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UPHL-BioNGS / Donut_Falls

Basic workflow for nanopore sequencing data
MIT License
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NOTE: Process `DONUT_FALLS:fastp (ATCC6258-FT)` terminated with an error exit status (137) #97

Open SeanSierra-Patev opened 4 hours ago

SeanSierra-Patev commented 4 hours ago

not executing successfully. Command was:

nextflow run UPHL-BioNGS/Donut_Falls -r 1.8.24207 -profile docker --sample_sheet samples.csv

here's the trace 

task_id hash    native_id   name    status  exit    submit  duration    realtime    %cpu    peak_rss    peak_vmem   rchar   wchar
1   d2/10c13a   1356809 DONUT_FALLS:fastp (ATCC6258-FT) FAILED  137 2024-11-01 12:06:47.587 16.5s   16.3s   -   -   -   -   -
3   20/770ed6   1357670 DONUT_FALLS:fastp (ATCC6258-FT) FAILED  137 2024-11-01 12:07:04.096 17.1s   17.1s   -   -   -   -   -
2   9e/6512f1   1356816 DONUT_FALLS:nanoplot (ATCC6258-FT)  COMPLETED   0   2024-11-01 12:06:47.595 1m 35s  9s  203.9%  2.2 GB  57.9 GB 73.1 MB 4.6 MB
4   4c/f61892   1363151 DONUT_FALLS:versions (extracting versions)  COMPLETED   0   2024-11-01 12:08:22.677 567ms   54ms    93.0%   6.9 MB  16.1 MB 681.2 KB    955 B
5   b6/333f3f   1363375 DONUT_FALLS:summary (Creating summary)  COMPLETED   0   2024-11-01 12:08:23.297 616ms   48ms    114.8%  6.2 MB  15.9 MB 553.6 KB    900 B
6   5d/c0486b   1363383 DONUT_FALLS:multiqc (combining reports) COMPLETED   0   2024-11-01 12:08:23.306 4.4s    3.7s    117.9%  83.5 MB 1014.7 MB   59.4 MB 2.4 MB
erinyoung commented 4 hours ago

!!!

This is a problem!!!

Can you share the full error message?

SeanSierra-Patev commented 3 hours ago

I think that's all it said

nextflow run UPHL-BioNGS/Donut_Falls -r 1.8.24207 -profile docker --sample_sheet samples.csv 

 N E X T F L O W   ~  version 24.10.0

Launching `https://github.com/UPHL-BioNGS/Donut_Falls` [nostalgic_blackwell] DSL2 - revision: 54982d3c21 [1.8.24207]

 __                    ___          
|  ) _   _      _)_    )_ _   ) ) _ 
|_/ (_) ) ) (_( (_    (  (_( ( ( (  
                                 _) 
Currently using the Donut Falls workflow for use with nanopore sequencing
Author: Erin Young
email: eriny@utah.gov
Version: 1.8.24207
executor >  local (3)
[-        ] DONUT_FALLS:mash                   -
[f3/b2a699] DONUT_FALLS:fastp (ATCC6258-FT)    | 1 of 2, failed: 1, retries: 1
[-        ] DONUT_FALLS:rasusa                 -
[-        ] DONUT_FALLS:flye                   -
[-        ] DONUT_FALLS:bandage                -
[-        ] DONUT_FALLS:gfastats               -
[-        ] DONUT_FALLS:gfa_to_fasta           -
executor >  local (3)
[-        ] DONUT_FALLS:mash                   -
[f3/b2a699] DONUT_FALLS:fastp (ATCC6258-FT)    | 1 of 2, failed: 1, retries: 1
[-        ] DONUT_FALLS:rasusa                 -
[-        ] DONUT_FALLS:flye                   -
[-        ] DONUT_FALLS:bandage                -
[-        ] DONUT_FALLS:gfastats               -
[-        ] DONUT_FALLS:gfa_to_fasta           -
[-        ] DONUT_FALLS:dnaapler               -
[-        ] DONUT_FALLS:medaka                 -
[-        ] DONUT_FALLS:bwa                    -
[-        ] DONUT_FALLS:polypolish             -
[-        ] DONUT_FALLS:pypolca                -
[81/241ffe] DONUT_FALLS:nanoplot (ATCC6258-FT) | 0 of 1
[-        ] DONUT_FALLS:busco                  -
[-        ] DONUT_FALLS:png                    -
[-        ] DONUT_FALLS:circulocov             -
[-        ] DONUT_FALLS:versions               -
[-        ] DONUT_FALLS:summary                -
[-        ] DONUT_FALLS:multiqc                -
[-        ] DONUT_FALLS:copy                   -
[76/0d5ea4] NOTE: Process `DONUT_FALLS:fastp (ATCC6258-FT)` terminated with an error exit status (137) -- Execution is retried (1)
erinyoung commented 3 hours ago

That's mysterious. Can you share your .nextflow.log file?

If I remember correctly, you either need to copy the contents as a message or change the file extension to something like .txt

SeanSierra-Patev commented 3 hours ago 
Nov-01 12:06:43.088 [main] DEBUG nextflow.cli.Launcher - $> nextflow run UPHL-BioNGS/Donut_Falls -r 1.8.24207 -profile docker --sample_sheet samples.csv
Nov-01 12:06:43.164 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.10.0
Nov-01 12:06:43.183 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/sean/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2
Nov-01 12:06:43.221 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Nov-01 12:06:43.222 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Nov-01 12:06:43.224 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Nov-01 12:06:43.235 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Nov-01 12:06:43.244 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/sean/.nextflow/scm
Nov-01 12:06:43.734 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/sean/.nextflow/assets/UPHL-BioNGS/Donut_Falls/.git/config; branch: main; remote: origin; url: https://github.com/UPHL-BioNGS/Donut_Falls.git
Nov-01 12:06:43.765 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Nov-01 12:06:43.780 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/sean/.nextflow/assets/UPHL-BioNGS/Donut_Falls/.git/config; branch: main; remote: origin; url: https://github.com/UPHL-BioNGS/Donut_Falls.git
Nov-01 12:06:44.350 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/sean/.nextflow/assets/UPHL-BioNGS/Donut_Falls/nextflow.config
Nov-01 12:06:44.352 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/sean/.nextflow/assets/UPHL-BioNGS/Donut_Falls/nextflow.config
Nov-01 12:06:44.359 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/sean/.nextflow/secrets/store.json
Nov-01 12:06:44.366 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2ec99035] - activable => nextflow.secret.LocalSecretsProvider@2ec99035
Nov-01 12:06:44.377 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Nov-01 12:06:44.507 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [test, campy, singularity, docker]
Nov-01 12:06:44.556 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Nov-01 12:06:44.557 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/UPHL-BioNGS/Donut_Falls` [irreverent_jang] DSL2 - revision: 54982d3c21 [1.8.24207]
Nov-01 12:06:44.558 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Nov-01 12:06:44.558 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Nov-01 12:06:44.601 [main] DEBUG nextflow.Session - Session UUID: 4433dfab-ea1c-4191-aece-eccdc5abf273
Nov-01 12:06:44.602 [main] DEBUG nextflow.Session - Run name: irreverent_jang
Nov-01 12:06:44.602 [main] DEBUG nextflow.Session - Executor pool size: 20
Nov-01 12:06:44.609 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Nov-01 12:06:44.614 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=60; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Nov-01 12:06:44.628 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 24.10.0 build 5928
  Created: 27-10-2024 18:36 UTC (14:36 EDT)
  System: Linux 6.8.0-47-generic
  Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 21.0.4+7-Ubuntu-1ubuntu224.04
  Encoding: UTF-8 (UTF-8)
  Process: 1356658@DOH-LAB-LNX1 [127.0.1.1]
  CPUs: 20 - Mem: 125.5 GB (84.6 GB) - Swap: 8 GB (6 GB)
Nov-01 12:06:44.644 [main] DEBUG nextflow.Session - Work-dir: /home/sean/Workdir/GridION/SP241030/work [ext2/ext3]
Nov-01 12:06:44.671 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Nov-01 12:06:44.678 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Nov-01 12:06:44.745 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Nov-01 12:06:44.774 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 21; maxThreads: 1000
Nov-01 12:06:44.860 [main] DEBUG nextflow.Session - Session start
Nov-01 12:06:44.863 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/sean/Workdir/GridION/SP241030/trace-20241101-43604681.txt
Nov-01 12:06:46.725 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Nov-01 12:06:46.733 [main] INFO  nextflow.script.BaseScript - 
Nov-01 12:06:46.733 [main] INFO  nextflow.script.BaseScript -  __                    ___          
Nov-01 12:06:46.734 [main] INFO  nextflow.script.BaseScript - |  ) _   _      _)_    )_ _   ) ) _ 
Nov-01 12:06:46.734 [main] INFO  nextflow.script.BaseScript - |_/ (_) ) ) (_( (_    (  (_( ( ( (  
Nov-01 12:06:46.734 [main] INFO  nextflow.script.BaseScript -                                  _) 
Nov-01 12:06:46.734 [main] INFO  nextflow.script.BaseScript - 
Nov-01 12:06:46.734 [main] INFO  nextflow.script.BaseScript - Currently using the Donut Falls workflow for use with nanopore sequencing
Nov-01 12:06:46.735 [main] INFO  nextflow.script.BaseScript - Author: Erin Young
Nov-01 12:06:46.735 [main] INFO  nextflow.script.BaseScript - email: eriny@utah.gov
Nov-01 12:06:46.735 [main] INFO  nextflow.script.BaseScript - Version: 1.8.24207
Nov-01 12:06:46.736 [main] INFO  nextflow.script.BaseScript - 
Nov-01 12:06:46.946 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:mash
Nov-01 12:06:46.958 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:46.959 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:46.965 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Nov-01 12:06:46.976 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=20; memory=125.5 GB; capacity=20; pollInterval=100ms; dumpInterval=5m
Nov-01 12:06:46.980 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Nov-01 12:06:47.066 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:fastp
Nov-01 12:06:47.068 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.068 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.084 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:rasusa
Nov-01 12:06:47.085 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.085 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.100 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name DONUT_FALLS:flye
Nov-01 12:06:47.102 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.102 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.129 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:bandage
Nov-01 12:06:47.130 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.131 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.138 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:gfastats
Nov-01 12:06:47.140 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.140 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.151 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:gfa_to_fasta
Nov-01 12:06:47.152 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.152 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.157 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:dnaapler
Nov-01 12:06:47.159 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.159 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.172 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:medaka
Nov-01 12:06:47.173 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.173 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.185 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name DONUT_FALLS:bwa
Nov-01 12:06:47.187 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.187 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.192 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:polypolish
Nov-01 12:06:47.194 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.194 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.208 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:pypolca
Nov-01 12:06:47.210 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.210 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.227 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:nanoplot
Nov-01 12:06:47.229 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.229 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.241 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:busco
Nov-01 12:06:47.242 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.242 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.276 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:png
Nov-01 12:06:47.278 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.278 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.284 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name DONUT_FALLS:circulocov
Nov-01 12:06:47.285 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.285 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.294 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:versions
Nov-01 12:06:47.296 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.296 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.325 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:summary
Nov-01 12:06:47.327 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.327 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.337 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:multiqc
Nov-01 12:06:47.339 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.339 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.353 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name DONUT_FALLS:copy
Nov-01 12:06:47.354 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-01 12:06:47.354 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-01 12:06:47.357 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: unicycler, DONUT_FALLS:medaka, DONUT_FALLS:versions, DONUT_FALLS:copy, rasusa, bandage, pypolca, polypolish, DONUT_FALLS:bandage, medaka, nanoplot, gfastats, DONUT_FALLS:fastp, mash, copy, multiqc, DONUT_FALLS:rasusa, DONUT_FALLS:circulocov, fastp, summary, DONUT_FALLS:nanoplot, flye, DONUT_FALLS:multiqc, raven, test, DONUT_FALLS:gfa_to_fasta, dnaapler, png, DONUT_FALLS:mash, DONUT_FALLS:pypolca, DONUT_FALLS:gfastats, DONUT_FALLS:bwa, gfa_to_fasta, DONUT_FALLS:flye, bwa, nanoplot_summary, DONUT_FALLS:png, DONUT_FALLS:polypolish, DONUT_FALLS:busco, versions, busco, DONUT_FALLS:dnaapler, DONUT_FALLS:summary, circulocov
Nov-01 12:06:47.359 [main] DEBUG nextflow.Session - Igniting dataflow network (26)
Nov-01 12:06:47.363 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:mash
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:fastp
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:rasusa
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:flye
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:bandage
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:gfastats
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:gfa_to_fasta
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:dnaapler
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:medaka
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:bwa
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:polypolish
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:pypolca
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:nanoplot
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:busco
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:png
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:circulocov
Nov-01 12:06:47.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:versions
Nov-01 12:06:47.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:summary
Nov-01 12:06:47.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:multiqc
Nov-01 12:06:47.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DONUT_FALLS:copy
Nov-01 12:06:47.365 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_0dc632d2faa2652a: /home/sean/.nextflow/assets/UPHL-BioNGS/Donut_Falls/donut_falls.nf
Nov-01 12:06:47.365 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Nov-01 12:06:47.365 [main] DEBUG nextflow.Session - Session await
Nov-01 12:06:47.394 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Nov-01 12:06:47.585 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-01 12:06:47.587 [Task submitter] INFO  nextflow.Session - [d2/10c13a] Submitted process > DONUT_FALLS:fastp (ATCC6258-FT)
Nov-01 12:06:47.595 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-01 12:06:47.596 [Task submitter] INFO  nextflow.Session - [9e/6512f1] Submitted process > DONUT_FALLS:nanoplot (ATCC6258-FT)
Nov-01 12:07:04.042 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: DONUT_FALLS:fastp (ATCC6258-FT); status: COMPLETED; exit: 137; error: -; workDir: /home/sean/Workdir/GridION/SP241030/work/d2/10c13a393ba1e8e184164ff2947b3e]
Nov-01 12:07:04.044 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=60; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Nov-01 12:07:04.062 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=DONUT_FALLS:fastp (ATCC6258-FT); work-dir=/home/sean/Workdir/GridION/SP241030/work/d2/10c13a393ba1e8e184164ff2947b3e
  error [nextflow.exception.ProcessFailedException]: Process `DONUT_FALLS:fastp (ATCC6258-FT)` terminated with an error exit status (137)
Nov-01 12:07:04.076 [TaskFinalizer-1] INFO  nextflow.processor.TaskProcessor - [d2/10c13a] NOTE: Process `DONUT_FALLS:fastp (ATCC6258-FT)` terminated with an error exit status (137) -- Execution is retried (1)
Nov-01 12:07:04.096 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-01 12:07:04.097 [Task submitter] INFO  nextflow.Session - [20/770ed6] Re-submitted process > DONUT_FALLS:fastp (ATCC6258-FT)
Nov-01 12:07:21.199 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: DONUT_FALLS:fastp (ATCC6258-FT); status: COMPLETED; exit: 137; error: -; workDir: /home/sean/Workdir/GridION/SP241030/work/20/770ed655dab0c04de7f75fe5ce44a3]
Nov-01 12:07:21.203 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=DONUT_FALLS:fastp (ATCC6258-FT); work-dir=/home/sean/Workdir/GridION/SP241030/work/20/770ed655dab0c04de7f75fe5ce44a3
  error [nextflow.exception.ProcessFailedException]: Process `DONUT_FALLS:fastp (ATCC6258-FT)` terminated with an error exit status (137)
Nov-01 12:07:21.205 [TaskFinalizer-2] INFO  nextflow.processor.TaskProcessor - [20/770ed6] NOTE: Process `DONUT_FALLS:fastp (ATCC6258-FT)` terminated with an error exit status (137) -- Error is ignored
Nov-01 12:07:21.210 [Actor Thread 11] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Nov-01 12:07:21.211 [Actor Thread 13] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Nov-01 12:07:21.216 [Actor Thread 16] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Nov-01 12:07:21.218 [Actor Thread 13] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Nov-01 12:08:22.566 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: DONUT_FALLS:nanoplot (ATCC6258-FT); status: COMPLETED; exit: 0; error: -; workDir: /home/sean/Workdir/GridION/SP241030/work/9e/6512f1071876f15db9839858ecdb60]
Nov-01 12:08:22.613 [TaskFinalizer-3] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=60; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Nov-01 12:08:22.647 [Actor Thread 13] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.01 s; total time: 0.011 s
Nov-01 12:08:22.647 [Actor Thread 7] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.01 s; total time: 0.011 s
Nov-01 12:08:22.654 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/sean/Workdir/GridION/SP241030/work/collect-file/9d1a3ac0125638112a9eac6842dbe13b
Nov-01 12:08:22.654 [Actor Thread 7] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/sean/Workdir/GridION/SP241030/work/collect-file/511b618f5430a0365a84bbefe40767b7
Nov-01 12:08:22.659 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-9288820374715413236
Nov-01 12:08:22.659 [Actor Thread 7] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-15108572825948055919
Nov-01 12:08:22.677 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-01 12:08:22.678 [Task submitter] INFO  nextflow.Session - [4c/f61892] Submitted process > DONUT_FALLS:versions (extracting versions)
Nov-01 12:08:23.245 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: DONUT_FALLS:versions (extracting versions); status: COMPLETED; exit: 0; error: -; workDir: /home/sean/Workdir/GridION/SP241030/work/4c/f61892251e1679adca09a7041341b2]
Nov-01 12:08:23.296 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-01 12:08:23.297 [Task submitter] INFO  nextflow.Session - [b6/333f3f] Submitted process > DONUT_FALLS:summary (Creating summary)
Nov-01 12:08:23.306 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-01 12:08:23.306 [Task submitter] INFO  nextflow.Session - [5d/c0486b] Submitted process > DONUT_FALLS:multiqc (combining reports)
Nov-01 12:08:23.913 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: DONUT_FALLS:summary (Creating summary); status: COMPLETED; exit: 0; error: -; workDir: /home/sean/Workdir/GridION/SP241030/work/b6/333f3f56cba337cfbfae612e51cb82]
Nov-01 12:08:27.685 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: DONUT_FALLS:multiqc (combining reports); status: COMPLETED; exit: 0; error: -; workDir: /home/sean/Workdir/GridION/SP241030/work/5d/c0486b8e527bb3a3be6714d2f83eb9]
Nov-01 12:08:27.696 [main] DEBUG nextflow.Session - Session await > all processes finished
Nov-01 12:08:27.785 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Nov-01 12:08:27.786 [main] DEBUG nextflow.Session - Session await > all barriers passed
Nov-01 12:08:27.789 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Nov-01 12:08:27.790 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Nov-01 12:08:27.794 [main] INFO  nextflow.script.BaseScript - Pipeline completed at: 2024-11-01T12:08:27.790894720-04:00
Nov-01 12:08:27.795 [main] INFO  nextflow.script.BaseScript - The multiqc report can be found at donut_falls/multiqc/multiqc_report.html
Nov-01 12:08:27.795 [main] INFO  nextflow.script.BaseScript - The consensus fasta files can be found in donut_falls/sample/consensus
Nov-01 12:08:27.796 [main] INFO  nextflow.script.BaseScript - The fasta files are from each phase of assembly. polca > polypolish > medaka > unpolished
Nov-01 12:08:27.796 [main] INFO  nextflow.script.BaseScript - Execution status: OK
Nov-01 12:08:27.803 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=4; failedCount=2; ignoredCount=1; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=1; abortedCount=0; succeedDuration=25.6s; failedDuration=1m 7s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=4; peakMemory=24 GB; ]
Nov-01 12:08:27.804 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Nov-01 12:08:27.806 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Nov-01 12:08:28.513 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Nov-01 12:08:28.831 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Nov-01 12:08:28.853 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Nov-01 12:08:28.855 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
erinyoung commented 3 hours ago

Thank you!

I'm not seeing anything really informative as to why fastp failed, unfortunately.

What is in /home/sean/Workdir/GridION/SP241030/work/d2/10c13a393ba1e8e184164ff2947b3e ?

Other things:

What does your sample sheet look like?

Fastp should run on fastq files, but perhaps your files aren't getting read in correctly. This should throw an error in fastp, though.

How old are your fastq files?

Donut Falls will not run on R9 flow cell and prior reads because the quality is too low. This should also throw a more informative error.

SeanSierra-Patev commented 2 hours ago

ah yes these are R9s! That would do it

the sample sheet was just one fastq as input. a multifastq of all the individual reads out of this run for this library

I had already deleted the work directory (I'm operating on the razor's edge of storage availability, sorry!)

fastp runs on the fastqs individually, but most of them fail out. I have a hunch this is some kind of strange RAM bug (inexplicably gobbling up 128gb RAM and then also maxing out my SWAP). I'm re-running on the fastp filtered fastqs only and the error seems to have disappeared!

my appologies for using the program incorrectly!