ifremer-bioinformatics / samba Goto Github PK
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Home Page: https://gitlab.ifremer.fr/bioinfo/SAMBA-nextflow
License: MIT License
Standardized and Automated MetaBarcoding Analyses workflow (Mirror)
Home Page: https://gitlab.ifremer.fr/bioinfo/SAMBA-nextflow
License: MIT License
Hello,
Samba-LR does LCA only if there are several mapping hits with the same score but if there is only one hit it gives the species of the hit as identification even if there is only 80% identity and that is a problem I think ... so in the output it would be best to have an assignment score or a LCA corresponding to the percentage of identity of the hit. Would it be possible to implement this in Samba for next release?
Best,
Germain
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 - ----------------------------------------------------
__ __ __ . __ __
\ |_ |) | |/| |_ |)
\ | |) | | | | | \
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
Hello,
When use longreads = true parameter to activate Samba LR it is necessary to deactivate many short-reads specific option. It would be useful to have a list of option needed to be deactivated when running Samba LR.
Best
Germain
Hello,
Would it be possible to implement microDecon in Samba-LR ?
Best
Germain
Upon following the instructions, it seems that samba has disappeared from the nextflow core, is that correct?
$ nextflow run nf-core/samba -profile test,singularity
N E X T F L O W ~ version 20.10.0
Pulling nf-core/samba ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/nf-core/samba/contents/nextflow.config
Remote resource not found: https://api.github.com/repos/nf-core/samba/contents/main.nf
Is there a proposed alternative?
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