Getting an error [nextflow.exception.ProcessFailedException]. Same code works on local nextflow

[BhumiChitroda]

Jul-10 02:04:51.748 [main] DEBUG nextflow.cli.Launcher - $> nextflow run 'https://github.com/UGenome/Nextflow_Tower' -name adoring_torvalds -params-file 'https://api.tower.nf/ephemeral/rPT_-W-E6zh9Sc6yMX3pbQ.json' -with-tower
Jul-10 02:04:51.797 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.2
Jul-10 02:04:51.839 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.3
Jul-10 02:04:51.857 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-10 02:04:51.858 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-10 02:04:51.864 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jul-10 02:04:51.891 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-10 02:04:51.923 [main] DEBUG nextflow.scm.ProviderConfig - Detected SCM custom path: https://api.tower.nf/ephemeral/NPrQG4PnPpDwKmZml23KoA
Jul-10 02:04:54.683 [main] DEBUG nextflow.scm.ProviderConfig - Detected SCM config: [providers:[github:[user:bhumichitroda, password:ghp****, platform:github]]]
Jul-10 02:04:54.700 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jul-10 02:04:54.748 [main] DEBUG nextflow.scm.RepositoryFactory - Git url=nextflow.scm.GitUrl(https, null, github.com, UGenome/Nextflow_Tower) -> config=ProviderConfig[name: github, platform: github, server: https://github.com]
Jul-10 02:04:54.749 [main] DEBUG nextflow.scm.AssetManager - Repository URL: https://github.com/UGenome/Nextflow_Tower; Project: UGenome/Nextflow_Tower; Hub provider: github
Jul-10 02:04:54.764 [main] INFO nextflow.cli.CmdRun - Pulling UGenome/Nextflow_Tower ...
Jul-10 02:04:54.765 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials bhu****:ghp****] -> https://api.github.com/repos/UGenome/Nextflow_Tower/contents/nextflow.config
Jul-10 02:04:55.425 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials bhu****:ghp****] -> https://api.github.com/repos/UGenome/Nextflow_Tower/contents/main.nf
Jul-10 02:04:55.710 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials bhu****:ghp****] -> https://api.github.com/repos/UGenome/Nextflow_Tower
Jul-10 02:04:55.931 [main] DEBUG nextflow.scm.AssetManager - Pulling UGenome/Nextflow_Tower -- Using remote clone url: https://github.com/UGenome/Nextflow_Tower.git
Jul-10 02:05:17.870 [main] INFO nextflow.cli.CmdRun - downloaded from https://github.com/UGenome/Nextflow_Tower.git
Jul-10 02:05:17.925 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /.nextflow/assets/UGenome/Nextflow_Tower/nextflow.config
Jul-10 02:05:17.926 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /nextflow.config
Jul-10 02:05:17.927 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /.nextflow/assets/UGenome/Nextflow_Tower/nextflow.config
Jul-10 02:05:17.927 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /nextflow.config
Jul-10 02:05:18.393 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Jul-10 02:05:18.516 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Jul-10 02:05:18.647 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jul-10 02:05:18.648 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/UGenome/Nextflow_Tower [adoring_torvalds] DSL2 - revision: 7ea5226f8a [master]
Jul-10 02:05:18.650 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[nf-tower@1.5.12, nf-amazon@1.16.2, xpack-amzn]
Jul-10 02:05:18.650 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.5.12, nf-amazon@1.16.2, xpack-amzn]
Jul-10 02:05:18.650 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.5.12
Jul-10 02:05:18.662 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.5.12' resolved
Jul-10 02:05:18.662 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.5.12'
Jul-10 02:05:18.682 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.5.12
Jul-10 02:05:18.682 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-amazon version: 1.16.2
Jul-10 02:05:18.689 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@1.16.2' resolved
Jul-10 02:05:18.689 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-amazon@1.16.2'
Jul-10 02:05:18.706 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-amazon@1.16.2
Jul-10 02:05:18.737 [main] DEBUG nextflow.file.FileHelper - > Added 'S3FileSystemProvider' to list of installed providers [s3]
Jul-10 02:05:18.739 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin xpack-amzn version: latest
Jul-10 02:05:19.067 [main] DEBUG nextflow.plugin.PluginUpdater - Plugin xpack-amzn requires nf-amazon supported version: >=1.14.0 - found version: 1.16.2
Jul-10 02:05:19.068 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'xpack-amzn@1.2.1' resolved
Jul-10 02:05:19.069 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'xpack-amzn@1.2.1'
Jul-10 02:05:19.085 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started xpack-amzn@1.2.1
Jul-10 02:05:19.798 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /.nextflow/secrets/store.json
Jul-10 02:05:21.893 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.cloud.aws.secrets.AwsSecretsProvider@2801827a, nextflow.secret.LocalSecretsProvider@50bc3219] - activable => nextflow.cloud.aws.secrets.AwsSecretsProvider@2801827a
Jul-10 02:05:21.995 [main] DEBUG nextflow.Session - Session UUID: cfeafd7d-1d7c-4640-bb3e-72d491ba9a35
Jul-10 02:05:21.996 [main] DEBUG nextflow.Session - Run name: adoring_torvalds
Jul-10 02:05:21.997 [main] DEBUG nextflow.Session - Executor pool size: 2
Jul-10 02:05:22.019 [main] DEBUG n.cloud.aws.file.S3PathFactoryPro - Installing S3 path factory
Jul-10 02:05:22.026 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider
Jul-10 02:05:22.060 [main] DEBUG nextflow.file.FileHelper - AWS S3 config details: {upload_chunk_size=10485760, region=us-west-1, max_error_retry=10}
Jul-10 02:05:22.776 [main] DEBUG com.upplication.s3fs.AmazonS3Client - Setting S3 upload chunk size=10485760
Jul-10 02:05:22.776 [main] DEBUG com.upplication.s3fs.AmazonS3Client - Setting S3 glacierRetrievalTier=null
Jul-10 02:05:22.833 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-10 02:05:22.839 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /.nextflow/assets/UGenome/Nextflow_Tower/nextflow.config
Jul-10 02:05:22.839 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /nextflow.config
Jul-10 02:05:22.840 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /.nextflow/assets/UGenome/Nextflow_Tower/nextflow.config
Jul-10 02:05:22.840 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /nextflow.config
Jul-10 02:05:22.840 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Jul-10 02:05:22.975 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard
Jul-10 02:05:23.036 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.04.2 build 5870
Created: 08-06-2023 08:29 UTC
System: Linux 4.14.311-233.529.amzn2.x86_64
Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.7+7-LTS
Encoding: UTF-8 (UTF-8)
Process: 121@ip-172-31-30-6.us-west-1.compute.internal [172.31.30.6]
CPUs: 2 - Mem: 3.7 GB (2.6 GB) - Swap: 3.7 GB (3.7 GB)
Jul-10 02:05:23.037 [main] DEBUG nextflow.script.ScriptRunner - Nextflow history file tracking disabled
Jul-10 02:05:23.436 [main] DEBUG nextflow.file.FileHelper - Can't check if specified path is NFS (1): s3://ugenome-data/scratch/37ZgSiJzRC6jqR

Jul-10 02:05:23.436 [main] DEBUG nextflow.Session - Work-dir: s3://ugenome-data/scratch/37ZgSiJzRC6jqR [null]
Jul-10 02:05:23.494 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[AwsBatchExecutor, AwsBatchExecutorPro]
Jul-10 02:05:23.495 [main] DEBUG nextflow.executor.ExecutorFactory - Replacing executor AwsBatchExecutor with class nextflow.cloud.aws.batch.AwsBatchExecutorPro
Jul-10 02:05:23.515 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-10 02:05:23.523 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jul-10 02:05:23.667 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-10 02:05:23.687 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000
Jul-10 02:05:23.808 [main] DEBUG nextflow.Session - Session start
Jul-10 02:05:23.817 [main] DEBUG io.seqera.tower.plugin.TowerClient - Creating Tower observer -- endpoint=https://api.tower.nf; requestInterval=1s; aliveInterval=1m; maxRetries=5; backOffBase=3; backOffDelay=250
Jul-10 02:05:26.428 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-10 02:05:26.484 [main] INFO nextflow.Nextflow - K A L L I S T O - N F ~ version 0.9
Jul-10 02:05:26.485 [main] INFO nextflow.Nextflow - =====================================
Jul-10 02:05:26.485 [main] INFO nextflow.Nextflow - name : RNA-Seq Abundance Analysis
Jul-10 02:05:26.486 [main] INFO nextflow.Nextflow - reads : /.nextflow/assets/UGenome/Nextflow_Tower/tutorial/reads/*.fastq
Jul-10 02:05:26.486 [main] INFO nextflow.Nextflow - transcriptome : /.nextflow/assets/UGenome/Nextflow_Tower/tutorial/transcriptome/transcriptome.fa
Jul-10 02:05:26.487 [main] INFO nextflow.Nextflow - fragment length : 180 nt
Jul-10 02:05:26.487 [main] INFO nextflow.Nextflow - fragment SD : 20 nt
Jul-10 02:05:26.487 [main] INFO nextflow.Nextflow - bootstraps : 100
Jul-10 02:05:26.487 [main] INFO nextflow.Nextflow - experimental design : /.nextflow/assets/UGenome/Nextflow_Tower/tutorial/experiment/hiseq_info.txt
Jul-10 02:05:26.487 [main] INFO nextflow.Nextflow - output : /.nextflow/assets/UGenome/Nextflow_Tower/results/
Jul-10 02:05:26.489 [main] INFO nextflow.Nextflow -

Jul-10 02:05:26.835 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch
Jul-10 02:05:26.837 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch'
Jul-10 02:05:26.842 [main] DEBUG nextflow.executor.Executor - [warm up] executor > awsbatch (pro)
Jul-10 02:05:26.860 [main] DEBUG nextflow.util.ThrottlingExecutor - Creating throttling executor with opts: nextflow.util.ThrottlingExecutor$Options(poolName:AWSBatch-executor, limiter:RateLimiter[stableRate=50.0qps], poolSize:10, maxPoolSize:10, queueSize:5000, maxRetries:10, keepAlive:1m, autoThrottle:true, errorBurstDelay:1s, rampUpInterval:100, rampUpFactor:1.2, rampUpMaxRate:1.7976931348623157E308, backOffFactor:2.0, backOffMinRate:0.0166666667, retryDelay:1s)
Jul-10 02:05:26.872 [main] DEBUG nextflow.util.ThrottlingExecutor - Creating throttling executor with opts: nextflow.util.ThrottlingExecutor$Options(poolName:AWSBatch-reaper, limiter:RateLimiter[stableRate=50.0qps], poolSize:10, maxPoolSize:10, queueSize:5000, maxRetries:10, keepAlive:1m, autoThrottle:true, errorBurstDelay:1s, rampUpInterval:100, rampUpFactor:1.2, rampUpMaxRate:1.7976931348623157E308, backOffFactor:2.0, backOffMinRate:0.0166666667, retryDelay:1s)
Jul-10 02:05:26.875 [main] DEBUG n.cloud.aws.batch.AwsBatchExecutor - Creating parallel monitor for executor 'awsbatch' > pollInterval=10s; dumpInterval=5m
Jul-10 02:05:26.890 [main] DEBUG n.c.aws.batch.AwsBatchExecutorPro - [AWS BATCH PRO] work-dir=s3://ugenome-data/scratch/37ZgSiJzRC6jqR; default file system scheme=file; is FSx compatible=false
Jul-10 02:05:27.118 [main] INFO n.cloud.aws.batch.AwsBatchExecutor - Uploading local bin scripts folder to s3://ugenome-data/scratch/37ZgSiJzRC6jqR/tmp/14/9b1c9e766813c137790e4cbbfcefd2/bin
Jul-10 02:05:27.175 [main] DEBUG c.u.s3fs.S3FileSystemProvider - S3 upload directory from=/.nextflow/assets/UGenome/Nextflow_Tower/bin to=s3://ugenome-data/scratch/37ZgSiJzRC6jqR/tmp/14/9b1c9e766813c137790e4cbbfcefd2/bin
Jul-10 02:05:27.175 [main] DEBUG com.upplication.s3fs.AmazonS3Client - Creating S3 transfer manager pool - chunk-size=10485760; max-treads=10;
Jul-10 02:05:27.176 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'S3TransferManager' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-10 02:05:28.067 [main] DEBUG n.cloud.aws.batch.AwsBatchExecutor - [AWS BATCH] Executor options=AwsOptions(cliPath:/home/ec2-user/miniconda/bin/aws, storageClass:null, storageEncryption:null, storageKmsKeyId:null, remoteBinDir:/ugenome-data/scratch/37ZgSiJzRC6jqR/tmp/14/9b1c9e766813c137790e4cbbfcefd2/bin, region:us-west-1, maxParallelTransfers:4, maxTransferAttempts:10, delayBetweenAttempts:10s, retryMode:standard, maxSpotAttempts:5, debug:null, fetchInstanceType:true, jobRole:null, logsGroup:null, volumes:[], shareIdentifier:null, schedulingPriority:0, s3Acl:null, awsCli:/home/ec2-user/miniconda/bin/aws --region us-west-1)
Jul-10 02:05:28.207 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch
Jul-10 02:05:28.207 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch'
Jul-10 02:05:28.227 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: mapping, index, fastp, reportgeneration
Jul-10 02:05:28.557 [main] INFO io.seqera.tower.plugin.TowerClient - Monitor the execution with Nextflow Tower using this URL: https://tower.nf/orgs/UGenome/workspaces/nextflow-pipeline/watch/37ZgSiJzRC6jqR
Jul-10 02:05:28.557 [main] DEBUG nextflow.Session - Igniting dataflow network (3)
Jul-10 02:05:28.569 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastp
Jul-10 02:05:28.572 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > mapping
Jul-10 02:05:28.573 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-10 02:05:28.573 [main] DEBUG nextflow.Session - Session await
Jul-10 02:05:28.575 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /.nextflow/assets/UGenome/Nextflow_Tower/tutorial/reads/; pattern: *.fastq; options: [:]
Jul-10 02:05:28.691 [Actor Thread 1] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /.nextflow/assets/UGenome/Nextflow_Tower/tutorial/reads/SRR493371.fastq
Jul-10 02:05:29.181 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file /.nextflow/assets/UGenome/Nextflow_Tower/tutorial/reads/SRR493371.fastq to work dir: s3://ugenome-data/scratch/37ZgSiJzRC6jqR/stage-cfeafd7d-1d7c-4640-bb3e-72d491ba9a35/fd/1b43ecc4d44c3f089b9a25183adb05/SRR493371.fastq
Jul-10 02:05:29.207 [FileTransfer-1] DEBUG c.u.s3fs.S3FileSystemProvider - S3 upload file from=/.nextflow/assets/UGenome/Nextflow_Tower/tutorial/reads/SRR493371.fastq to=s3://ugenome-data/scratch/37ZgSiJzRC6jqR/stage-cfeafd7d-1d7c-4640-bb3e-72d491ba9a35/fd/1b43ecc4d44c3f089b9a25183adb05/SRR493371.fastq
Jul-10 02:05:30.338 [Actor Thread 1] WARN nextflow.script.ScriptBinding - Access to undefined parameter ontreads -- Initialise it to a default value eg. params.ontreads = some_value
Jul-10 02:05:31.093 [AWSBatch-executor-1] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] [AWS BATCH] Found job definition name=nf-cbcrg-kallisto-nf-sha256-9f840127392d04c9f8e39cb72bcd62ff53cfe0492dde02dc3749bf15f1c547f1:1; container=cbcrg/kallisto-nf@sha256:9f840127392d04c9f8e39cb72bcd62ff53cfe0492dde02dc3749bf15f1c547f1
Jul-10 02:05:31.208 [AWSBatch-executor-1] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] submitted > job=6ce617f0-a848-44d0-bc25-87d97e70a408; work-dir=s3://ugenome-data/scratch/37ZgSiJzRC6jqR/8d/0d498f7b114c7fffe3f3c1d1b86349
Jul-10 02:05:31.208 [AWSBatch-executor-1] INFO nextflow.Session - [8d/0d498f] Submitted process > fastp (fastp on SRR493371)
Jul-10 02:10:36.903 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor awsbatch > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: fastp (fastp on SRR493371); status: SUBMITTED; exit: -; error: -; workDir: s3://ugenome-data/scratch/37ZgSiJzRC6jqR/8d/0d498f7b114c7fffe3f3c1d1b86349]
Jul-10 02:11:17.862 [Task monitor] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] Cannot read exitstatus for task: fastp (fastp on SRR493371) | /ugenome-data/scratch/37ZgSiJzRC6jqR/8d/0d498f7b114c7fffe3f3c1d1b86349/.exitcode
Jul-10 02:11:17.863 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: fastp (fastp on SRR493371); status: COMPLETED; exit: -; error: -; workDir: s3://ugenome-data/scratch/37ZgSiJzRC6jqR/8d/0d498f7b114c7fffe3f3c1d1b86349]
Jul-10 02:11:17.868 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=fastp (fastp on SRR493371); work-dir=s3://ugenome-data/scratch/37ZgSiJzRC6jqR/8d/0d498f7b114c7fffe3f3c1d1b86349
error [nextflow.exception.ProcessFailedException]: Process fastp (fastp on SRR493371) terminated for an unknown reason -- Likely it has been terminated by the external system
Jul-10 02:11:17.894 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'fastp (fastp on SRR493371)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-11663889587439241117/.command.out
Jul-10 02:11:17.912 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'fastp (fastp on SRR493371)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-17643401686929566865/.command.err
Jul-10 02:11:17.915 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'fastp (fastp on SRR493371)'

Caused by:
Process fastp (fastp on SRR493371) terminated for an unknown reason -- Likely it has been terminated by the external system

Command executed:

apt-get -y install fastp
mkdir fastp_trimmed
fastp -q 15 -i SRR493371.fastq -o fastp_trimmed/trim_SRR493371.fastq -j /.nextflow/assets/UGenome/Nextflow_Tower/SRR493371_fastp.json

Command exit status:

Command output:
(empty)

Work dir:
s3://ugenome-data/scratch/37ZgSiJzRC6jqR/8d/0d498f7b114c7fffe3f3c1d1b86349

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
Jul-10 02:11:17.923 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-10 02:11:17.979 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process fastp (fastp on SRR493371) terminated for an unknown reason -- Likely it has been terminated by the external system
Jul-10 02:11:18.031 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'fastp (fastp on SRR493371)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-4173578845630338999/.command.err
Jul-10 02:11:18.048 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'fastp (fastp on SRR493371)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-1698332082576509144/.command.out
Jul-10 02:11:18.050 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-10 02:11:18.062 [main] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'fastp (fastp on SRR493371)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-6168706018270338195/.command.err
Jul-10 02:11:18.073 [main] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'fastp (fastp on SRR493371)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-17824598314372832187/.command.out
Jul-10 02:11:18.081 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=902ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Jul-10 02:11:18.081 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-10 02:11:18.662 [main] DEBUG c.u.s3fs.S3FileSystemProvider - S3 upload file from=/nf-37ZgSiJzRC6jqR-reports.tsv to=s3://ugenome-data/scratch/37ZgSiJzRC6jqR/nf-37ZgSiJzRC6jqR-reports.tsv
Jul-10 02:11:18.687 [main] DEBUG io.seqera.tower.plugin.TowerReports - Saved reports file s3://ugenome-data/scratch/37ZgSiJzRC6jqR/nf-37ZgSiJzRC6jqR-reports.tsv
Jul-10 02:11:19.485 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-10 02:11:19.485 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'xpack-amzn@1.2.1'
Jul-10 02:11:19.485 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped xpack-amzn
Jul-10 02:11:19.485 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@1.16.2'
Jul-10 02:11:19.485 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon
Jul-10 02:11:19.485 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.5.12'
Jul-10 02:11:19.485 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Jul-10 02:11:19.492 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye