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

No response

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

epi2me-labs / wf-pore-c

Failed to pull singularity image #64

Operating System

Other Linux

Workflow Version

Workflow Execution

EPI2ME Version

CLI command run

Workflow Execution - CLI Execution Profile

What happened?

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

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

Relevant log output

Application activity log entry

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

Other demo data information

epi2me-labs / wf-pore-c

Failed to pull singularity image #64

Operating System

Other Linux

Workflow Version

Workflow Execution

EPI2ME Version

CLI command run

Workflow Execution - CLI Execution Profile

What happened?

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

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

Relevant log output

Application activity log entry

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

Other demo data information

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