submitted from host by user in cluster at Tue Jun 25 03:37:27 2024 Job was executed on host(s) <25*c05n06>, in queue , as user in cluster at Tue Jun 25 03:37:27 2024 </public/home/yqming> was used as the home directory. </public/home/yqming/Work_plate/Cotton_data/Pore_data> was used as the working directory. Started at Tue Jun 25 03:37:27 2024 Terminated at Tue Jun 25 03:37:53 2024 Results reported at Tue Jun 25 03:37:53 2024

Your job looked like:

LSBATCH: User input

nextflow run ~/Software/wf-pore-c-1.1.0 --fastq ../raw_data/Pore-C_part1.fq.gz --ref ../Gh_genome.fa --cutter DpnII -c increase_memory.config --threads 60 --paired

Exited with exit code 1.

Resource usage summary:

CPU time :                                   88.18 sec.
Max Memory :                                 1742 MB
Average Memory :                             482.40 MB
Total Requested Memory :                     -
Delta Memory :                               -
Max Swap :                                   -
Max Processes :                              7
Max Threads :                                141
Run time :                                   26 sec.
Turnaround time :                            26 sec.

The output (if any) follows:

N E X T F L O W ~ version 23.10.1 Launching /public/home/yqming/Software/wf-pore-c-1.1.0/main.nf [cheesy_knuth] DSL2 - revision: cc183d633a

|||||||||| _ __ _ __ ____ |||||||||| | ____| _ | | \/ | __| | | | | ||||| | | | |) | | ) | |\/| | _| ___| |/ ` | ' \/ | ||||| | |_| /| | / /| | | | |_|| | (| | |) _ \ |||||||||| |____|_| |_|___|| ||| ||\,|._/|/ |||||||||| wf-pore-c v1.1.0

Core Nextflow options runName : cheesy_knuth containerEngine : singularity container : [withLabel:wfporec:ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0, withLabel:pore_c_py:ontresearch/pore-c-py:shad launchDir : /public/home/yqming/Work_plate/Cotton_data/Pore_data workDir : /public/home/yqming/Work_plate/Cotton_data/Pore_data/work ...skipping... [- ] process > POREC:merge_pairs - [- ] process > POREC:merge_pairs_stats - [- ] process > POREC:pair_stats_report - [- ] process > POREC:merge_paired_end_bams - [- ] process > POREC:getVersions - [- ] process > POREC:getParams - [- ] process > POREC:makeReport - [- ] process > POREC:prepare_hic - [- ] process > POREC:get_filtered_out_bam - [- ] process > output - Pulling Singularity image docker://ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9 [cache /public/home/yqming/Work_plate/Cotton_data/Pore_data/wo Pulling Singularity image docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0 [cache /public/home/yqming/Work_plate/Cotton_data/Pore_data/wo WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /public/home/yqming/Work_plate/Cotton_data/Pore_data/work/singul ERROR ~ Error executing process > 'POREC:getVersions'

Caused by: Failed to pull singularity image command: singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1719257860451 docker://ontresearch/wf-pore-c:sha3 status : 255 message: FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

-- Check '.nextflow.log' file for details

PS:

Read file for stderr output of this job.

Waiting for data... (interrupt to abort)

Relevant log output

Jun-25 03:37:31.365 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /public/home/yqming/Software/wf-pore-c-1.1.0 --fastq ../raw_data/Pore-C_part1.fq.gz --ref 
Jun-25 03:37:31.624 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.10.1
Jun-25 03:37:31.659 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/public/home/yqming/.nextflow/p
Jun-25 03:37:31.675 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-25 03:37:31.677 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-25 03:37:31.683 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jun-25 03:37:31.701 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-25 03:37:33.008 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /public/home/yqming/Software/wf-pore-c-1.1.0/nextflow.config
Jun-25 03:37:33.013 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /public/home/yqming/Work_plate/Cotton_data/Pore_data/increase_memory.config
Jun-25 03:37:33.013 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /public/home/yqming/Software/wf-pore-c-1.1.0/nextflow.config
Jun-25 03:37:33.013 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /public/home/yqming/Work_plate/Cotton_data/Pore_data/increase_memory.config
Jun-25 03:37:33.027 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jun-25 03:37:33.260 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jun-25 03:37:33.303 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, conda, singularity, awsbatch, local]
Jun-25 03:37:33.355 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jun-25 03:37:33.386 [main] INFO  nextflow.cli.CmdRun - Launching `/public/home/yqming/Software/wf-pore-c-1.1.0/main.nf` [cheesy_knuth] DSL2 - revision: cc183d633a
Jun-25 03:37:33.387 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-25 03:37:33.387 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-25 03:37:33.402 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /public/home/yqming/.nextflow/secrets/store.json
Jun-25 03:37:33.408 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@1e1232cf] - activable => nextf
Jun-25 03:37:33.508 [main] DEBUG nextflow.Session - Session UUID: 18c8c5fd-6f1e-408d-aafa-93c18b33342b
Jun-25 03:37:33.508 [main] DEBUG nextflow.Session - Run name: cheesy_knuth
Jun-25 03:37:33.509 [main] DEBUG nextflow.Session - Executor pool size: 36
Jun-25 03:37:33.520 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-25 03:37:33.526 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=108; workQueue=LinkedBlockingQueue[10000
Jun-25 03:37:33.583 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.10.1 build 5891
  Created: 12-01-2024 22:01 UTC (13-01-2024 06:01 CDT)
  System: Linux 3.10.0-862.el7.x86_64
  Runtime: Groovy 3.0.19 on Java HotSpot(TM) 64-Bit Server VM 11.0.8+10-LTS
  Encoding: UTF-8 (UTF-8)
  Process: 311382@c05n06 [10.1.5.6]
  CPUs: 36 - Mem: 150 GB (149.5 GB) - Swap: 0 (0)
Jun-25 03:37:33.621 [main] DEBUG nextflow.Session - Work-dir: /public/home/yqming/Work_plate/Cotton_data/Pore_data/work [gpfs]
Jun-25 03:37:33.650 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-25 03:37:33.664 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-25 03:37:33.724 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-25 03:37:33.739 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 37; maxThreads: 1000
Jun-25 03:37:33.931 [main] DEBUG nextflow.Session - Session start
Jun-25 03:37:33.940 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /public/home/yqming/Work_plate/Cotton_data/Pore_data/PoreC_part
Jun-25 03:37:33.962 [main] DEBUG nextflow.Session - Using default localLib path: /public/home/yqming/Software/wf-pore-c-1.1.0/lib
Jun-25 03:37:33.970 [main] DEBUG nextflow.Session - Adding to the classpath library: /public/home/yqming/Software/wf-pore-c-1.1.0/lib
Jun-25 03:37:33.971 [main] DEBUG nextflow.Session - Adding to the classpath library: /public/home/yqming/Software/wf-pore-c-1.1.0/lib/nfcore_external_java_deps.jar
Jun-25 03:37:37.061 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-25 03:37:39.472 [main] INFO  nextflow.Nextflow - 
ESC[0;92m||||||||||   ESC[0mESC[2m_____ ____ ___ ____  __  __ _____      _       _
ESC[0;92m||||||||||  ESC[0mESC[2m| ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
ESC[0;33m|||||       ESC[0mESC[2m|  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
ESC[0;33m|||||       ESC[0mESC[2m| |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
ESC[0;94m||||||||||  ESC[0mESC[2m|_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
ESC[0;94m||||||||||  ESC[0mESC[1mwf-pore-c v1.1.0ESC[0m
ESC[2m--------------------------------------------------------------------------------ESC[0m
ESC[1mCore Nextflow optionsESC[0m
  ESC[0;34mrunName                    : ESC[0;32mcheesy_knuthESC[0m
  ESC[0;34mcontainerEngine            : ESC[0;32msingularityESC[0m
  ESC[0;34mcontainer                  : ESC[0;32m[withLabel:wfporec:ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0, withLabel:pore_c_py:ontresea
  ESC[0;34mlaunchDir                  : ESC[0;32m/public/home/yqming/Work_plate/Cotton_data/Pore_dataESC[0m
  ESC[0;34mworkDir                    : ESC[0;32m/public/home/yqming/Work_plate/Cotton_data/Pore_data/workESC[0m
  ESC[0;34mprojectDir                 : ESC[0;32m/public/home/yqming/Software/wf-pore-c-1.1.0ESC[0m
  ESC[0;34muserName                   : ESC[0;32myqmingESC[0m
  ESC[0;34mprofile                    : ESC[0;32msingularityESC[0m
  ESC[0;34mconfigFiles                : ESC[0;32m/public/home/yqming/Software/wf-pore-c-1.1.0/nextflow.config, /public/home/yqming/Work_plate/Cotton_data/Pore_data

ESC[1mInput OptionsESC[0m
  ESC[0;34mfastq                      : ESC[0;32m../raw_data/Pore-C_part1.fq.gzESC[0m
  ESC[0;34mref                        : ESC[0;32m../Gh_genome.faESC[0m
  ESC[0;34mcutter                     : ESC[0;32mDpnIIESC[0m

ESC[1mOutput OptionsESC[0m
  ESC[0;34mout_dir                    : ESC[0;32mPoreC_part1ESC[0m
  ESC[0;34mhi_c                       : ESC[0;32mtrueESC[0m

ESC[1mAdvanced OptionsESC[0m
  ESC[0;34mchunk_size                 : ESC[0;32m10000ESC[0m
  ESC[0;34mthreads                    : ESC[0;32m60ESC[0m

ESC[1mPaired-end BAM OptionsESC[0m
  ESC[0;34mpaired_end                 : ESC[0;32mtrueESC[0m
  ESC[0;34mfilter_pairs               : ESC[0;32mtrueESC[0m
  ESC[0;34mpaired_end_minimum_distance: ESC[0;32m100ESC[0m
  ESC[0;34mpaired_end_maximum_distance: ESC[0;32m200ESC[0m

!! Only displaying parameters that differ from the pipeline defaults !!
ESC[2m--------------------------------------------------------------------------------ESC[0m
If you use epi2me-labs/wf-pore-c for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

ESC[2m--------------------------------------------------------------------------------ESC[0m
This is epi2me-labs/wf-pore-c v1.1.0.
ESC[2m--------------------------------------------------------------------------------ESC[0m
Jun-25 03:37:39.650 [main] INFO  nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Jun-25 03:37:39.867 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `ingress,wf_common` for process with name POR
Jun-25 03:37:39.877 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:39.877 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:39.886 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jun-25 03:37:39.893 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=36; memory=150 GB; capacity=36; pollInte
Jun-25 03:37:39.896 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jun-25 03:37:40.009 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:index_bam
Jun-25 03:37:40.011 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.011 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.031 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:prepare_g
Jun-25 03:37:40.032 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.032 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.057 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:prepare_g
Jun-25 03:37:40.059 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.059 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.096 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pore_c_py` matches labels `pore_c_py` for process with name POREC:diges
Jun-25 03:37:40.097 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.098 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.120 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:haplotag_
Jun-25 03:37:40.122 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.122 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.140 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:merge_coo
Jun-25 03:37:40.140 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:merge_coordsorted_bams|merge_namesorted_bams` matches process POREC:merg
Jun-25 03:37:40.142 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.142 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.151 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:merge_nam
Jun-25 03:37:40.152 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:merge_coordsorted_bams|merge_namesorted_bams` matches process POREC:merg
Jun-25 03:37:40.152 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.152 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.180 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:create_re
Jun-25 03:37:40.181 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_s
Jun-25 03:37:40.182 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.182 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.198 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:to_pairs_
Jun-25 03:37:40.199 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.199 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.208 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:merge_pai
Jun-25 03:37:40.209 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_s
Jun-25 03:37:40.209 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.209 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.216 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:merge_pai
Jun-25 03:37:40.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_s
Jun-25 03:37:40.219 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.219 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.223 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:pair_stat
Jun-25 03:37:40.224 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:merge_pairs|merge_pairs_stats|merge_mcools|create_restriction_bed|pair_s
Jun-25 03:37:40.224 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.225 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.231 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:merge_pai
Jun-25 03:37:40.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:merge_coordsorted_bams|merge_namesorted_bams` matches process POREC:merg
Jun-25 03:37:40.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:merge_paired_end_bams` matches process POREC:merge_paired_end_bams
Jun-25 03:37:40.233 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.233 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.236 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:getVersio
Jun-25 03:37:40.237 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.237 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.241 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:getParams
Jun-25 03:37:40.242 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.242 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.258 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:makeRepor
Jun-25 03:37:40.258 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:makeReport` matches process POREC:makeReport
Jun-25 03:37:40.259 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.259 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:prepare_h
Jun-25 03:37:40.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:prepare_hic` matches process POREC:prepare_hic
Jun-25 03:37:40.265 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.265 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.279 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name POREC:get_filte
Jun-25 03:37:40.279 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:get_filtered_out_bam` matches process POREC:get_filtered_out_bam
Jun-25 03:37:40.280 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.280 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.284 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfporec` matches labels `wfporec` for process with name output
Jun-25 03:37:40.285 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-25 03:37:40.285 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-25 03:37:40.288 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: move_or_compress_fq_file, haplotag_alignments, pair_stats_report, haplotagReads,
Jun-25 03:37:40.290 [main] DEBUG nextflow.Session - Igniting dataflow network (23)
Jun-25 03:37:40.290 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:fastcat
Jun-25 03:37:40.291 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:index_bam
Jun-25 03:37:40.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:prepare_genome:index_ref_fai
Jun-25 03:37:40.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:prepare_genome:index_ref_mmi
Jun-25 03:37:40.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:digest_align_annotate
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:haplotag_alignments
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_coordsorted_bams
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_namesorted_bams
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:create_restriction_bed
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:to_pairs_file
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_pairs
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_pairs_stats
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:pair_stats_report
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:merge_paired_end_bams
Jun-25 03:37:40.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:getVersions
Jun-25 03:37:40.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:getParams
Jun-25 03:37:40.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:makeReport
Jun-25 03:37:40.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:prepare_hic
Jun-25 03:37:40.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > POREC:get_filtered_out_bam
Jun-25 03:37:40.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output
Jun-25 03:37:40.307 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_6183ff06cb5d1fd0: /public/home/yqming/Software/wf-pore-c-1.1.0/main.nf
  Script_a004c86652788981: /public/home/yqming/Software/wf-pore-c-1.1.0/./modules/local/4dn.nf
  Script_e8e8e89ec33b6973: /public/home/yqming/Software/wf-pore-c-1.1.0/./subworkflows/local/../../modules/local/common.nf
  Script_88e1f22baeec41c5: /public/home/yqming/Software/wf-pore-c-1.1.0/./modules/local/pore-c.nf
  Script_6f2dfe738e879fd7: /public/home/yqming/Software/wf-pore-c-1.1.0/./subworkflows/local/prepare_genome.nf
  Script_52f11d1ddf9ca2a2: /public/home/yqming/Software/wf-pore-c-1.1.0/./lib/ingress.nf
Jun-25 03:37:40.307 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Jun-25 03:37:40.307 [main] DEBUG nextflow.Session - Session await
Jun-25 03:37:40.448 [Actor Thread 26] WARN  nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored i
Jun-25 03:37:40.451 [Actor Thread 26] INFO  nextflow.container.SingularityCache - Pulling Singularity image docker://ontresearch/wf-common:sha1c5febff9f75143710826
Jun-25 03:37:40.451 [Actor Thread 23] INFO  nextflow.container.SingularityCache - Pulling Singularity image docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67fb
Jun-25 03:37:43.843 [Actor Thread 30] 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.1719257860451 docker://ontresearch/wf-pore-c:sha3
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

Jun-25 03:37:43.843 [Actor Thread 32] 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.1719257860451 docker://ontresearch/wf-pore-c:sha3
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

Jun-25 03:37:43.843 [Actor Thread 33] 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.1719257860451 docker://ontresearch/wf-pore-c:sha3
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

Jun-25 03:37:43.843 [Actor Thread 31] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=POREC:prepare_genome:index_ref_fai (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.1719257860451 docker://ontresearch/wf-pore-c:sha3
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

Jun-25 03:37:43.852 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=POREC:prepare_genome:index_ref_fai; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jun-25 03:37:43.852 [Actor Thread 34] 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
Jun-25 03:37:43.852 [Actor Thread 37] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=POREC:getParams; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jun-25 03:37:43.873 [Actor Thread 30] ERROR nextflow.processor.TaskProcessor - Error executing process > 'POREC:getVersions'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1719257860451 docker://ontresearch/wf-pore-c:sha3
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

java.lang.IllegalStateException: java.lang.IllegalStateException: Failed to pull singularity image
  command: singularity pull  --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1719257860451 docker://ontresearch/wf-pore-c:sha3
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

        at nextflow.container.SingularityCache.getCachePathFor(SingularityCache.groovy:354)
        at nextflow.container.ContainerHandler.createSingularityCache(ContainerHandler.groovy:101)
        at nextflow.container.ContainerHandler.normalizeImageName(ContainerHandler.groovy:73)
        at nextflow.container.resolver.DefaultContainerResolver.resolveImage(DefaultContainerResolver.groovy:44)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
        at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSite.invoke(PogoMetaMethodSite.java:166)
        at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.call(PogoMetaMethodSite.java:69)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
        at nextflow.processor.TaskRun.containerInfo0(TaskRun.groovy:634)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:362)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
        at nextflow.processor.TaskRun$_containerInfo_closure7.doCall(TaskRun.groovy:620)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at groovy.lang.Closure.call(Closure.java:427)
        at org.codehaus.groovy.runtime.ConvertedClosure.invokeCustom(ConvertedClosure.java:50)
        at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:112)
        at com.sun.proxy.$Proxy29.apply(Unknown Source)
        at java.base/java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1705)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoCachedMethodSiteNoUnwrap.invoke(PojoMetaMethodSite.java:198)
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:51)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
        at nextflow.processor.TaskRun.containerInfo(TaskRun.groovy:620)
        at nextflow.processor.TaskRun.getContainer(TaskRun.groovy:642)
        at nextflow.processor.TaskRun.isContainerEnabled(TaskRun.groovy:687)
        at nextflow.processor.TaskRun$isContainerEnabled$12.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
        at nextflow.processor.TaskProcessor.createTaskHashKey(TaskProcessor.groovy:2109)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
        at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
        at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
        at nextflow.processor.TaskProcessor.invokeTask(TaskProcessor.groovy:638)
        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$1.run(ForkingDataflowOperatorActor.java:58)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.IllegalStateException: Failed to pull singularity image
  command: singularity pull  --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1719257860451 docker://ontresearch/wf-pore-c:sha3
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

        at nextflow.container.SingularityCache.runCommand(SingularityCache.groovy:306)
        at nextflow.container.SingularityCache.downloadContainerImage0(SingularityCache.groovy:273)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1036)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1019)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
        at nextflow.container.SingularityCache$_downloadContainerImage_closure1.doCall(SingularityCache.groovy:241)
        at nextflow.container.SingularityCache$_downloadContainerImage_closure1.call(SingularityCache.groovy)
        at nextflow.file.FileMutex.lock(FileMutex.groovy:106)
        at nextflow.container.SingularityCache.downloadContainerImage(SingularityCache.groovy:241)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1036)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1019)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
        at nextflow.container.SingularityCache$_getLazyImagePath_closure2.doCall(SingularityCache.groovy:331)
        at nextflow.container.SingularityCache$_getLazyImagePath_closure2.call(SingularityCache.groovy)
        at groovyx.gpars.dataflow.LazyDataflowVariable$1.run(LazyDataflowVariable.java:70)
        ... 3 common frames omitted
Jun-25 03:37:43.883 [Actor Thread 30] 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.1719257860451 docker://ontresearch/wf-pore-c:sha3
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://ontresearch/wf-pore-c:sha3787c234c0cacf66a67f

Jun-25 03:37:43.906 [Actor Thread 30] DEBUG nextflow.Session - The following nodes are still active:
[process] POREC:fastcat
  status=ACTIVE
  port 0: (queue) closed; channel: -
  port 1: (value) bound ; channel: extra_args
  port 2: (cntrl) -     ; channel: $

[process] POREC:index_bam
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: chunk_size
  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: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:merge_paired_end_bams
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] POREC:getVersions
  status=ACTIVE
  port 0: (cntrl) -     ; channel: $

[process] POREC:makeReport
  status=ACTIVE
  port 0: (value) OPEN  ; channel: metadata
  port 1: (value) OPEN  ; channel: per_read_stats/{?}.gz
  port 2: (value) OPEN  ; channel: versions/*
  port 3: (value) OPEN  ; channel: params.json
  port 4: (cntrl) -     ; channel: $

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

Jun-25 03:37:43.914 [main] DEBUG nextflow.Session - Session await > all processes finished
Jun-25 03:37:43.916 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-25 03:37:43.916 [Actor Thread 35] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=POREC:fastcat; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jun-25 03:37:43.916 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jun-25 03:37:43.923 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=POREC:getVersions; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jun-25 03:37:43.941 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0;
Jun-25 03:37:43.941 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jun-25 03:37:43.944 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jun-25 03:37:44.820 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jun-25 03:37:44.931 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jun-25 03:37:44.955 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
(END)

Application activity log entry

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Were you able to successfully run the latest version of the workflow with the demo data?

other (please describe below)

Other demo data information

No response

wangguiqian commented 5 months ago

Due to, My computer is LSF System to run,My computer did not connect network.

sarahjeeeze commented 4 months ago

Hi, did you manage to resolve this? It does look like an issue with the singularity set up on the system you are running it on.

sarahjeeeze commented 4 months ago

also see https://labs.epi2me.io/singularity/ for guidance

wangguiqian commented 4 months ago

Hi, did you manage to resolve this? It does look like an issue with the singularity set up on the system you are running it on. I am testing much times, But I don’t resolve this. Do you know how did resolve the question ?

wangguiqian commented 4 months ago

also see https://labs.epi2me.io/singularity/ for guidance

I carefully read the link you sent me, but I still can't download the container tools used by singularity, and my server can only run offline. Do you have any other way to solve the problem?

sarahjeeeze commented 4 months ago

have you tried export NXF_OFFLINE='true' before running the nextflow cmd above

wangguiqian commented 4 months ago

have you tried export NXF_OFFLINE='true' before running the nextflow cmd above Thank you for your answer. I checked the nextflow process later and found that it can be run offline. NXF_OFFLINE='true' But I need to download the image file of pore-c specified singularity before running it. Is that right? Or do I need to download other files? I am still trying to download the image file, but I cannot download this file at the moment. I feel so strange.

sarahjeeeze commented 4 months ago

Can you download the image to any location? If so then you can specify wherever you have downloaded it to using NXF_SINGULARITY_CACHEDIR=nameofidrectory and this along with the export NXF_OFFLINE='true' should all you to run it offline. Let me know how it goes.

wangguiqian commented 4 months ago

Can you download the image to any location? If so then you can specify wherever you have downloaded it to using NXF_SINGULARITY_CACHEDIR=nameofidrectory and this along with the export NXF_OFFLINE='true' should all you to run it offline. Let me know how it goes.

