testmanifest issue

[weber8thomas]

Hi,

I'm getting the following issue when runing:

nextflow run main.nf -profile shortreadstest,singularity

May-13 20:12:38.785 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf -profile shortreadstest,singularity
May-13 20:12:38.886 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.1
May-13 20:12:38.913 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/tweber/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
May-13 20:12:38.928 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
May-13 20:12:38.929 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
May-13 20:12:38.934 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
May-13 20:12:38.952 [main] INFO org.pf4j.AbstractPluginManager - No plugins
May-13 20:12:38.974 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /g/korbel2/weber/workspace/nextflow-samba/samba/nextflow.config
May-13 20:12:38.975 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /g/korbel2/weber/workspace/nextflow-samba/samba/nextflow.config
May-13 20:12:39.002 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: shortreadstest,singularity
May-13 20:12:40.559 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [custom, conda, longreadstest, singularity, shortreadstest, docker]
May-13 20:12:40.634 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
May-13 20:12:40.669 [main] INFO nextflow.cli.CmdRun - Launching main.nf [pensive_faggin] DSL2 - revision: 435bd2eede
May-13 20:12:40.669 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
May-13 20:12:40.669 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
May-13 20:12:40.681 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/tweber/.nextflow/secrets/store.json
May-13 20:12:40.685 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2a334bac] - activable => nextflow.secret.LocalSecretsProvider@2a334bac
May-13 20:12:40.753 [main] DEBUG nextflow.Session - Session UUID: 67fbece7-36f9-4ca5-9d09-2e721c0c01c8
May-13 20:12:40.753 [main] DEBUG nextflow.Session - Run name: pensive_faggin
May-13 20:12:40.754 [main] DEBUG nextflow.Session - Executor pool size: 128
May-13 20:12:40.768 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=384; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-13 20:12:40.809 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.04.1 build 5866
Created: 15-04-2023 06:51 UTC (08:51 CEST)
System: Linux 4.18.0-425.3.1.el8.x86_64
Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)
Process: [email protected] [10.11.8.232]
CPUs: 128 - Mem: 2 TB (349.9 GB) - Swap: 4 GB (0)
May-13 20:12:40.903 [main] DEBUG nextflow.Session - Work-dir: /g/korbel2/weber/workspace/nextflow-samba/samba/work/training_shortreads [nfs]
May-13 20:12:40.937 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
May-13 20:12:40.949 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
May-13 20:12:41.059 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
May-13 20:12:41.077 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 129; maxThreads: 1000
May-13 20:12:41.179 [main] DEBUG nextflow.Session - Session start
May-13 20:12:41.185 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /g/korbel2/weber/workspace/nextflow-samba/samba/results/training_shortreads/pipeline_info/trace.tsv
May-13 20:12:44.903 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
May-13 20:12:45.012 [main] INFO nextflow.Nextflow - ----------------------------------------------------
__ __ __ . __ __
\ |_ |) | |/| |_ |)
\ | |) | | | | | \

samba v3.1.0: Standardized and Automated MetaBarcoding Analyses workflow

May-13 20:12:45.019 [main] INFO nextflow.Nextflow - Run Name : pensive_faggin
Project Name : training_shortreads
Manifest File : /g/korbel2/weber/workspace/nextflow-samba/samba/training_dataset/shortreads/q2_manifest
Metadata File : /g/korbel2/weber/workspace/nextflow-samba/samba/training_dataset/shortreads/q2_metadata
Data Type : Paired-End
Container : singularity
Output dir : /g/korbel2/weber/workspace/nextflow-samba/samba/results/training_shortreads
Launch dir : /g/korbel2/weber/workspace/nextflow-samba/samba
Working dir : /g/korbel2/weber/workspace/nextflow-samba/samba/work/training_shortreads
Script dir : /g/korbel2/weber/workspace/nextflow-samba/samba
User : tweber
Config Profile : shortreadstest,singularity
Data integrity : Data integrity checking process enabled
Primer removal : Primer removal process enabled
Clustering : Distribution based-clustering process enabled
Decontamination : Sample decontamination process enabled
Prediction : Functionnal prediction process enabled
Ancom : Differential abundance ANCOM analysis process enabled
Alpha div : Alpha diversity indexes process enabled
Beta div : Beta diversity statistics processes enabled
Desc comp : Descriptive comparisons statistics process enabled
May-13 20:12:45.020 [main] INFO nextflow.Nextflow - ----------------------------------------------------
May-13 20:12:45.112 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: testmanifest for class: Script_836238c5
May-13 20:12:45.136 [main] DEBUG nextflow.Session - The following nodes are still active:
[operator] map
[operator] reduce
[operator] map

May-13 20:12:45.162 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: No such property: testmanifest for class: Script_836238c5
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:65)
at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:341)
at Script_836238c5.runScript(Script_836238c5:437)
at nextflow.script.BaseScript.run0(BaseScript.groovy:145)
at nextflow.script.BaseScript.run(BaseScript.groovy:192)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:229)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:224)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:130)
at nextflow.cli.CmdRun.run(CmdRun.groovy:368)
at nextflow.cli.Launcher.run(Launcher.groovy:494)
at nextflow.cli.Launcher.main(Launcher.groovy:653)

---

Config:

N E X T F L O W ~ version 23.04.1
Launching main.nf [pensive_faggin] DSL2 - revision: 435bd2eede