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error fetching mash screen database (on a plant and nac) #150

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LucileSol opened this issue Jan 15, 2025 · 0 comments
Open

error fetching mash screen database (on a plant and nac) #150

LucileSol opened this issue Jan 15, 2025 · 0 comments

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@LucileSol
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Jan-15 14:40:07.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop
Jan-15 14:40:07.655 [main] ERROR nextflow.cli.Launcher - https://gembox.cbcb.umd.edu/mash/refseq.genomes%2Bplasmid.k21s1000.msh
java.nio.file.NoSuchFileException: https://gembox.cbcb.umd.edu/mash/refseq.genomes%2Bplasmid.k21s1000.msh
        at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at nextflow.Nextflow.file(Nextflow.groovy:115)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at Script_a98122854d6bc4d1$_runScript_closure1$_closure2.doCall(Script_a98122854d6bc4d1:22)
        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:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at groovy.lang.Closure.call(Closure.java:433)
        at groovy.lang.Closure.call(Closure.java:412)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
        at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
        at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
        at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:103)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:651)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:391)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:330)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at Script_8f961c85aa6fc363$_runScript_closure1$_closure2.doCall(Script_8f961c85aa6fc363:93)
        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:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at groovy.lang.Closure.call(Closure.java:433)
        at groovy.lang.Closure.call(Closure.java:412)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)

wget https://gembox.cbcb.umd.edu/mash/refseq.genomes%2Bplasmid.k21s1000.msh

Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
ERROR: could not open HSTS store at '/home/lucso605/.wget-hsts'. HSTS will be disabled.
--2025-01-15 14:41:53--  https://gembox.cbcb.umd.edu/mash/refseq.genomes%2Bplasmid.k21s1000.msh
Resolving gembox.cbcb.umd.edu (gembox.cbcb.umd.edu)... 128.8.120.25
Connecting to gembox.cbcb.umd.edu (gembox.cbcb.umd.edu)|128.8.120.25|:443... connected.
Unable to establish SSL connection.

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