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It appears that PLOT_EXPLORATORY is trying to use an attribute view that this not supported.
The error:
[e7/f55d34] Cached process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (genes)[ba/c482a3] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (samples.csv)[23/2750fc] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study])[14/4084dd] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL ([id:time_series, variable:condition, reference:control, target:treatment, blocking:replicate])[b7/fb11ce] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM ([id:time_series, variable:condition, reference:control, target:treatment, blocking:replicate])[58/00dc1a] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)ERROR ~ PosixFileAttributeView -- Check '.nextflow.log' file for details
The relevant section from the nextflow.log:
Apr-12 18:41:31.762 [Task submitter] INFO nextflow.Session - [58/00dc1a] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)Apr-12 18:41:36.838 [Task monitor] DEBUG n.c.g.batch.GoogleBatchTaskHandler - [GOOGLE BATCH] Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL ([id:time_series, variable:condition, reference:control, target:treatment, blocking:replicate])` - terminated job=nf-144084dd-1712947138681; state=SUCCEEDEDApr-12 18:41:36.923 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL ([id:time_series, variable:condition, reference:control, target:treatment, blocking:replicate]); status: COMPLETED; exit: 0; error: -; workDir: gs://arc-genomics-nextflow/differentialabundance/work/14/4084dd744f455abfc18a0834878f56]Apr-12 18:41:40.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>Apr-12 18:41:41.075 [Actor Thread 217] ERROR nextflow.extension.OperatorImpl - @unknownjava.lang.UnsupportedOperationException: PosixFileAttributeView at com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider.getFileAttributeView(CloudStorageFileSystemProvider.java:855) at java.base/java.nio.file.Files.getFileAttributeView(Files.java:1790) at java.base/java.nio.file.CopyMoveHelper.copyToForeignTarget(CopyMoveHelper.java:151) at java.base/java.nio.file.CopyMoveHelper.moveToForeignTarget(CopyMoveHelper.java:193) at java.base/java.nio.file.Files.move(Files.java:1433) at nextflow.file.SimpleFileCollector.saveFile(SimpleFileCollector.groovy:102) at nextflow.file.FileCollector.saveTo0(FileCollector.groovy:228) at nextflow.file.FileCollector.saveTo(FileCollector.groovy:251) at nextflow.file.FileCollector$saveTo.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139) at nextflow.extension.CollectFileOp.emitItems(CollectFileOp.groovy:187) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254) at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1042) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1128) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:416) at groovy.lang.Closure$call.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139) at nextflow.extension.DataflowHelper$3.afterStop(DataflowHelper.groovy:257) at groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324) at groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:1024) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1015) at groovyx.gpars.actor.Actor.callDynamic(Actor.java:369) at groovyx.gpars.actor.Actor.handleTermination(Actor.java:320) at groovyx.gpars.actor.AbstractLoopingActor.terminate(AbstractLoopingActor.java:204) at groovyx.gpars.dataflow.operator.DataflowProcessor.terminate(DataflowProcessor.java:147) at groovyx.gpars.dataflow.operator.DataflowProcessorActor.checkPoison(DataflowProcessorActor.java:115) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:83) at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43) at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293) at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30) at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93) at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) at java.base/java.util.concurrent.ThreadPerTaskExecutor$TaskRunner.run(ThreadPerTaskExecutor.java:314) at java.base/java.lang.Thread.run(Thread.java:1583)Apr-12 18:41:41.082 [Actor Thread 217] DEBUG nextflow.Session - Session aborted -- Cause: PosixFileAttributeViewApr-12 18:41:41.097 [Actor Thread 217] DEBUG nextflow.Session - The following nodes are still active:[process] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS status=ACTIVE port 0: (queue) OPEN ; channel: versions port 1: (cntrl) - ; channel: $[process] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP status=ACTIVE port 0: (value) bound ; channel: - port 1: (queue) OPEN ; channel: - port 2: (value) bound ; channel: contrast_stats_assay port 3: (cntrl) - ; channel: $[process] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (queue) OPEN ; channel: parameters port 2: (queue) OPEN ; channel: input_files port 3: (cntrl) - ; channel: $[process] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
I'm guessing it has something to do with the plotting in the PLOT_EXPLORATORY R code.
Command used and terminal output
I'm running the pipeline on output from the `nf-core/rnaseq` pipeline. My command:nextflow run main.nf \ -ansi-log false \ -profile docker,gcp \ -work-dir gs://arc-genomics-nextflow/differentialabundance/work \ --gtf gs://arc-genomics-references/cellranger/refdata-gex-GRCh38-2024-A/genes/genes.gtf \ --matrix gs://arc-genomics-nextflow/bulk-rna/KL-NPC-Differentiation/star_salmon/salmon.merged.gene_counts.tsv \ --transcript_length_matrix gs://arc-genomics-nextflow/bulk-rna/KL-NPC-Differentiation/star_salmon/salmon.merged.gene_lengths.tsv \ --input gs://arc-genomics-nextflow/bulk-rna/KL-NPC-Differentiation/diff-abund/samples.csv \ --contrasts gs://arc-genomics-nextflow/bulk-rna/KL-NPC-Differentiation/diff-abund/contrasts.csv \ --outdir gs://arc-genomics-nextflow/bulk-rna/KL-NPC-Differentiation/diff-abund
Relevant files
No response
System information
Nextflow: 23.10.1
Hardware: GCP Batch
Container engine: Docker
I'm running the Nextflow job on a Linux VM running on a GCP Compute Engine VM
The text was updated successfully, but these errors were encountered:
Description of the bug
I'm running the pipeline with GCP Batch. My GCP profile:
It appears that
PLOT_EXPLORATORY
is trying to use an attribute view that this not supported.The error:
The relevant section from the nextflow.log:
I'm guessing it has something to do with the plotting in the
PLOT_EXPLORATORY
R code.Command used and terminal output
Relevant files
No response
System information
The text was updated successfully, but these errors were encountered: