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guppy image missing? #11

Closed gokalpyildirir closed 2 years ago

gokalpyildirir commented 2 years ago

What happened?

Hi, this is my first time running an epi2me workflow. I can see how this will help me (if I can get it to work!)

I am working on a diploid organism, and I am trying to phase variants + basecall methylations on the phased reads. Normally I would use megalodon for this, but as the phase variant is not being supported anymore I want to try this workflow. When I run the script, because ontresearch/guppy image does not exist, the workflow fails. What am I missing? Should I run this workflow in any other way? This is my script:

OUTPUT=output.oct18 ~/nextflow run epi2me-labs/wf-human-variation \ -w ${OUTPUT}/workspace \ -profile standard \ --snp \ --fast5_dir ../A4_fast5/fast5 \ --guppy_device cuda:all:80% \ --guppy_cfg /home/science/rerio/basecall_models/res_dna_r941_min_modbases_5mC_CpG_v001.cfg \ --guppy_map_threads 3 \ --guppy_basemod_threads 4 \ --ref ../A4_diploid_sorted.fasta.masked \ --model /home/science/Clair3/models/r941_prom_sup_g5014 \ --out_dir ${OUTPUT}

Operating System

ubuntu 18.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - Execution Profile

Docker

Workflow Version

v0.3.0

Relevant log output

Oct.-20 13:24:42.348 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-human-variation -w output.oct18/workspace -profile standard --snp --fast5_dir ../A4_fast5/fast5 --guppy_device 'cuda:all:80%' --guppy_cfg /home/science/rerio/basecall_models/res_dna_r941_min_modbases_5mC_CpG_v001.cfg --guppy_map_threads 3 --guppy_basemod_threads 4 --ref ../A4_diploid_sorted.fasta.masked --model /home/science/Clair3/models/r941_prom_sup_g5014 --out_dir output.oct18
Oct.-20 13:24:42.398 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.10.0
Oct.-20 13:24:42.411 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/science/.nextflow/plugins; core-plugins: nf-amazon@1.11.0,nf-azure@0.14.2,nf-codecommit@0.1.2,nf-console@1.0.4,nf-ga4gh@1.0.4,nf-google@1.4.4,nf-tower@1.5.5,nf-wave@0.5.2
Oct.-20 13:24:42.419 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct.-20 13:24:42.419 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct.-20 13:24:42.421 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct.-20 13:24:42.428 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Oct.-20 13:24:42.437 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/science/.nextflow/scm
Oct.-20 13:24:43.046 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/science/.nextflow/assets/epi2me-labs/wf-human-variation/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-human-variation.git
Oct.-20 13:24:43.060 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Oct.-20 13:24:43.065 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/science/.nextflow/assets/epi2me-labs/wf-human-variation/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-human-variation.git
Oct.-20 13:24:43.581 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/science/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config
Oct.-20 13:24:43.582 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/science/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config
Oct.-20 13:24:43.590 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Oct.-20 13:24:43.732 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Oct.-20 13:24:43.732 [main] INFO  nextflow.cli.CmdRun - Launching `https://github.com/epi2me-labs/wf-human-variation` [voluminous_murdock] DSL2 - revision: b743889177 [master]
Oct.-20 13:24:43.733 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct.-20 13:24:43.733 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct.-20 13:24:43.735 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/science/.nextflow/secrets/store.json
Oct.-20 13:24:43.737 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@4e22368c] - activable => nextflow.secret.LocalSecretsProvider@4e22368c
Oct.-20 13:24:43.778 [main] DEBUG nextflow.Session - Session UUID: 49a9f469-59f8-413b-bf53-c02a5d86ff82
Oct.-20 13:24:43.778 [main] DEBUG nextflow.Session - Run name: voluminous_murdock
Oct.-20 13:24:43.778 [main] DEBUG nextflow.Session - Executor pool size: 8
Oct.-20 13:24:43.785 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct.-20 13:24:43.799 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 22.10.0 build 5826
  Created: 13-10-2022 05:44 UTC (01:44 EDT)
  System: Linux 5.4.0-126-generic
  Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 11.0.16+8-post-Ubuntu-0ubuntu118.04
  Encoding: UTF-8 (UTF-8)
  Process: 5905@1703-R-20KA00 [127.0.1.1]
  CPUs: 8 - Mem: 15.5 GB (683 MB) - Swap: 2 GB (1.7 GB)
Oct.-20 13:24:43.808 [main] DEBUG nextflow.Session - Work-dir: /media/science/Storage/A4/epi2me/output.oct18/workspace [fuseblk]
Oct.-20 13:24:43.818 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct.-20 13:24:43.824 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct.-20 13:24:43.877 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct.-20 13:24:43.883 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Oct.-20 13:24:43.953 [main] DEBUG nextflow.Session - Session start
Oct.-20 13:24:43.957 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /media/science/Storage/A4/epi2me/output.oct18/execution/trace.txt
Oct.-20 13:24:43.963 [main] DEBUG nextflow.Session - Using default localLib path: /home/science/.nextflow/assets/epi2me-labs/wf-human-variation/lib
Oct.-20 13:24:43.965 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/science/.nextflow/assets/epi2me-labs/wf-human-variation/lib
Oct.-20 13:24:43.965 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/science/.nextflow/assets/epi2me-labs/wf-human-variation/lib/nfcore_external_java_deps.jar
Oct.-20 13:24:45.071 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct.-20 13:24:46.306 [main] INFO  nextflow.Nextflow - Core Nextflow options
  revision             : master
  runName              : voluminous_murdock
  containerEngine      : docker
  container            : ontresearch/wf-human-variation:shab3358c08b332f9d113caa258b6daea245184bc00
  launchDir            : /media/science/Storage/A4/epi2me
  workDir              : /media/science/Storage/A4/epi2me/output.oct18/workspace
  projectDir           : /home/science/.nextflow/assets/epi2me-labs/wf-human-variation
  userName             : science
  profile              : standard
  configFiles          : /home/science/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config