I now fully understand what you mean, that is, to run this program by downloading the image first. But I am in China, and I don’t know why I can’t download the image singularity pull --name ontresearch-wf-pore-c docker://ontresearch/wf-pore-c:sha3

wangguiqian commented 4 months ago

Can you download the image to any location? If so then you can specify wherever you have downloaded it to using NXF_SINGULARITY_CACHEDIR=nameofidrectory and this along with the export NXF_OFFLINE='true' should all you to run it offline. Let me know how it goes.

Thank you very much

wangguiqian commented 4 months ago

I downloaded the image,but get some errs result
(work) [yqming@login01 Pore_data]$ singularity pull --name ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.img.pulling.1719257860451 docker://ontresearch/wf-pore-c:shab20d0656e02c0f4dac3054ae6c0e1f816de2ff90
INFO: Converting OCI blobs to SIF format INFO: Starting build... Getting image source signatures Copying blob 4f4fb700ef54 skipped: already exists
Copying blob 4f4fb700ef54 skipped: already exists
Copying blob 4f4fb700ef54 skipped: already exists
Copying blob 4f4fb700ef54 skipped: already exists
Copying blob 4f4fb700ef54 skipped: already exists
Copying blob 4f4fb700ef54 [--------------------------------------] 0.0b / 0.0b
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: Error initializing source oci:/public/home/yqming/.singularity/cache/blob:5c188ea4969a72d550a610b2dcd23b9ba491dd5b0b314a90628d1e4ab159f2c8: Error reading blob sha256:ca1778b6935686ad781c27472c4668fc61ec3aeb85494f72deb1921892b9d39e: Get "https://production.cloudflare.docker.com/registry-v2/docker/registry/v2/blobs/sha256/ca/ca1778b6935686ad781c27472c4668fc61ec3aeb85494f72deb1921892b9d39e/data?verify=1721135596-R71uIw7PR2Lp5ZKdvabmITlKdsE%3D": dial tcp 31.13.73.169:443: i/o timeout

wangguiqian commented 4 months ago

Can you download the image to any location? If so then you can specify wherever you have downloaded it to using NXF_SINGULARITY_CACHEDIR=nameofidrectory and this along with the export NXF_OFFLINE='true' should all you to run it offline. Let me know how it goes.

Hi ,Thank you very much for your help.Just I solved my problem ,I tried many times.I use offonline to run . Finally I use the command: nextflow run ~/Software/wf-pore-c-1.1.0/ --fastq ../raw_data/Pore-C_part2.fq.gz --ref ../Gh_genome.fa --cutter DpnII -c increase_memory.config --threads 60 --paired_end_minimum_distance 100 --paired_end_maximum_distance 200 --chunk_size 10000 --filter_pairs --paired_end --hi_c --out_dir PoreC_part1 -profile singularity -with-singularity '~/Software/wf-pore-c-1.1.0/ontresearch-wf-pore-c-sha3787c234c0cacf66a67fb77da223cc2e1cb0baf0.sif' -with-trace -resume

sarahjeeeze commented 4 months ago

ah ok thanks for letting us know

wangguiqian commented 4 months ago

ah ok thanks for letting us know

But I personal have a question that to download wfporec.sif 、wf_common.sif and pore_c_py.sif files is very difficult in China. Advised for you,please you put the 3 files on specific path to download. Thank you so much

Blosers commented 3 months ago

您好，我也在使用该软件，在下载的过程中出现了问题，请问您是如何解决的该问题的，可以不吝赐教吗？非常感谢。