Closed MauriAndresMU1313 closed 1 week ago
MauriAndresMU1313
commented
4 months ago Any ideas? I had tried to use different options that involve installing TF with conda, installing old versions, etc. Some instructions support the idea that "You can compile a Tensorflow from the source that does not use the AVX instruction set." However, I'm unfamiliar with that kind of workflow in TF, so any comment from you guys will help solve this issue. Would you happen to need more information from me?
cjalder
commented
4 months ago Hi @MauriAndresMU1313 - The tensorflow warning might be a red herring and not necessarily the cause of the worklow crashing. If possible could you send the nextflow.log file? Also any details on your machines specs would be useful. Thanks!
MauriAndresMU1313
commented
4 months ago Thank you for your comment. Here is the nextlow.log file:
cat .nextflow.log.3
Jun-21 18:49:11.167 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-flu --fastq /home/mmora30/workspace/nextflow_pipelines/wf-flu/wf-flu-demo/fastq -profile standard
Jun-21 18:49:11.254 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.2
Jun-21 18:49:11.284 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/mmora30/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
Jun-21 18:49:11.299 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-21 18:49:11.301 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-21 18:49:11.304 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-21 18:49:11.321 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jun-21 18:49:11.341 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/mmora30/.nextflow/scm
Jun-21 18:49:11.381 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-21 18:49:11.395 [main] INFO nextflow.cli.CmdRun - Pulling epi2me-labs/wf-flu ...
Jun-21 18:49:11.401 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/epi2me-labs/wf-flu/contents/nextflow.config
Jun-21 18:49:12.703 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/epi2me-labs/wf-flu/contents/main.nf
Jun-21 18:49:12.810 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/epi2me-labs/wf-flu
Jun-21 18:49:12.893 [main] DEBUG nextflow.scm.AssetManager - Pulling epi2me-labs/wf-flu -- Using remote clone url: https://github.com/epi2me-labs/wf-flu.git
Jun-21 18:49:34.590 [main] INFO nextflow.cli.CmdRun - downloaded from https://github.com/epi2me-labs/wf-flu.git
Jun-21 18:49:34.633 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/nextflow.config
Jun-21 18:49:34.636 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/nextflow.config
Jun-21 18:49:34.644 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/mmora30/.nextflow/secrets/store.json
Jun-21 18:49:34.647 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3b41e1bf] - activable => nextflow.secret.LocalSecretsProvider@3b41e1bf
Jun-21 18:49:34.658 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jun-21 18:49:34.849 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-21 18:49:34.851 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/epi2me-labs/wf-flu` [furious_monod] DSL2 - revision: d2de117c4f [master]
Jun-21 18:49:34.853 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-21 18:49:34.853 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-21 18:49:34.919 [main] DEBUG nextflow.Session - Session UUID: f2277c09-dd41-40c0-9de9-3ced4f63d470
Jun-21 18:49:34.920 [main] DEBUG nextflow.Session - Run name: furious_monod
Jun-21 18:49:34.920 [main] DEBUG nextflow.Session - Executor pool size: 24
Jun-21 18:49:34.930 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-21 18:49:34.937 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=72; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-21 18:49:34.957 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.04.2 build 5914
Created: 29-05-2024 06:19 UTC
System: Linux 5.15.0-112-generic
Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 11.0.23+9-post-Ubuntu-1ubuntu122.04.1
Encoding: UTF-8 (UTF-8)
Process: 195267@medina-lab [127.0.1.1]
CPUs: 24 - Mem: 122.8 GB (78.6 GB) - Swap: 8 GB (8 GB)
Jun-21 18:49:34.983 [main] DEBUG nextflow.Session - Work-dir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work [ext2/ext3]
Jun-21 18:49:35.020 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-21 18:49:35.035 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-21 18:49:35.110 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-21 18:49:35.123 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000
Jun-21 18:49:35.201 [main] DEBUG nextflow.Session - Session start
Jun-21 18:49:35.204 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/mmora30/workspace/nextflow_pipelines/wf-flu/output/execution/trace.txt
Jun-21 18:49:35.213 [main] DEBUG nextflow.Session - Using default localLib path: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/lib
Jun-21 18:49:35.217 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/lib
Jun-21 18:49:35.218 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/lib/nfcore_external_java_deps.jar
Jun-21 18:49:37.545 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-21 18:49:38.324 [main] INFO nextflow.Nextflow -
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-flu v1.1.0-gd2de117
--------------------------------------------------------------------------------
Core Nextflow options
revision : master
runName : furious_monod
containerEngine: docker
container : [withLabel:wf_common:ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9, withLabel:wfflu:ontresearch/wf-flu:sha5eeb2cd0a75a6cc0f47d689d2926e0d9922ceda8, withLabel:wfflutyping:ontresearch/abricate:shacd6e6b77d14424d746c3d7332dfa13e3bda9034f, withLabel:nextclade:ontresearch/nextclade:shad0a8a0bf027edec8d452def0f29275fd67def643, withLabel:medaka:ontresearch/medaka:sha4f35e9f6f231dc8343c98e04d43517d4a38528a2]
launchDir : /home/mmora30/workspace/nextflow_pipelines/wf-flu
workDir : /home/mmora30/workspace/nextflow_pipelines/wf-flu/work
projectDir : /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu
userName : mmora30
profile : standard
configFiles : /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/nextflow.config
Input Options
fastq : /home/mmora30/workspace/nextflow_pipelines/wf-flu/wf-flu-demo/fastq
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-flu for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-flu v1.1.0-gd2de117.
--------------------------------------------------------------------------------
Jun-21 18:49:38.878 [main] INFO nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Jun-21 18:49:39.100 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `ingress,wf_common` for process with name fastcat
Jun-21 18:49:39.112 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.112 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.119 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jun-21 18:49:39.125 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=24; memory=122.8 GB; capacity=24; pollInterval=100ms; dumpInterval=5m
Jun-21 18:49:39.128 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jun-21 18:49:39.252 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:alignReads
Jun-21 18:49:39.254 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.254 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:coverageCalc
Jun-21 18:49:39.266 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.266 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.272 [main] INFO nextflow.script.BaseScript - NOT Downsampling!!!
Jun-21 18:49:39.287 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:lookup_medaka_consensus_model
Jun-21 18:49:39.289 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.289 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.310 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name pipeline:medakaVariants
Jun-21 18:49:39.312 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.312 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.326 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:makeConsensus
Jun-21 18:49:39.328 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.328 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.335 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflutyping` matches labels `wfflutyping` for process with name pipeline:typeFlu
Jun-21 18:49:39.337 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.337 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.342 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:processType
Jun-21 18:49:39.343 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.343 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.356 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:prepNextclade
Jun-21 18:49:39.358 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.358 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.383 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextclade` matches labels `nextclade` for process with name pipeline:nextclade
Jun-21 18:49:39.384 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.385 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.389 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:getVersions
Jun-21 18:49:39.390 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.390 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.414 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:getParams
Jun-21 18:49:39.415 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.415 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.435 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name pipeline:collectFilesInDir
Jun-21 18:49:39.436 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.436 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `wf_common` for process with name pipeline:makeReport
Jun-21 18:49:39.482 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.482 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.529 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfflu` matches labels `wfflu` for process with name output
Jun-21 18:49:39.530 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-21 18:49:39.530 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-21 18:49:39.534 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: move_or_compress_fq_file, pipeline:getParams, pipeline:collectFilesInDir, sortBam, validate_sample_sheet, pipeline:medakaVariants, nextclade, makeConsensus, pipeline:nextclade, pipeline:makeReport, checkBamHeaders, pipeline:makeConsensus, downSample, alignReads, mergeBams, output, pipeline:lookup_medaka_consensus_model, makeReport, getVersions, processType, lookup_medaka_consensus_model, pipeline:alignReads, prepNextclade, bamstats, pipeline:getVersions, pipeline:processType, pipeline:coverageCalc, typeFlu, medakaVariants, coverageCalc, fastcat, pipeline:prepNextclade, collectFilesInDir, pipeline:typeFlu, getParams, catSortBams
Jun-21 18:49:39.536 [main] DEBUG nextflow.Session - Igniting dataflow network (18)
Jun-21 18:49:39.544 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastcat
Jun-21 18:49:39.546 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:alignReads
Jun-21 18:49:39.546 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:coverageCalc
Jun-21 18:49:39.547 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:lookup_medaka_consensus_model
Jun-21 18:49:39.547 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:medakaVariants
Jun-21 18:49:39.547 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:makeConsensus
Jun-21 18:49:39.547 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:typeFlu
Jun-21 18:49:39.547 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:processType
Jun-21 18:49:39.548 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:prepNextclade
Jun-21 18:49:39.548 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:nextclade
Jun-21 18:49:39.548 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getVersions
Jun-21 18:49:39.548 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getParams
Jun-21 18:49:39.549 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:collectFilesInDir
Jun-21 18:49:39.552 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:makeReport
Jun-21 18:49:39.554 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output
Jun-21 18:49:39.557 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_e66d6bf3f45767ef: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/main.nf
Script_52f11d1ddf9ca2a2: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/./lib/ingress.nf
Jun-21 18:49:39.558 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jun-21 18:49:39.558 [main] DEBUG nextflow.Session - Session await
Jun-21 18:49:39.808 [Actor Thread 23] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/data/medaka_models.tsv
Jun-21 18:49:39.814 [Actor Thread 23] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/bin/workflow-glue
Jun-21 18:49:39.886 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.889 [Task submitter] INFO nextflow.Session - [bb/4fa5e8] Submitted process > pipeline:getVersions
Jun-21 18:49:39.910 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.911 [Task submitter] INFO nextflow.Session - [48/c63379] Submitted process > fastcat (5)
Jun-21 18:49:39.920 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.920 [Task submitter] INFO nextflow.Session - [e5/f87404] Submitted process > fastcat (3)
Jun-21 18:49:39.928 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.929 [Task submitter] INFO nextflow.Session - [ea/71782b] Submitted process > fastcat (4)
Jun-21 18:49:39.937 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.938 [Task submitter] INFO nextflow.Session - [c1/9daece] Submitted process > fastcat (8)
Jun-21 18:49:39.945 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.946 [Task submitter] INFO nextflow.Session - [3d/5df3e8] Submitted process > fastcat (2)
Jun-21 18:49:39.954 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.955 [Task submitter] INFO nextflow.Session - [e2/35f742] Submitted process > fastcat (1)
Jun-21 18:49:39.970 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.971 [Task submitter] INFO nextflow.Session - [d8/e5364d] Submitted process > fastcat (9)
Jun-21 18:49:39.981 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.983 [Task submitter] INFO nextflow.Session - [84/b2662b] Submitted process > pipeline:getParams
Jun-21 18:49:39.991 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:39.992 [Task submitter] INFO nextflow.Session - [da/d809de] Submitted process > pipeline:lookup_medaka_consensus_model (1)
Jun-21 18:49:42.014 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: fastcat (2); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/3d/5df3e84b74490f855d40daddf76800]
Jun-21 18:49:42.015 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=72; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-21 18:49:42.020 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:42.021 [Task submitter] INFO nextflow.Session - [76/2dbdce] Submitted process > fastcat (7)
Jun-21 18:49:42.115 [Actor Thread 19] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/./data/primer_schemes/V1/consensus_irma.fasta
Jun-21 18:49:42.936 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: fastcat (1); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/e2/35f7424a14233da49b23ed741f79a7]
Jun-21 18:49:42.946 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:42.947 [Task submitter] INFO nextflow.Session - [44/fc3c0e] Submitted process > fastcat (6)
Jun-21 18:49:43.250 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: fastcat (3); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/e5/f87404bf478c31e9e51a745240716a]
Jun-21 18:49:43.257 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:43.258 [Task submitter] INFO nextflow.Session - [a7/054328] Submitted process > pipeline:alignReads (1)
Jun-21 18:49:43.731 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: fastcat (4); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/ea/71782bdcb93ff1b4aa6ab1840b9c81]
Jun-21 18:49:43.739 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:43.740 [Task submitter] INFO nextflow.Session - [bf/daa9b0] Submitted process > pipeline:alignReads (2)
Jun-21 18:49:43.747 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:43.748 [Task submitter] INFO nextflow.Session - [ad/c9a154] Submitted process > pipeline:alignReads (3)
Jun-21 18:49:43.907 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: fastcat (8); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/c1/9daeceedc98e79cf95b67e2c82492f]
Jun-21 18:49:43.914 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:43.915 [Task submitter] INFO nextflow.Session - [13/215cb8] Submitted process > pipeline:alignReads (4)
Jun-21 18:49:44.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: fastcat (7); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/76/2dbdce59d6466a8dc44931be7aba5f]
Jun-21 18:49:44.062 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:44.063 [Task submitter] INFO nextflow.Session - [5b/fd72d3] Submitted process > pipeline:alignReads (5)
Jun-21 18:49:44.084 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:44.085 [Task submitter] INFO nextflow.Session - [ef/babd22] Submitted process > pipeline:alignReads (6)
Jun-21 18:49:44.410 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: fastcat (5); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/48/c633791d3beb857c7e7d25a5c241b8]
Jun-21 18:49:44.416 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: fastcat (9); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/d8/e5364de78a88e2da77798ed3605834]
Jun-21 18:49:44.436 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:44.437 [Task submitter] INFO nextflow.Session - [0e/164540] Submitted process > pipeline:alignReads (7)
Jun-21 18:49:44.445 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:44.446 [Task submitter] INFO nextflow.Session - [30/f53f84] Submitted process > pipeline:alignReads (8)
Jun-21 18:49:46.186 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: fastcat (6); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/44/fc3c0e3a996b001be1011fb9007eb8]
Jun-21 18:49:46.206 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:49:46.206 [Task submitter] INFO nextflow.Session - [6d/f885aa] Submitted process > pipeline:alignReads (9)
Jun-21 18:50:41.408 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: pipeline:getVersions; status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/bb/4fa5e814228a1fc0d9d9caa4f93f20]
Jun-21 18:50:42.081 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: pipeline:getParams; status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/84/b2662b8eef6b63427af778cd12d176]
Jun-21 18:50:44.191 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: pipeline:alignReads (1); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/a7/0543285b2c2693e4b372704f3054f2]
Jun-21 18:50:44.213 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:44.213 [Task submitter] INFO nextflow.Session - [50/60e0c4] Submitted process > pipeline:coverageCalc (1)
Jun-21 18:50:45.024 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: pipeline:coverageCalc (1); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/50/60e0c4c5f0ccec39b58bdc565cf89a]
Jun-21 18:50:54.436 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: pipeline:alignReads (6); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/ef/babd22daa6ffadeca0353e10d99117]
Jun-21 18:50:54.465 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:54.466 [Task submitter] INFO nextflow.Session - [e0/2b66b7] Submitted process > pipeline:coverageCalc (2)
Jun-21 18:50:55.236 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: pipeline:alignReads (3); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/ad/c9a154ca324c51ec7f9d341747c406]
Jun-21 18:50:55.258 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:55.259 [Task submitter] INFO nextflow.Session - [9e/01fd31] Submitted process > pipeline:coverageCalc (3)
Jun-21 18:50:55.461 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: pipeline:coverageCalc (2); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/e0/2b66b784104158d9ba857ab647091c]
Jun-21 18:50:56.506 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: pipeline:coverageCalc (3); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/9e/01fd3110022ccc17b1b5eee31e8aa6]
Jun-21 18:50:57.097 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: pipeline:alignReads (8); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/30/f53f8435744a5ee08d09fe35c62bd7]
Jun-21 18:50:57.118 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:57.118 [Task submitter] INFO nextflow.Session - [8b/068f78] Submitted process > pipeline:coverageCalc (4)
Jun-21 18:50:57.942 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: pipeline:alignReads (4); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/13/215cb8a77443f91b7600f3293b8057]
Jun-21 18:50:57.960 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:57.960 [Task submitter] INFO nextflow.Session - [3a/618501] Submitted process > pipeline:coverageCalc (5)
Jun-21 18:50:58.246 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: pipeline:coverageCalc (4); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/8b/068f78de8386cda26cf37aba97078d]
Jun-21 18:50:58.733 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: pipeline:alignReads (7); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/0e/164540c9f302df9e29425790f761df]
Jun-21 18:50:58.760 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:58.761 [Task submitter] INFO nextflow.Session - [05/ebc182] Submitted process > pipeline:coverageCalc (6)
Jun-21 18:50:58.869 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: pipeline:alignReads (5); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/5b/fd72d33e9b2223570cd6aba1ba2c92]
Jun-21 18:50:58.891 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:58.891 [Task submitter] INFO nextflow.Session - [34/899edb] Submitted process > pipeline:coverageCalc (7)
Jun-21 18:50:58.963 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: pipeline:lookup_medaka_consensus_model (1); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/da/d809deee41d435c20b79ca84ffc9d0]
Jun-21 18:50:59.010 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:59.010 [Task submitter] INFO nextflow.Session - [55/328e02] Submitted process > pipeline:medakaVariants (6)
Jun-21 18:50:59.023 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:59.026 [Task submitter] INFO nextflow.Session - [5d/1a7da9] Submitted process > pipeline:medakaVariants (2)
Jun-21 18:50:59.040 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:59.040 [Task submitter] INFO nextflow.Session - [12/b35d02] Submitted process > pipeline:medakaVariants (7)
Jun-21 18:50:59.046 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:59.047 [Task submitter] INFO nextflow.Session - [20/f57be5] Submitted process > pipeline:medakaVariants (5)
Jun-21 18:50:59.053 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:59.053 [Task submitter] INFO nextflow.Session - [bd/6030f6] Submitted process > pipeline:medakaVariants (3)
Jun-21 18:50:59.063 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:59.064 [Task submitter] INFO nextflow.Session - [37/59782b] Submitted process > pipeline:medakaVariants (4)
Jun-21 18:50:59.075 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:50:59.076 [Task submitter] INFO nextflow.Session - [54/fc0a97] Submitted process > pipeline:medakaVariants (1)
Jun-21 18:50:59.664 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: pipeline:coverageCalc (5); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/3a/618501fb1db73ff4b3554d6d68ee2f]
Jun-21 18:51:02.200 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: pipeline:coverageCalc (6); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/05/ebc182f4e93f284f603d71afaa25a4]
Jun-21 18:51:02.244 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: pipeline:coverageCalc (7); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/34/899edbbf045638ae88ab3c131ea8a3]
Jun-21 18:51:02.659 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: pipeline:alignReads (9); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/6d/f885aae217be9a2ff6a2b8b6170a62]
Jun-21 18:51:02.690 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:51:02.690 [Task submitter] INFO nextflow.Session - [05/3c4330] Submitted process > pipeline:medakaVariants (8)
Jun-21 18:51:02.697 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:51:02.697 [Task submitter] INFO nextflow.Session - [a5/4aff81] Submitted process > pipeline:coverageCalc (8)
Jun-21 18:51:05.594 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: pipeline:alignReads (2); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/bf/daa9b07e08fab0832c205e33228cd7]
Jun-21 18:51:05.610 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:51:05.611 [Task submitter] INFO nextflow.Session - [d6/303130] Submitted process > pipeline:coverageCalc (9)
Jun-21 18:51:05.619 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-21 18:51:05.619 [Task submitter] INFO nextflow.Session - [7a/f2bb2f] Submitted process > pipeline:medakaVariants (9)
Jun-21 18:51:06.172 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: pipeline:coverageCalc (8); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/a5/4aff81099f601ea828bc3e43912ad2]
Jun-21 18:51:06.868 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: pipeline:coverageCalc (9); status: COMPLETED; exit: 0; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/d6/3031309527d1c22d5055a58843ba20]
Jun-21 18:53:43.911 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: pipeline:medakaVariants (7); status: COMPLETED; exit: 134; error: -; workDir: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/12/b35d02326108319c0ab44b433068e9]
Jun-21 18:53:43.918 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:medakaVariants (7); work-dir=/home/mmora30/workspace/nextflow_pipelines/wf-flu/work/12/b35d02326108319c0ab44b433068e9
error [nextflow.exception.ProcessFailedException]: Process `pipeline:medakaVariants (7)` terminated with an error exit status (134)
Jun-21 18:53:43.946 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'pipeline:medakaVariants (7)'
Caused by:
Process `pipeline:medakaVariants (7)` terminated with an error exit status (134)
Command executed:
medaka consensus downsample.bam consensus.hdf --model "r1041_e82_400bps_hac_g632"
medaka variant --gvcf reference.fasta consensus.hdf variants.vcf --verbose
medaka tools annotate --debug --pad 25 variants.vcf reference.fasta downsample.bam variants.annotated.vcf
bcftools filter -e "ALT='.'" variants.annotated.vcf | bcftools filter -o variants.annotated.filtered.vcf -O v -e "INFO/DP<20" -
Command exit status:
134
Command output:
(empty)
Command error:
f636889572e8: Download complete
bd838845df2f: Verifying Checksum
bd838845df2f: Download complete
56e0351b9876: Pull complete
34388bf37a91: Verifying Checksum
34388bf37a91: Download complete
4f4fb700ef54: Download complete
2863766b5fd4: Pull complete
8d19aae6b9e8: Download complete
ea1a434b99ca: Verifying Checksum
ea1a434b99ca: Download complete
827c444d8f44: Pull complete
0f07d929085f: Pull complete
95ba63acee01: Pull complete
2ff148fb209c: Download complete
be18c90380e8: Download complete
e4dca7d7b1d7: Download complete
f39cce9b5942: Download complete
d1c43d64a0da: Verifying Checksum
d1c43d64a0da: Download complete
3aa6278d569b: Download complete
0bcba66e5b75: Download complete
6296ffe2c3d4: Verifying Checksum
6296ffe2c3d4: Download complete
ae716de67ab4: Download complete
ae716de67ab4: Pull complete
a7476cc8e8fe: Pull complete
754fa580d193: Pull complete
16ed58043377: Pull complete
0bcba66e5b75: Pull complete
e6afbf71047c: Pull complete
812991d2a8b3: Pull complete
e78fb8d98984: Pull complete
f636889572e8: Pull complete
bd838845df2f: Pull complete
34388bf37a91: Pull complete
4f4fb700ef54: Pull complete
8d19aae6b9e8: Pull complete
ea1a434b99ca: Pull complete
2ff148fb209c: Pull complete
be18c90380e8: Pull complete
e4dca7d7b1d7: Pull complete
f39cce9b5942: Pull complete
d1c43d64a0da: Pull complete
3aa6278d569b: Pull complete
6296ffe2c3d4: Pull complete
Digest: sha256:4d3a1078b1104ec76698dc02383492ed6fb3b2664ef9a0385d4c14abdc004e6c
Status: Image is up to date for ontresearch/medaka:sha4f35e9f6f231dc8343c98e04d43517d4a38528a2
The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine.
.command.sh: line 2: 30 Aborted (core dumped) medaka consensus downsample.bam consensus.hdf --model "r1041_e82_400bps_hac_g632"
Work dir:
/home/mmora30/workspace/nextflow_pipelines/wf-flu/work/12/b35d02326108319c0ab44b433068e9
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Jun-21 18:53:43.954 [TaskFinalizer-1] DEBUG nextflow.Session - Session aborted -- Cause: Process `pipeline:medakaVariants (7)` terminated with an error exit status (134)
Jun-21 18:53:43.975 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jun-21 18:53:43.999 [TaskFinalizer-1] DEBUG nextflow.Session - The following nodes are still active:
[process] pipeline:makeConsensus
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: reference.fasta
port 2: (cntrl) - ; channel: $
[process] pipeline:typeFlu
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: blast_db
port 2: (cntrl) - ; channel: $
[process] pipeline:processType
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] pipeline:prepNextclade
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: nextclade_data
port 2: (cntrl) - ; channel: $
[process] pipeline:nextclade
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] pipeline:collectFilesInDir
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] pipeline:makeReport
status=ACTIVE
port 0: (value) bound ; channel: metadata
port 1: (value) bound ; channel: fastcat_stats/?.gz
port 2: (value) OPEN ; channel: data/*
port 3: (value) OPEN ; channel: nextclade/*
port 4: (value) bound ; channel: nextclade_datasets
port 5: (value) OPEN ; channel: versions/*
port 6: (value) bound ; channel: params.json
port 7: (cntrl) - ; channel: $
[process] output
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
Jun-21 18:53:44.637 [main] DEBUG nextflow.Session - Session await > all processes finished
Jun-21 18:53:44.637 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-21 18:53:44.688 [Actor Thread 19] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.005 s; external sort time: 0.017 s; total time: 0.022 s
Jun-21 18:53:44.696 [Actor Thread 19] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/mmora30/workspace/nextflow_pipelines/wf-flu/work/collect-file/c784976cde95796aca1966c246097a88
Jun-21 18:53:44.708 [Actor Thread 19] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-9397918069979095492
Jun-21 18:53:44.784 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (8)
Jun-21 18:53:44.808 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill pipeline:medakaVariants (2) -- command: kill -TERM 214486; exit: 1
bash: line 1: kill: (214486) - No such process
Jun-21 18:53:44.816 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill pipeline:medakaVariants (5) -- command: kill -TERM 214534; exit: 1
bash: line 1: kill: (214534) - No such process
Jun-21 18:53:44.823 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill pipeline:medakaVariants (3) -- command: kill -TERM 214560; exit: 1
bash: line 1: kill: (214560) - No such process
Jun-21 18:53:44.830 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill pipeline:medakaVariants (4) -- command: kill -TERM 214603; exit: 1
bash: line 1: kill: (214603) - No such process
Jun-21 18:53:44.839 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill pipeline:medakaVariants (1) -- command: kill -TERM 214653; exit: 1
bash: line 1: kill: (214653) - No such process
Jun-21 18:53:44.848 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill pipeline:medakaVariants (8) -- command: kill -TERM 215174; exit: 1
bash: line 1: kill: (215174) - No such process
Jun-21 18:53:44.858 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill pipeline:medakaVariants (9) -- command: kill -TERM 215517; exit: 1
bash: line 1: kill: (215517) - No such process
Jun-21 18:53:44.863 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=30; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=8; succeedDuration=5m 49s; failedDuration=2m 45s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=12; peakCpus=24; peakMemory=24 GB; ]
Jun-21 18:53:44.864 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jun-21 18:53:44.867 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jun-21 18:53:45.427 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jun-21 18:53:45.495 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jun-21 18:53:45.517 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbyehere is information about the remote server that I'm using:
lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Address sizes: 40 bits physical, 48 bits virtual
Byte Order: Little Endian
CPU(s): 24
On-line CPU(s) list: 0-23
Vendor ID: GenuineIntel
Model name: QEMU Virtual CPU version 2.5+
CPU family: 15
Model: 107
Thread(s) per core: 1
Core(s) per socket: 12
Socket(s): 2
Stepping: 1
BogoMIPS: 4190.16
Flags: fpu de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2
ht syscall nx lm constant_tsc nopl xtopology cpuid tsc_known_freq pni ssse3 cx16 sse4_1 sse4_2
x2apic popcnt aes hypervisor lahf_lm cpuid_fault pti
Virtualization features:
Hypervisor vendor: KVM
Virtualization type: full
Caches (sum of all):
L1d: 768 KiB (24 instances)
L1i: 768 KiB (24 instances)
L2: 96 MiB (24 instances)
L3: 32 MiB (2 instances)
NUMA:
NUMA node(s): 1
NUMA node0 CPU(s): 0-23
Vulnerabilities:
Gather data sampling: Not affected
Itlb multihit: KVM: Mitigation: VMX unsupported
L1tf: Mitigation; PTE Inversion
Mds: Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown
Meltdown: Mitigation; PTI
Mmio stale data: Unknown: No mitigations
Retbleed: Not affected
Spec rstack overflow: Not affected
Spec store bypass: Vulnerable
Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Spectre v2: Mitigation; Retpolines; STIBP disabled; RSB filling; PBRSB-eIBRS Not affected; BHI Retpoline
Srbds: Not affected
Tsx async abort: Not affectedAny ideas? Please let me now if you need more information, thank you again
cjalder
commented
4 months ago Hi @MauriAndresMU1313 - so it does look like the AVX instructions are part of the problem in this case. The remote server you're running from seems to be a Virtual machine so I would recommend speaking to the system administrator in charge on how to proceed.
MauriAndresMU1313
commented
4 months ago Thank you the information, I will check with him
MauriAndresMU1313
commented
2 weeks ago Hi again, I need to reopen the issue because I was able to run the pipeline using a conda enviroment with TF installed. However, now I'm trying to run the demo data again, but I do not have any output at all, neither in work or output_dir.
I tested the use of NXF_VER=23.10.1 and the 24.04.2, and right now I do not have any signal of error, or AVX instructions or medaka issues. Even if I look at the .nexflow.log file I can not find any information.
Here the file of the last run:
Oct-15 14:56:27.300 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-flu --downsample 50 --fastq demo_data/wf-flu-demo/fastq/ --out_dir /home/mmora30/localData/workspace_mm/nextflow_pipelines/epi2me-labs/wf-flu/output_dir --sample_sheet demo_data/wf-flu-demo/sample_sheet.csv -profile standard
Oct-15 14:56:27.376 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1
Oct-15 14:56:27.408 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/mmora30/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1
Oct-15 14:56:27.423 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-15 14:56:27.424 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-15 14:56:27.428 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-15 14:56:27.442 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Oct-15 14:56:27.463 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/mmora30/.nextflow/scm
Oct-15 14:56:28.494 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-flu.git
Oct-15 14:56:28.517 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Oct-15 14:56:28.527 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-flu.git
Oct-15 14:56:29.279 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/nextflow.config
Oct-15 14:56:29.280 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/nextflow.config
Oct-15 14:56:29.292 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Oct-15 14:56:29.461 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Oct-15 14:56:29.462 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/epi2me-labs/wf-flu` [happy_gates] DSL2 - revision: 5290f79553 [master]
Oct-15 14:56:29.463 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-15 14:56:29.463 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-15 14:56:29.466 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/mmora30/.nextflow/secrets/store.json
Oct-15 14:56:29.469 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3434a4f0] - activable => nextflow.secret.LocalSecretsProvider@3434a4f0
Oct-15 14:56:29.532 [main] DEBUG nextflow.Session - Session UUID: e7cd4b39-ed72-445e-a824-ee916c3a3533
Oct-15 14:56:29.532 [main] DEBUG nextflow.Session - Run name: happy_gates
Oct-15 14:56:29.533 [main] DEBUG nextflow.Session - Executor pool size: 32
Oct-15 14:56:29.541 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Oct-15 14:56:29.546 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct-15 14:56:29.573 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.10.1 build 5891
Created: 12-01-2024 22:01 UTC
System: Linux 5.15.0-119-generic
Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 11.0.24+8-post-Ubuntu-1ubuntu322.04
Encoding: UTF-8 (UTF-8)
Process: 472853@medina-lab [127.0.1.1]
CPUs: 32 - Mem: 250.9 GB (172.2 GB) - Swap: 8 GB (8 GB)
Oct-15 14:56:29.597 [main] DEBUG nextflow.Session - Work-dir: /localData/workspace_mm/nextflow_pipelines/epi2me-labs/wf-flu/work [ext2/ext3]
Oct-15 14:56:29.614 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-15 14:56:29.627 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-15 14:56:29.760 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-15 14:56:29.788 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Oct-15 14:56:30.068 [main] DEBUG nextflow.Session - Session start
Oct-15 14:56:30.086 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/mmora30/localData/workspace_mm/nextflow_pipelines/epi2me-labs/wf-flu/output_dir/execution/trace.txt
Oct-15 14:56:30.100 [main] DEBUG nextflow.Session - Using default localLib path: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/lib
Oct-15 14:56:30.104 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/lib
Oct-15 14:56:30.105 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/lib/nfcore_external_java_deps.jar
Oct-15 14:56:32.949 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-15 14:56:36.370 [main] INFO nextflow.Nextflow -
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-flu v1.2.3-g5290f79
--------------------------------------------------------------------------------
Core Nextflow options
revision : master
runName : happy_gates
containerEngine: docker
container : [withLabel:wf_common:ontresearch/wf-common:shad28e55140f75a68f59bbecc74e880aeab16ab158, withLabel:wfflu:ontresearch/wf-flu:sha5eeb2cd0a75a6cc0f47d689d2926e0d9922ceda8, withLabel:wfflutyping:ontresearch/abricate:sha671198c26ad22c97e3cdaa81a646ec0c215ebc43, withLabel:nextclade:ontresearch/nextclade:shab67652b34e898ec8dea18d0953a0b06b10466f76, withLabel:medaka:ontresearch/medaka:sha3486abaab0d3b90351617eb8622acf2028edb154]
launchDir : /localData/workspace_mm/nextflow_pipelines/epi2me-labs/wf-flu
workDir : /localData/workspace_mm/nextflow_pipelines/epi2me-labs/wf-flu/work
projectDir : /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu
userName : mmora30
profile : standard
configFiles : /home/mmora30/.nextflow/assets/epi2me-labs/wf-flu/nextflow.config
Input Options
fastq : demo_data/wf-flu-demo/fastq/
Sample Options
sample_sheet : demo_data/wf-flu-demo/sample_sheet.csv
Output Options
out_dir : /home/mmora30/localData/workspace_mm/nextflow_pipelines/epi2me-labs/wf-flu/output_dir
Advanced Options
downsample : 50
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-flu for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-flu v1.2.3-g5290f79.
--------------------------------------------------------------------------------
Oct-15 14:56:36.940 [main] INFO nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Oct-15 14:56:37.061 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `ingress,wf_common` for process with name validate_sample_sheet
Oct-15 14:56:37.088 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-15 14:56:37.088 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-15 14:56:37.096 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-15 14:56:37.102 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=250.8 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Oct-15 14:56:37.105 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Oct-15 14:56:37.344 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `ingress,wf_common` for process with name fastcat
Oct-15 14:56:37.346 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-15 14:56:37.346 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'Looks like everything is working properly, except for the analysis:
nextflow run epi2me-labs/wf-flu --help:
Nextflow 24.04.4 is available - Please consider updating your version to it
N E X T F L O W ~ version 24.04.2
Launching `https://github.com/epi2me-labs/wf-flu` [berserk_gilbert] DSL2 - revision: 5290f79553 [master]
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-flu v1.2.3-g5290f79
--------------------------------------------------------------------------------
Typical pipeline command:
nextflow run epi2me-labs/wf-flu \
--downsample 50 \
--fastq 'wf-flu-demo/fastq' \
--sample_sheet 'wf-flu-demo/sample_sheet.csv'
Input Options
--fastq [string] FASTQ files to use in the analysis.
--analyse_unclassified [boolean] Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified
directory.
Sample Options
--sample_sheet [string] A CSV file used to map barcodes to sample aliases. The sample sheet can be provided when the input data is a directory
containing sub-directories with FASTQ files.
Output Options
--out_dir [string] Directory for output of all workflow results. [default: output]
Advanced Options
--override_basecaller_cfg [choice] Override auto-detected basecaller model that processed the signal data; used to select an appropriate Medaka
model.
* dna_r10.4.1_e8.2_400bps_sup@v5.0.0
* dna_r10.4.1_e8.2_400bps_hac@v5.0.0
* dna_r10.4.1_e8.2_400bps_sup@v4.3.0
* dna_r10.4.1_e8.2_400bps_hac@v4.3.0
* dna_r10.4.1_e8.2_400bps_sup@v4.2.0
* dna_r10.4.1_e8.2_400bps_hac@v4.2.0
* dna_r10.4.1_e8.2_260bps_hac@v4.1.0
* dna_r10.4.1_e8.2_260bps_sup@v4.1.0
* dna_r10.4.1_e8.2_400bps_hac@v4.1.0
* dna_r10.4.1_e8.2_400bps_sup@v4.1.0
* dna_r10.4.1_e8.2_260bps_hac@v4.0.0
* dna_r10.4.1_e8.2_260bps_sup@v4.0.0
* dna_r10.4.1_e8.2_400bps_hac@v4.0.0
* dna_r10.4.1_e8.2_400bps_sup@v4.0.0
* dna_r10.4.1_e8.2_400bps_hac@v3.5.2
* dna_r10.4.1_e8.2_400bps_sup@v3.5.2
* dna_r9.4.1_e8_fast@v3.4
* dna_r9.4.1_e8_hac@v3.3
* dna_r9.4.1_e8_sup@v3.3
* dna_r10.4.1_e8.2_400bps_hac_prom
* dna_r9.4.1_450bps_hac_prom
* dna_r10.3_450bps_hac
* dna_r10.3_450bps_hac_prom
* dna_r10.4.1_e8.2_260bps_hac
* dna_r10.4.1_e8.2_260bps_hac_prom
* dna_r10.4.1_e8.2_400bps_hac
* dna_r9.4.1_450bps_hac
* dna_r9.4.1_e8.1_hac
* dna_r9.4.1_e8.1_hac_prom
--reference [string] Enter the full path to a custom reference genome you would like to use.
--blastdb [string] blastdb file used for typing.
--min_coverage [integer] Coverage threshold for masking bases in the consensus. [default: 20]
--min_qscore [number] Minimum read quality score for fastcat. [default: 9]
--downsample [integer] Number of reads to downsample to in each direction, leave blank for no downsampling.
--rbk [boolean] Set when using data created with the RBK protocol.
Miscellaneous Options
--disable_ping [boolean] Enable to prevent sending a workflow ping.
Other parameters
--monochrome_logs [boolean] null
--validate_params [boolean] null [default: true]
--show_hidden_params [boolean] null
!! Hiding 6 params, use --show_hidden_params to show them !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-flu for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-xAny comment or suggestion is welcome! Any advise to solve this issue?
MauriAndresMU1313
commented
2 weeks ago The workflow stays running without generating any output, and if I close the session (even if I'm running the job in the background), I get the error:
[Task monitor] DEBUG nextflow.Session - Unexpected error while dumping DAG status
error [java.lang.InterruptedException]: java.lang.InterruptedException
error [java.lang.InterruptedException]: java.lang.InterruptedException
error [java.lang.InterruptedException]: java.lang.InterruptedExceptionSo, if I check the output that is printed when I run the analysis:
This is epi2me-labs/wf-flu v1.2.3-g5290f79.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
[- ] validate_sample_sheet -
[- ] validate_sample_sheet -
[- ] fastcat -
[- ] pipeline:alignReads -
[- ] pipeline:coverageCalc -
[- ] pipeline:downSample -
[- ] pipeline:medakaVariants -
[- ] pipeline:makeConsensus -
[- ] pipeline:typeFlu -
[- ] pipeline:processType -
[- ] pipeline:prepNextclade -
[- ] pipeline:nextclade -
[- ] pipeline:getVersions -
Downsampling!!!
[- ] validate_sample_sheet -
[- ] fastcat -
[- ] pipeline:alignReads -
[- ] pipeline:coverageCalc -
[- ] pipeline:downSample -
[- ] pipeline:medakaVariants -
[- ] pipeline:makeConsensus -
[- ] pipeline:typeFlu -
[- ] pipeline:processType -
[- ] pipeline:prepNextclade -
[- ] pipeline:nextclade -
[- ] pipeline:getVersions -
[- ] pipeline:getParams -
[- ] pipeline:collectFilesInDir -
[- ] pipeline:makeReport -
[- ] output -
Downsampling!!!
[- ] validate_sample_sheet -
[- ] fastcat -
[- ] pipeline:alignReads -
[- ] pipeline:coverageCalc -
[- ] pipeline:downSample -
[- ] pipeline:medakaVariants -
[- ] pipeline:makeConsensus -
[- ] pipeline:typeFlu -
[- ] pipeline:processType -
[- ] pipeline:prepNextclade -
[- ] pipeline:nextclade -
[- ] pipeline:getVersions -
[- ] pipeline:getParams -
[- ] pipeline:collectFilesInDir -
[- ] pipeline:makeReport -
[- ] output -
Downsampling!!!So it is not running at all, is there any issue with the pipeline? Any version issue? Any incompatibility with next flow updates?
MauriAndresMU1313
commented
1 week ago Any comments about this? Any help or comment will be great and really appreciated. I know that in the second error that I shared last week, I do not see error related to Medaka, however, I have the feeling that maybe the virtual environment that I created could be related or maybe not, but as you can see the pipeline is not working at all in my case.
cjw85
commented
1 week ago @MauriAndresMU1313
Please open a new issue rather than reopening old unrelated issues.
I'm trying to run the test pipeline in Ubuntu 22.04 using the basic command line:
However, I got the following error:
Based on that error, I tried to install TensorFlow using three different approaches:
None of them worked so far, all show me the same error. If I try to check the version of TensorFlow for the second and third option (list above) using:
The output of the nextflow command line:
So far, I could not find a way to run the pipeline even when I used the options listed above What can I do in this particular case? Can I use a docker image to solve the issue? What do you recommend? Do you need more information to help me solve this issue?
Thank you for your help!