Basic Input/Output Options
  fast5_dir            : ../A4_fast5/fast5
  ref                  : ../A4_diploid_sorted.fasta.masked
  model                : /home/science/Clair3/models/r941_prom_sup_g5014
  out_dir              : output.oct18
  ubam_sort_threads    : 3
  ubam_bam2fq_threads  : 1

wf-human-snp options
  snp                  : true

Basecalling options
  guppy_cfg            : /home/science/rerio/basecall_models/res_dna_r941_min_modbases_5mC_CpG_v001.cfg
  guppy_device         : cuda:all:80%
  guppy_map_threads    : 3
  guppy_basemod_threads: 4

Other parameters
  process_label        : wfdefault

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use epi2me-labs/wf-human-variation for your analysis please cite:

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

Oct.-20 13:24:46.335 [main] WARN  nextflow.Nextflow - * Using basecalling subworkflow!
Oct.-20 13:24:46.336 [main] WARN  nextflow.Nextflow -   This subworkflow is experimental and we do not provide an official guppy image at this time.
Oct.-20 13:24:46.406 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_guppy` matches labels `wf_guppy` for process with name fast5:guppy
Oct.-20 13:24:46.409 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:46.409 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:46.414 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct.-20 13:24:46.417 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=8 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
Oct.-20 13:24:46.467 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_sv` matches labels `wf_human_sv` for process with name fast5:sort_calls
Oct.-20 13:24:46.467 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:46.467 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:46.475 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_sv` matches labels `wf_human_sv` for process with name fast5:merge_calls
Oct.-20 13:24:46.476 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:46.476 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:46.506 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:46.506 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.045 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.045 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.068 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.068 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.072 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.072 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.076 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.076 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.080 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:make_chunks
Oct.-20 13:24:47.080 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.080 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.095 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:pileup_variants
Oct.-20 13:24:47.104 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.104 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.105 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [0]
Oct.-20 13:24:47.110 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:aggregate_pileup_variants
Oct.-20 13:24:47.110 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.110 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.113 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:select_het_snps
Oct.-20 13:24:47.114 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.114 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.115 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [0]
Oct.-20 13:24:47.125 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:phase_contig
Oct.-20 13:24:47.125 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.125 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.128 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:get_qual_filter
Oct.-20 13:24:47.129 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.129 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.132 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:create_candidates
Oct.-20 13:24:47.133 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.133 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.134 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [0]
Oct.-20 13:24:47.147 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:evaluate_candidates
Oct.-20 13:24:47.148 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.148 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.157 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:aggregate_full_align_variants
Oct.-20 13:24:47.157 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.157 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.163 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:merge_pileup_and_full_vars
Oct.-20 13:24:47.164 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.164 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.165 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [0]
Oct.-20 13:24:47.170 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:aggregate_all_variants
Oct.-20 13:24:47.170 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.170 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.173 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:readStats
Oct.-20 13:24:47.173 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.173 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.175 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:getVersions
Oct.-20 13:24:47.175 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.175 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.176 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:getParams
Oct.-20 13:24:47.176 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.176 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.178 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:vcfStats
Oct.-20 13:24:47.178 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.178 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.180 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name snp:makeReport
Oct.-20 13:24:47.180 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.180 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_human_snp` matches labels `wf_human_snp` for process with name output_snp
Oct.-20 13:24:47.185 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.185 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.188 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct.-20 13:24:47.188 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct.-20 13:24:47.189 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: filterBam, snp:merge_pileup_and_full_vars, get_qual_filter, snp:evaluate_candidates, create_candidates, sortVCF, sort_calls, fast5:merge_calls, index_ref_gzi, indexVCF, snp:getParams, makeReport, hap, select_het_snps, getVersions, output_snp, pileup_variants, guppy, snp:makeReport, phase_contig, aggregate_full_align_variants, minimap2_ubam, post_clair_phase_contig, getAllChromosomesBed, check_for_alignment, getParams, merge_pileup_and_full_vars, snp:readStats, snp:pileup_variants, snp:aggregate_full_align_variants, mapula, snp:phase_contig, sniffles2, output_sv, readStats, fast5:guppy, evaluate_candidates, aggregate_pileup_variants, output_methyl, index_ref_fai, filterCalls, publish_artifact, make_chunks, snp:create_candidates, cram_cache, snp:get_qual_filter, fast5:sort_calls, vcfStats, merge_calls, snp:select_het_snps, mosdepth, snp:getVersions, snp:vcfStats, snp:make_chunks, aggregate_all_variants, decompress_ref, report, snp:aggregate_pileup_variants, snp:aggregate_all_variants, modbam2bed
Oct.-20 13:24:47.189 [main] DEBUG nextflow.Session - Igniting dataflow network (34)
Oct.-20 13:24:47.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fast5:guppy
Oct.-20 13:24:47.193 [PathVisitor-2] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: ../A4_fast5/; pattern: fast5**/*.fast5; options: [:]
Oct.-20 13:24:47.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fast5:sort_calls
Oct.-20 13:24:47.194 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fast5:merge_calls
Oct.-20 13:24:47.194 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > index_ref_fai
Oct.-20 13:24:47.194 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > cram_cache
Oct.-20 13:24:47.195 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > getAllChromosomesBed
Oct.-20 13:24:47.195 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > mosdepth
Oct.-20 13:24:47.195 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > mapula
Oct.-20 13:24:47.196 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:make_chunks
Oct.-20 13:24:47.196 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:pileup_variants
Oct.-20 13:24:47.196 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:pileup_variants
Oct.-20 13:24:47.197 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:aggregate_pileup_variants
Oct.-20 13:24:47.197 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:select_het_snps
Oct.-20 13:24:47.197 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:select_het_snps
Oct.-20 13:24:47.199 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:phase_contig
Oct.-20 13:24:47.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:get_qual_filter
Oct.-20 13:24:47.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:create_candidates
Oct.-20 13:24:47.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:create_candidates
Oct.-20 13:24:47.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:evaluate_candidates
Oct.-20 13:24:47.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:aggregate_full_align_variants
Oct.-20 13:24:47.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:merge_pileup_and_full_vars
Oct.-20 13:24:47.201 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:merge_pileup_and_full_vars
Oct.-20 13:24:47.201 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:aggregate_all_variants
Oct.-20 13:24:47.201 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:readStats
Oct.-20 13:24:47.203 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:getVersions
Oct.-20 13:24:47.203 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:getParams
Oct.-20 13:24:47.203 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:vcfStats
Oct.-20 13:24:47.203 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > snp:makeReport
Oct.-20 13:24:47.203 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output_snp
Oct.-20 13:24:47.203 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > publish_artifact
Oct.-20 13:24:47.203 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Oct.-20 13:24:47.203 [main] DEBUG nextflow.Session - Session await
Oct.-20 13:24:47.321 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct.-20 13:24:47.323 [Task submitter] INFO  nextflow.Session - [88/949e5a] Submitted process > index_ref_fai (1)
Oct.-20 13:24:47.331 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct.-20 13:24:47.331 [Task submitter] INFO  nextflow.Session - [f0/f3a523] Submitted process > cram_cache (1)
Oct.-20 13:24:47.337 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct.-20 13:24:47.337 [Task submitter] INFO  nextflow.Session - [52/fef14a] Submitted process > snp:getVersions
Oct.-20 13:24:47.343 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct.-20 13:24:47.343 [Task submitter] INFO  nextflow.Session - [2f/84ee23] Submitted process > snp:getParams
Oct.-20 13:24:47.356 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct.-20 13:24:47.356 [Task submitter] INFO  nextflow.Session - [61/943546] Submitted process > fast5:guppy (1)
Oct.-20 13:24:48.056 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: fast5:guppy (1); status: COMPLETED; exit: 125; error: -; workDir: /media/science/Storage/A4/epi2me/output.oct18/workspace/61/9435460a8804a11b44e448929d04c0]
Oct.-20 13:24:48.064 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'fast5:guppy (1)'

Caused by:
  Process `fast5:guppy (1)` terminated with an error exit status (125)

Command executed:

  guppy_basecaller         -a A4_diploid_sorted.fasta.masked         -q 0         --device cuda:all:80%         --num_alignment_threads 3         --num_base_mod_threads 4         --config /home/science/rerio/basecall_models/res_dna_r941_min_modbases_5mC_CpG_v001.cfg         --bam_out                  -i . -s guppy_out
  for bam in guppy_out/pass/*.bam ; do
      mv -v ${bam} ${bam%.bam}.0.bam
  done

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'ontresearch/guppy:sha7ee822e4c0349299d7049ea3faa9671d38c27cd8' locally
  docker: Error response from daemon: pull access denied for ontresearch/guppy, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
  See 'docker run --help'.

Work dir:
  /media/science/Storage/A4/epi2me/output.oct18/workspace/61/9435460a8804a11b44e448929d04c0

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Oct.-20 13:24:48.064 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct.-20 13:24:48.067 [Task submitter] INFO  nextflow.Session - [34/d5de95] Submitted process > fast5:guppy (3)
Oct.-20 13:24:48.088 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `fast5:guppy (1)` terminated with an error exit status (125)
Oct.-20 13:24:48.102 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] fast5:sort_calls
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] fast5:merge_calls
  status=ACTIVE
  port 0: (value) bound ; channel: ref
  port 1: (value) OPEN  ; channel: crams
  port 2: (cntrl) -     ; channel: $

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

[process] mosdepth
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (queue) OPEN  ; channel: target_bed
  port 2: (queue) OPEN  ; channel: -
  port 3: (cntrl) -     ; channel: $

[process] mapula
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (queue) OPEN  ; channel: target_bed
  port 2: (queue) OPEN  ; channel: -
  port 3: (cntrl) -     ; channel: $

[process] snp:make_chunks
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (queue) OPEN  ; channel: -
  port 2: (queue) OPEN  ; channel: bed
  port 3: (cntrl) -     ; channel: $

[process] snp:pileup_variants
  status=ACTIVE
  port 0: (value) OPEN  ; channel: __$eachinparam<0>
  port 1: (queue) OPEN  ; channel: -
  port 2: (queue) OPEN  ; channel: -
  port 3: (queue) OPEN  ; channel: model
  port 4: (cntrl) -     ; channel: $

[process] snp:aggregate_pileup_variants
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: input_vcfs/*
  port 2: (queue) OPEN  ; channel: contigs
  port 3: (cntrl) -     ; channel: $

[process] snp:select_het_snps
  status=ACTIVE
  port 0: (value) OPEN  ; channel: __$eachinparam<0>
  port 1: (queue) OPEN  ; channel: -
  port 2: (queue) OPEN  ; channel: split_folder/phase_qual
  port 3: (cntrl) -     ; channel: $

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

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

[process] snp:create_candidates
  status=ACTIVE
  port 0: (value) OPEN  ; channel: __$eachinparam<0>
  port 1: (queue) OPEN  ; channel: -
  port 2: (queue) OPEN  ; channel: -
  port 3: (queue) OPEN  ; channel: candidate_bed/qual
  port 4: (cntrl) -     ; channel: $

[process] snp:evaluate_candidates
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (queue) OPEN  ; channel: -
  port 2: (queue) OPEN  ; channel: -
  port 3: (queue) OPEN  ; channel: model
  port 4: (cntrl) -     ; channel: $

[process] snp:aggregate_full_align_variants
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: full_alignment/*
  port 2: (queue) OPEN  ; channel: contigs
  port 3: (value) OPEN  ; channel: gvcf_tmp_path/*
  port 4: (cntrl) -     ; channel: $

[process] snp:merge_pileup_and_full_vars
  status=ACTIVE
  port 0: (value) OPEN  ; channel: __$eachinparam<0>
  port 1: (queue) OPEN  ; channel: -
  port 2: (queue) OPEN  ; channel: -
  port 3: (queue) OPEN  ; channel: -
  port 4: (queue) OPEN  ; channel: non_var.gvcf
  port 5: (value) OPEN  ; channel: candidate_beds/*
  port 6: (cntrl) -     ; channel: $

[process] snp:aggregate_all_variants
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: merge_output/*
  port 2: (value) OPEN  ; channel: merge_outputs_gvcf/*
  port 3: (value) bound ; channel: phase_vcf
  port 4: (queue) OPEN  ; channel: contigs
  port 5: (cntrl) -     ; channel: $

[process] snp:readStats
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (queue) OPEN  ; channel: -
  port 2: (cntrl) -     ; channel: $

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

[process] snp:makeReport
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: read_summary
  port 1: (queue) OPEN  ; channel: -
  port 2: (queue) OPEN  ; channel: vcfstats
  port 3: (value) OPEN  ; channel: versions
  port 4: (value) OPEN  ; channel: params.json
  port 5: (cntrl) -     ; channel: $

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

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

Oct.-20 13:24:48.223 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct.-20 13:24:48.223 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct.-20 13:24:48.346 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (5)
Oct.-20 13:24:48.569 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=9; submittedCount=1; runningCount=0; retriesCount=0; abortedCount=4; succeedDuration=0ms; failedDuration=4.4s; cachedDuration=0ms;loadCpus=-7; loadMemory=0; peakRunning=5; peakCpus=11; peakMemory=0; ]
Oct.-20 13:24:48.569 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Oct.-20 13:24:48.570 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Oct.-20 13:24:48.591 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":null,"process":"guppy","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":623,"min":623,"q1":623,"q2":623,"q3":623,"max":623,"minLabel":"fast5:guppy (1)","maxLabel":"fast5:guppy (1)","q1Label":"fast5:guppy (1)","q2Label":"fast5:guppy (1)","q3Label":"fast5:guppy (1)"},"writes":null},{"cpuUsage":null,"process":"index_ref_fai","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null},{"cpuUsage":null,"process":"cram_cache","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null},{"cpuUsage":null,"process":"getVersions","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null},{"cpuUsage":null,"process":"getParams","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null}]
Oct.-20 13:24:49.035 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Oct.-20 13:24:49.083 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct.-20 13:24:49.093 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
SamStudio8 commented 2 years ago

Hi @gokalpyildirir, you are correct that the image is missing. Please see this line in the log you provided:

Oct.-20 13:24:46.336 [main] WARN  nextflow.Nextflow -   This subworkflow is experimental and we do not provide an official guppy image at this time.

However, you will hopefully be excited to hear that wf-human-variation v0.4.0 has just been released with support for our experimental Dorado basecaller (image included!). To update please run:

nextflow pull epi2me-labs/wf-human-variation