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Hi. I was trying to run this interesting script however I am getting this error while trying to execute it:
No such variable: msa_gard_ch
-- Check script '.nextflow/assets/brwnj/idplot/main.nf' at line: 85 or see '.nextflow.log' file for more details
Hopefully there is a quick fix for this. Thank you so much.
the log file is the following:
Jun-09 03:05:31.466 [main] DEBUG nextflow.cli.Launcher - $> nextflow run brwnj/idplot -latest --cpus 12 --window 500 --gard --reference ./data/MN996532.fasta --fasta './data/query_seqs/*.fasta' Jun-09 03:05:31.565 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.04.0 Jun-09 03:05:32.459 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/jovyan/.nextflow/assets/brwnj/idplot/.git/config; branch: master; remote: origin; url: https://github.com/brwnj/idplot.git Jun-09 03:05:32.479 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/jovyan/.nextflow/assets/brwnj/idplot/.git/config; branch: master; remote: origin; url: https://github.com/brwnj/idplot.git Jun-09 03:05:32.480 [main] INFO nextflow.cli.CmdRun - Pulling brwnj/idplot ... Jun-09 03:05:32.480 [main] DEBUG nextflow.scm.AssetManager - Pull pipeline brwnj/idplot -- Using local path: /home/jovyan/.nextflow/assets/brwnj/idplot Jun-09 03:05:33.485 [main] INFO nextflow.cli.CmdRun - Already-up-to-date Jun-09 03:05:33.498 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/jovyan/.nextflow/assets/brwnj/idplot/nextflow.config Jun-09 03:05:33.498 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/jovyan/work/idplot/nextflow.config Jun-09 03:05:33.499 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/jovyan/.nextflow/assets/brwnj/idplot/nextflow.config Jun-09 03:05:33.499 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/jovyan/work/idplot/nextflow.config Jun-09 03:05:33.508 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard Jun-09 03:05:33.581 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard Jun-09 03:05:33.621 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/brwnj/idplot [nostalgic_meninsky] DSL2 - revision: 355bb5f [master] Jun-09 03:05:33.636 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/jovyan/.nextflow/plugins; core-plugins: nf-amazon@1.7.1,nf-azure@0.13.1,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 Jun-09 03:05:33.637 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jun-09 03:05:33.649 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jun-09 03:05:33.651 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jun-09 03:05:33.656 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Jun-09 03:05:33.664 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jun-09 03:05:33.719 [main] DEBUG nextflow.Session - Session uuid: 28b6a58e-fd78-40c8-a763-cfe9a9bdbe42 Jun-09 03:05:33.719 [main] DEBUG nextflow.Session - Run name: nostalgic_meninsky Jun-09 03:05:33.719 [main] DEBUG nextflow.Session - Executor pool size: 40 Jun-09 03:05:33.749 [main] DEBUG nextflow.cli.CmdRun - Version: 22.04.0 build 5697 Created: 23-04-2022 18:00 UTC System: Linux 3.10.0-1160.49.1.el7.x86_64 Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.9.1-internal+0-adhoc..src Encoding: UTF-8 (UTF-8) Process: 16458@3c5b05d34503 [10.0.3.144] CPUs: 40 - Mem: 251.4 GB (10.2 GB) - Swap: 128 GB (128 GB) Jun-09 03:05:33.770 [main] DEBUG nextflow.Session - Work-dir: /home/jovyan/work/idplot/work [nfs] Jun-09 03:05:33.771 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/jovyan/.nextflow/assets/brwnj/idplot/bin Jun-09 03:05:33.781 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jun-09 03:05:33.795 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jun-09 03:05:33.852 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jun-09 03:05:33.864 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 41; maxThreads: 1000 Jun-09 03:05:33.963 [main] DEBUG nextflow.Session - Session start invoked Jun-09 03:05:33.968 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/jovyan/work/idplot/results/logs/trace.txt Jun-09 03:05:34.676 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jun-09 03:05:34.769 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: msa_gard_ch for class: Script_4d2b5c58 Jun-09 03:05:34.812 [main] ERROR nextflow.cli.Launcher - @unknown groovy.lang.MissingPropertyException: No such property: msa_gard_ch for class: Script_4d2b5c58 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_4d2b5c58.runScript(Script_4d2b5c58:85) at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170) at nextflow.script.BaseScript.run(BaseScript.groovy:203) 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:334) at nextflow.cli.Launcher.run(Launcher.groovy:480) at nextflow.cli.Launcher.main(Launcher.groovy:639)
standard
https://github.com/brwnj/idplot
The text was updated successfully, but these errors were encountered:
It was something related with my system configuration. so now is solved!!
Sorry, something went wrong.
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Hi.
I was trying to run this interesting script however I am getting this error while trying to execute it:
No such variable: msa_gard_ch
-- Check script '.nextflow/assets/brwnj/idplot/main.nf' at line: 85 or see '.nextflow.log' file for more details
Hopefully there is a quick fix for this.
Thank you so much.
the log file is the following:
Jun-09 03:05:31.466 [main] DEBUG nextflow.cli.Launcher - $> nextflow run brwnj/idplot -latest --cpus 12 --window 500 --gard --reference ./data/MN996532.fasta --fasta './data/query_seqs/*.fasta'
Jun-09 03:05:31.565 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.04.0
Jun-09 03:05:32.459 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/jovyan/.nextflow/assets/brwnj/idplot/.git/config; branch: master; remote: origin; url: https://github.com/brwnj/idplot.git
Jun-09 03:05:32.479 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/jovyan/.nextflow/assets/brwnj/idplot/.git/config; branch: master; remote: origin; url: https://github.com/brwnj/idplot.git
Jun-09 03:05:32.480 [main] INFO nextflow.cli.CmdRun - Pulling brwnj/idplot ...
Jun-09 03:05:32.480 [main] DEBUG nextflow.scm.AssetManager - Pull pipeline brwnj/idplot -- Using local path: /home/jovyan/.nextflow/assets/brwnj/idplot
Jun-09 03:05:33.485 [main] INFO nextflow.cli.CmdRun - Already-up-to-date
Jun-09 03:05:33.498 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/jovyan/.nextflow/assets/brwnj/idplot/nextflow.config
Jun-09 03:05:33.498 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/jovyan/work/idplot/nextflow.config
Jun-09 03:05:33.499 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/jovyan/.nextflow/assets/brwnj/idplot/nextflow.config
Jun-09 03:05:33.499 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/jovyan/work/idplot/nextflow.config
Jun-09 03:05:33.508 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:
standard
Jun-09 03:05:33.581 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:
standard
Jun-09 03:05:33.621 [main] INFO nextflow.cli.CmdRun - Launching
https://github.com/brwnj/idplot
[nostalgic_meninsky] DSL2 - revision: 355bb5f [master]Jun-09 03:05:33.636 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/jovyan/.nextflow/plugins; core-plugins: nf-amazon@1.7.1,nf-azure@0.13.1,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
Jun-09 03:05:33.637 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-09 03:05:33.649 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-09 03:05:33.651 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-09 03:05:33.656 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jun-09 03:05:33.664 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jun-09 03:05:33.719 [main] DEBUG nextflow.Session - Session uuid: 28b6a58e-fd78-40c8-a763-cfe9a9bdbe42
Jun-09 03:05:33.719 [main] DEBUG nextflow.Session - Run name: nostalgic_meninsky
Jun-09 03:05:33.719 [main] DEBUG nextflow.Session - Executor pool size: 40
Jun-09 03:05:33.749 [main] DEBUG nextflow.cli.CmdRun -
Version: 22.04.0 build 5697
Created: 23-04-2022 18:00 UTC
System: Linux 3.10.0-1160.49.1.el7.x86_64
Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.9.1-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)
Process: 16458@3c5b05d34503 [10.0.3.144]
CPUs: 40 - Mem: 251.4 GB (10.2 GB) - Swap: 128 GB (128 GB)
Jun-09 03:05:33.770 [main] DEBUG nextflow.Session - Work-dir: /home/jovyan/work/idplot/work [nfs]
Jun-09 03:05:33.771 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/jovyan/.nextflow/assets/brwnj/idplot/bin
Jun-09 03:05:33.781 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-09 03:05:33.795 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-09 03:05:33.852 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-09 03:05:33.864 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 41; maxThreads: 1000
Jun-09 03:05:33.963 [main] DEBUG nextflow.Session - Session start invoked
Jun-09 03:05:33.968 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/jovyan/work/idplot/results/logs/trace.txt
Jun-09 03:05:34.676 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-09 03:05:34.769 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: msa_gard_ch for class: Script_4d2b5c58
Jun-09 03:05:34.812 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: No such property: msa_gard_ch for class: Script_4d2b5c58
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_4d2b5c58.runScript(Script_4d2b5c58:85)
at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
at nextflow.script.BaseScript.run(BaseScript.groovy:203)
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:334)
at nextflow.cli.Launcher.run(Launcher.groovy:480)
at nextflow.cli.Launcher.main(Launcher.groovy:639)
The text was updated successfully, but these errors were encountered: