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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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[Bug]: wf-artic v0.3.21 on epi2melabs v4.0.0 looks for primer scheme in directory that doesn't exist #73

Closed kneubehl closed 1 year ago

kneubehl commented 1 year ago

What happened?

wf-artic fails to find the primer scheme directory. It looks for a directory that does not exist in a very weird path that seems to be merging two different paths, see log info below. The demo data also fails to download properly to test out the workflow. The error returned is "Error:Untar failed: C:\Users\Alex\epi2melabs\demo\epi2m3-labs\wf-artic\demo_data.tar.gz". Not sure if both issues are related but we are experiencing both issues on our desktop in the lab and our laptop in the field (both are running the same OS and versions of epi2melabs and wf-artic). With previous versions of epi2melabs and wf-artic we ran the workflow just fine on both the desktop and laptop. The data we are using are data we had previously run on an older version of epi2melabs and wf-artic and it worked fine. Any guidance on how to resolve this would be appreciated. Thanks.

Operating System

Windows 11

Workflow Execution

EPI2ME Labs desktop application

Workflow Execution - EPI2ME Labs Versions

there is no blue help icon in the bottom left but the epi2melabs is V4.0.0

Workflow Execution - CLI Execution Profile

None

Workflow Version

v0.3.21

Relevant log output

Jan-18 18:40:29.959 [main] DEBUG nextflow.cli.Launcher - $> /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/404e70a77444be71a9a52298e2edb320428d142c511183b87a2f28696c475f8e/AppData/Local/EPI2MELabs/app-4.0.0/resources/nextflow-all -log /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_71c5ffa9-ece1-4e31-8f19-d987513f2c15/nextflow.log run /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/main.nf -params-file /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_71c5ffa9-ece1-4e31-8f19-d987513f2c15/params.json -w /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_71c5ffa9-ece1-4e31-8f19-d987513f2c15/work -ansi-log false -offline -profile standard -name cranky_golick
Jan-18 18:40:30.016 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.04.5
Jan-18 18:40:30.039 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/nextflow.config
Jan-18 18:40:30.042 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/nextflow.config
Jan-18 18:40:30.082 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jan-18 18:40:30.970 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jan-18 18:40:31.008 [main] INFO  nextflow.cli.CmdRun - Launching `/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/main.nf` [cranky_golick] DSL2 - revision: 86b7bb70f5
Jan-18 18:40:31.028 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/.nextflow/plugins; core-plugins: nf-amazon@1.7.2,nf-azure@0.13.2,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.4.0,nf-tower@1.4.0
Jan-18 18:40:31.031 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jan-18 18:40:31.055 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-18 18:40:31.058 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-18 18:40:31.063 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jan-18 18:40:31.078 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jan-18 18:40:31.162 [main] DEBUG nextflow.Session - Session uuid: 17bf3b8d-e7f7-4186-bb0f-39e906e4cef1
Jan-18 18:40:31.163 [main] DEBUG nextflow.Session - Run name: cranky_golick
Jan-18 18:40:31.164 [main] DEBUG nextflow.Session - Executor pool size: 6
Jan-18 18:40:31.190 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 22.04.5 build 5709
  Created: 15-07-2022 16:22 UTC (11:22 CDT)
  System: Linux 5.10.102.1-microsoft-standard-WSL2
  Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.15+10-Ubuntu-0ubuntu0.20.04.1
  Encoding: UTF-8 (UTF-8)
  Process: 10548@kneubehl-alienw [127.0.1.1]
  CPUs: 6 - Mem: 19.5 GB (5.9 GB) - Swap: 5 GB (5 GB)
Jan-18 18:40:31.226 [main] DEBUG nextflow.Session - Work-dir: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_71c5ffa9-ece1-4e31-8f19-d987513f2c15/work [v9fs]
Jan-18 18:40:31.290 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, AwsBatchExecutor]
Jan-18 18:40:31.303 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-18 18:40:31.320 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jan-18 18:40:31.362 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jan-18 18:40:31.379 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 7; maxThreads: 1000
Jan-18 18:40:31.523 [main] DEBUG nextflow.Session - Session start invoked
Jan-18 18:40:31.527 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_71c5ffa9-ece1-4e31-8f19-d987513f2c15/output/execution/trace.txt
Jan-18 18:40:31.540 [main] DEBUG nextflow.Session - Using default localLib path: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/lib
Jan-18 18:40:31.561 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/lib
Jan-18 18:40:31.563 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/lib/nfcore_external_java_deps.jar
Jan-18 18:40:33.406 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-18 18:40:34.201 [main] INFO  nextflow.Nextflow - 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-artic v0.3.21
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : cranky_golick
  containerEngine: docker
  launchDir      : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_71c5ffa9-ece1-4e31-8f19-d987513f2c15
  workDir        : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_71c5ffa9-ece1-4e31-8f19-d987513f2c15/work
  projectDir     : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic
  userName       : lopez_lab
  profile        : standard
  configFiles    : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/nextflow.config

Input Options
  fastq          : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/404e70a77444be71a9a52298e2edb320428d142c511183b87a2f28696c475f8e/Desktop/midnight_lib16_demux_ont_v3

Primer Scheme Selection
  scheme_version : Midnight-ONT/V3
  scheme_dir     : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/404e70a77444be71a9a52298e2edb320428d142c511183b87a2f28696c475f8e/AppData/Local/EPI2MELabs/app-4.0.0/primer_schemes

Output Options
  out_dir        : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_71c5ffa9-ece1-4e31-8f19-d987513f2c15/output

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

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

--------------------------------------------------------------------------------
This is epi2me-labs/wf-artic v0.3.21.
--------------------------------------------------------------------------------
Jan-18 18:40:34.980 [main] INFO  nextflow.Nextflow - 
      ------------------------------------
      Available Primer Schemes:
      ------------------------------------

Jan-18 18:40:34.980 [main] INFO  nextflow.Nextflow -   Name     Version
Jan-18 18:40:34.981 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V1    
Jan-18 18:40:34.981 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V2    
Jan-18 18:40:34.982 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V3    
Jan-18 18:40:34.982 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V4    
Jan-18 18:40:34.982 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V4.1  
Jan-18 18:40:34.983 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    Midnight-IDT/V1 
Jan-18 18:40:34.983 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    Midnight-ONT/V1 
Jan-18 18:40:34.983 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    Midnight-ONT/V2 
Jan-18 18:40:34.983 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    Midnight-ONT/V3 
Jan-18 18:40:34.984 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    NEB-VarSkip/v1a 
Jan-18 18:40:34.984 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    NEB-VarSkip/v1a-long    
Jan-18 18:40:34.984 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    NEB-VarSkip/v2  
Jan-18 18:40:34.985 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    NEB-VarSkip/v2b 
Jan-18 18:40:34.985 [main] INFO  nextflow.Nextflow -   spike-seq ONT/V1  
Jan-18 18:40:34.985 [main] INFO  nextflow.Nextflow -   spike-seq ONT/V4.1    
Jan-18 18:40:34.985 [main] INFO  nextflow.Nextflow - 
      ------------------------------------

Jan-18 18:40:34.991 [main] DEBUG nextflow.Session - Session aborted -- Cause: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/data/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/404e70a77444be71a9a52298e2edb320428d142c511183b87a2f28696c475f8e/AppData/Local/EPI2MELabs/app-4.0.0/primer_schemes/SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.scheme.bed
Jan-18 18:40:35.146 [main] ERROR nextflow.cli.Launcher - /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/data/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/404e70a77444be71a9a52298e2edb320428d142c511183b87a2f28696c475f8e/AppData/Local/EPI2MELabs/app-4.0.0/primer_schemes/SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.scheme.bed
java.nio.file.NoSuchFileException: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/data/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/404e70a77444be71a9a52298e2edb320428d142c511183b87a2f28696c475f8e/AppData/Local/EPI2MELabs/app-4.0.0/primer_schemes/SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.scheme.bed
    at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1036)
    at nextflow.file.FileHelper$checkIfExists$1.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
    at nextflow.Nextflow.file(Nextflow.groovy:159)
    at nextflow.Nextflow$file.callStatic(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240)
    at Script_03ed4be9$_runScript_closure20$_closure62.doCall(Script_03ed4be9:598)
    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:1035)
    at groovy.lang.Closure.call(Closure.java:412)
    at groovy.lang.Closure.call(Closure.java:406)
    at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205)
    at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189)
    at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
    at nextflow.script.IterableDef$invoke_a.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:139)
    at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:208)
    at nextflow.script.BaseScript.run(BaseScript.groovy:217)
    at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:220)
    at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:212)
    at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:120)
    at nextflow.cli.CmdRun.run(CmdRun.groovy:337)
    at nextflow.cli.Launcher.run(Launcher.groovy:480)
    at nextflow.cli.Launcher.main(Launcher.groovy:639)
kneubehl commented 1 year ago

I tried the wf-tb-amr workflow as well and attempted to do a demo run of that and I ran into the same issue with the "Error:Untar failed: C:\Users\Alex\epi2melabs\demo\epi2m3-labs\wf-tb-amr\demo_data.tar.gz". I was able to run the demo for both wf-artic and wf-tb-amr on epi2melabs v4.0.0 on my Linux machine so I am wondering if it is something with Windows11. I checked the WSL2, Java, Docker, etc in the epi2me app and it says they are all good to go. However, I did notice that with the Docker check while it says it is ready to use it will not let me 'Continue'. The 'Continue' button is greyed out. Not sure if that is normal or something is amiss there. I might be able to try this out on a Windows 10 computer tomorrow. Will report back.

mattdmem commented 1 year ago

thanks @kneubehl - please do let us know how you get on. We do not currently test on Windows 11.

kneubehl commented 1 year ago

Our windows 10 desktop is returning the same error when we try to do the demo run and the same weird path issue when we try to run our own data.

EmaOMV commented 1 year ago

HI, i've been trough the same error in windows 10. The problem was in lines 597-601 of 'main.nf' script. the two overlapping path were generated apparently by 'params.scheme_dir' and 'params.scheme_name'. I managed to temporarily solve the issue by removing the first one. Then it stopped again with the same problem in the tutorial in the old version, the path and the folders the unzipped from the downloaded primer schemes werenot matching

No such file: /mnt/c/Users/admineo/epi2melabs/workflows/epi2me-labs/wf-artic/data/ARTIC/V4.1/SARS-CoV-2.reference.fasta

so i had to manually reorder the folders in the correct order to macth the path and rename reference fasta and bed files. But then stopped again with this:

Error executing process > 'pipeline:copySchemeDir'
Caused by:
  Process `pipeline:copySchemeDir` terminated with an error exit status (1)
Command executed:
  cp -RL primer_schemes scheme_dir
Command exit status:
  1
Command output:
  (empty)
Command error:
  cp: cannot stat 'primer_schemes': No such file or directory

Can you please tell how long will it take to adjust the script? thank you

mattdmem commented 1 year ago

@EmaOMV could you please start a new issue - I don't think this is related. When you submit you new issue can you please let me know what you changed and also the command/settings you're using to run the workflow! Thanks!

kneubehl commented 1 year ago

v4.1.0 has fixed running the demo issue which completes with no problem. However, when we go to run our data we still run into the same issue as before. It is looking for the primer scheme in a path that does not exist. See log below:

Jan-26 19:31:18.953 [main] DEBUG nextflow.cli.Launcher - $> /mnt/c/Users/Alex/AppData/Local/EPI2MELabs/app-4.1.0/resources/nextflow-all -log /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_3c0906a2-3acb-4096-a36a-5dec0582eccc/nextflow.log run /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/main.nf -params-file /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_3c0906a2-3acb-4096-a36a-5dec0582eccc/params.json -w /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_3c0906a2-3acb-4096-a36a-5dec0582eccc/work -ansi-log false -offline -profile standard -name ecstatic_mayer
Jan-26 19:31:19.017 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.04.5
Jan-26 19:31:19.046 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/nextflow.config
Jan-26 19:31:19.049 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/nextflow.config
Jan-26 19:31:19.102 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jan-26 19:31:20.066 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jan-26 19:31:20.108 [main] INFO  nextflow.cli.CmdRun - Launching `/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/main.nf` [ecstatic_mayer] DSL2 - revision: 86b7bb70f5
Jan-26 19:31:20.127 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/.nextflow/plugins; core-plugins: nf-amazon@1.7.2,nf-azure@0.13.2,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.4.0,nf-tower@1.4.0
Jan-26 19:31:20.130 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jan-26 19:31:20.155 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-26 19:31:20.158 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-26 19:31:20.165 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jan-26 19:31:20.186 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jan-26 19:31:20.277 [main] DEBUG nextflow.Session - Session uuid: 5a682b1d-a0cd-4490-8c2e-8e86dea58b48
Jan-26 19:31:20.277 [main] DEBUG nextflow.Session - Run name: ecstatic_mayer
Jan-26 19:31:20.278 [main] DEBUG nextflow.Session - Executor pool size: 6
Jan-26 19:31:20.304 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 22.04.5 build 5709
  Created: 15-07-2022 16:22 UTC (11:22 CDT)
  System: Linux 5.15.79.1-microsoft-standard-WSL2
  Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.17+8-post-Ubuntu-1ubuntu220.04
  Encoding: UTF-8 (UTF-8)
  Process: 13142@kneubehl-alienw [127.0.1.1]
  CPUs: 6 - Mem: 19.5 GB (9.4 GB) - Swap: 5 GB (5 GB)
Jan-26 19:31:20.350 [main] DEBUG nextflow.Session - Work-dir: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_3c0906a2-3acb-4096-a36a-5dec0582eccc/work [v9fs]
Jan-26 19:31:20.425 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, AwsBatchExecutor]
Jan-26 19:31:20.443 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-26 19:31:20.463 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jan-26 19:31:20.506 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jan-26 19:31:20.530 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 7; maxThreads: 1000
Jan-26 19:31:20.733 [main] DEBUG nextflow.Session - Session start invoked
Jan-26 19:31:20.739 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_3c0906a2-3acb-4096-a36a-5dec0582eccc/output/execution/trace.txt
Jan-26 19:31:20.753 [main] DEBUG nextflow.Session - Using default localLib path: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/lib
Jan-26 19:31:20.774 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/lib
Jan-26 19:31:20.776 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/lib/nfcore_external_java_deps.jar
Jan-26 19:31:22.648 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-26 19:31:23.465 [main] WARN  nextflow.Nextflow - Found unexpected parameters:
* --wf.agent: epi2melabs/4.1.0
Jan-26 19:31:23.466 [main] INFO  nextflow.Nextflow - - Ignore this warning: params.schema_ignore_params = "wf.agent" 
Jan-26 19:31:23.482 [main] INFO  nextflow.Nextflow - 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-artic v0.3.21
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : ecstatic_mayer
  containerEngine: docker
  launchDir      : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_3c0906a2-3acb-4096-a36a-5dec0582eccc
  workDir        : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_3c0906a2-3acb-4096-a36a-5dec0582eccc/work
  projectDir     : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic
  userName       : lopez_lab
  profile        : standard
  configFiles    : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/nextflow.config

Input Options
  fastq          : /mnt/c/Users/Alex/Desktop/midnight_lib16_demux_ont_v3

Primer Scheme Selection
  scheme_version : Midnight-ONT/V3
  scheme_dir     : /mnt/c/Users/Alex/AppData/Local/EPI2MELabs/app-4.1.0/primer_schemes

Output Options
  out_dir        : /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/instances/wf-artic_3c0906a2-3acb-4096-a36a-5dec0582eccc/output

Advanced Options
  update_data    : true

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

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

--------------------------------------------------------------------------------
This is epi2me-labs/wf-artic v0.3.21.
--------------------------------------------------------------------------------
Jan-26 19:31:24.929 [main] INFO  nextflow.Nextflow - 
      ------------------------------------
      Available Primer Schemes:
      ------------------------------------

Jan-26 19:31:24.930 [main] INFO  nextflow.Nextflow -   Name     Version
Jan-26 19:31:24.930 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V1    
Jan-26 19:31:24.931 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V2    
Jan-26 19:31:24.931 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V3    
Jan-26 19:31:24.932 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V4    
Jan-26 19:31:24.932 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    ARTIC/V4.1  
Jan-26 19:31:24.933 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    Midnight-IDT/V1 
Jan-26 19:31:24.933 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    Midnight-ONT/V1 
Jan-26 19:31:24.933 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    Midnight-ONT/V2 
Jan-26 19:31:24.934 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    Midnight-ONT/V3 
Jan-26 19:31:24.934 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    NEB-VarSkip/v1a 
Jan-26 19:31:24.934 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    NEB-VarSkip/v1a-long    
Jan-26 19:31:24.935 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    NEB-VarSkip/v2  
Jan-26 19:31:24.935 [main] INFO  nextflow.Nextflow -   SARS-CoV-2    NEB-VarSkip/v2b 
Jan-26 19:31:24.936 [main] INFO  nextflow.Nextflow -   spike-seq ONT/V1  
Jan-26 19:31:24.936 [main] INFO  nextflow.Nextflow -   spike-seq ONT/V4.1    
Jan-26 19:31:24.936 [main] INFO  nextflow.Nextflow - 
      ------------------------------------

Jan-26 19:31:24.942 [main] DEBUG nextflow.Session - Session aborted -- Cause: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/data/mnt/c/Users/Alex/AppData/Local/EPI2MELabs/app-4.1.0/primer_schemes/SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.scheme.bed
Jan-26 19:31:25.246 [main] ERROR nextflow.cli.Launcher - /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/data/mnt/c/Users/Alex/AppData/Local/EPI2MELabs/app-4.1.0/primer_schemes/SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.scheme.bed
java.nio.file.NoSuchFileException: /mnt/wsl/docker-desktop-bind-mounts/Ubuntu/91d938b66991dd2c6301bf97e5bcf00449432574eb61e679b69a60334f3ef5da/workflows/epi2me-labs/wf-artic/data/mnt/c/Users/Alex/AppData/Local/EPI2MELabs/app-4.1.0/primer_schemes/SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.scheme.bed
    at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1036)
    at nextflow.file.FileHelper$checkIfExists$1.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
    at nextflow.Nextflow.file(Nextflow.groovy:159)
    at nextflow.Nextflow$file.callStatic(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240)
    at Script_03ed4be9$_runScript_closure20$_closure62.doCall(Script_03ed4be9:598)
    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:1035)
    at groovy.lang.Closure.call(Closure.java:412)
    at groovy.lang.Closure.call(Closure.java:406)
    at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205)
    at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189)
    at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
    at nextflow.script.ChainableDef$invoke_a.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:139)
    at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:208)
    at nextflow.script.BaseScript.run(BaseScript.groovy:217)
    at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:220)
    at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:212)
    at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:120)
    at nextflow.cli.CmdRun.run(CmdRun.groovy:337)
    at nextflow.cli.Launcher.run(Launcher.groovy:480)
    at nextflow.cli.Launcher.main(Launcher.groovy:639)
kneubehl commented 1 year ago

Regarding what @EmaOMV encountered, when we do give the correct path to the primer scheme in the 'Custom Scheme' field we encounter the same error.

"Error executing process > 'pipeline:copySchemeDir'
Caused by:
  Process `pipeline:copySchemeDir` terminated with an error exit status (1)"
mattdmem commented 1 year ago

Do you have your own primer scheme or are you just using one of the defaults?

If using one of your own could you send me the Instance parameters on the overview page?

If using the defaults which one and what are you entering for scheme_dir etc?

EmaOMV commented 1 year ago

I'm using the default primer scheme for SARS-CoV-2 ARTIC/V4.1 Core Nextflow options runName : laughing_einstein containerEngine : docker launchDir : /mnt/c/Users/admineo/epi2melabs/instances/wf-artic_2fc04f4e-38e2-40b7-8ce9-0855345d4fa5 workDir : /mnt/c/Users/admineo/epi2melabs/instances/wf-artic_2fc04f4e-38e2-40b7-8ce9-0855345d4fa5/work projectDir : /mnt/c/Users/admineo/epi2melabs/workflows/epi2me-labs/wf-artic userName : root profile : standard configFiles : /mnt/c/Users/admineo/epi2melabs/workflows/epi2me-labs/wf-artic/nextflow.config Input Options fastq : /mnt/c/Users/admineo/epi2melabs-data/20221219_SARS-CoV-2 Primer Scheme Selection scheme_version : ARTIC/V4.1 scheme_dir : /mnt/c/Users/admineo/AppData/Local/EPI2MELabs/app-4.0.0/primer_schemes Output Options out_dir : /mnt/c/Users/admineo/epi2melabs/instances/wf-artic_2fc04f4e-38e2-40b7-8ce9-0855345d4fa5/output Advanced Options artic_threads : 8 pangolin_threads: 8

kneubehl commented 1 year ago

Sorry I just had a second to get back to this. The path I put in for the scheme was right to the directory: /mnt/c/Users/Alex/epi2melabs/workflows/epi2me-labs/wf-artic/data/primer_schemes/SARS-CoV-2/Midnight-ONT/V3 At this point I suspect it is a Docker issue. There are no containers running when I try to use Epi2MeLabs and that seems off despite Epi2MeLab v4.1.2 saying that Docker is good to go. We are still having issues on Win10 and Win11.

mattdmem commented 1 year ago

We've fixed this internally - I just need to release it. Will try and get it out soon!

kneubehl commented 1 year ago

Still encountering the same issue (see Issue #46)

EmaOMV commented 1 year ago

We've fixed this internally - I just need to release it. Will try and get it out soon!

now it works for me, thank you

mattdmem commented 1 year ago

Fix coming in v0.3.23 today hopefully! @kneubehl

mattdmem commented 1 year ago

@kneubehl - let us know if v0.3.23 fixes your issue - it's out now!