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.nextflow.log
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Nov-06 09:05:07.351 [main] DEBUG nextflow.cli.Launcher - $> nextflow run intogen.nf -resume -profile local --input /home/kairos/intogen-plus-2024/test/ --output ./output1
Nov-06 09:05:07.443 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.03.0-edge
Nov-06 09:05:07.470 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/kairos/intogen-plus-2024/nextflow.config
Nov-06 09:05:07.471 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/kairos/intogen-plus-2024/nextflow.config
Nov-06 09:05:07.494 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `local`
Nov-06 09:05:08.227 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bbglab, local]
Nov-06 09:05:08.284 [main] INFO nextflow.cli.CmdRun - Launching `intogen.nf` [infallible_goodall] DSL1 - revision: 9ff16beb38
Nov-06 09:05:08.296 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/kairos/.nextflow/plugins; core-plugins: nf-amazon@1.6.0,nf-azure@0.13.0,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.3.0,nf-tower@1.4.0
Nov-06 09:05:08.298 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Nov-06 09:05:08.311 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Nov-06 09:05:08.312 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Nov-06 09:05:08.316 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Nov-06 09:05:08.324 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Nov-06 09:05:08.376 [main] DEBUG nextflow.Session - Session uuid: e2e32fda-11c5-4119-bda0-17c6d1618b9a
Nov-06 09:05:08.376 [main] DEBUG nextflow.Session - Run name: infallible_goodall
Nov-06 09:05:08.377 [main] DEBUG nextflow.Session - Executor pool size: 22
Nov-06 09:05:08.414 [main] DEBUG nextflow.cli.CmdRun -
Version: 22.03.0-edge build 5693
Created: 27-03-2022 19:42 UTC (28-03-2022 06:42 AEDT)
System: Linux 5.15.153.1-microsoft-standard-WSL2
Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.24+8-post-Ubuntu-1ubuntu322.04
Encoding: UTF-8 (UTF-8)
Process: 662682@Kairos [127.0.1.1]
CPUs: 22 - Mem: 27.4 GB (24 GB) - Swap: 8 GB (7.9 GB)
Nov-06 09:05:08.443 [main] DEBUG nextflow.Session - Work-dir: /home/kairos/intogen-plus-2024/work [ext2/ext3]
Nov-06 09:05:08.444 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/kairos/intogen-plus-2024/bin
Nov-06 09:05:08.453 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Nov-06 09:05:08.461 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Nov-06 09:05:08.487 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Nov-06 09:05:08.503 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 23; maxThreads: 1000
Nov-06 09:05:08.607 [main] DEBUG nextflow.Session - Session start invoked
Nov-06 09:05:08.614 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/kairos/intogen-plus-2024/trace.txt
Nov-06 09:05:09.553 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Nov-06 09:05:09.684 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name ParseInput
Nov-06 09:05:09.686 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ParseInput` matches process ParseInput
Nov-06 09:05:09.689 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.689 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.693 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Nov-06 09:05:09.704 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=22; memory=27.4 GB; capacity=22; pollInterval=100ms; dumpInterval=5m
Nov-06 09:05:09.882 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name LoadCancer
Nov-06 09:05:09.884 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.885 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.895 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name LoadPlatform
Nov-06 09:05:09.896 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.896 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.904 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name LoadGenome
Nov-06 09:05:09.906 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.906 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.937 [Actor Thread 5] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /home/kairos/config/annotations.txt -- Cause: java.nio.file.NoSuchFileException: /home/kairos/config/annotations.txt
Nov-06 09:05:09.947 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name ProcessVariants
Nov-06 09:05:09.947 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.947 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.959 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatSignature
Nov-06 09:05:09.959 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.959 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.967 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:bgsignature` matches labels `bgsignature` for process with name ComputeProfile
Nov-06 09:05:09.967 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.967 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.974 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatFML
Nov-06 09:05:09.975 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.975 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.983 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:OncodriveFML` matches process OncodriveFML
Nov-06 09:05:09.983 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.984 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatCLUSTL
Nov-06 09:05:09.988 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.988 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.994 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:OncodriveCLUSTL` matches process OncodriveCLUSTL
Nov-06 09:05:09.994 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.994 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:09.997 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatDNDSCV
Nov-06 09:05:09.998 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:09.998 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.004 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:dNdScv` matches process dNdScv
Nov-06 09:05:10.004 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.004 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.011 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatVEP
Nov-06 09:05:10.012 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.012 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.016 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VEP` matches process VEP
Nov-06 09:05:10.017 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.017 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.022 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name ProcessVEPoutput
Nov-06 09:05:10.022 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.022 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.027 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [18/d90fa8] Cached process > ParseInput (Parse input test)
Nov-06 09:05:10.028 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FilterNonSynonymous
Nov-06 09:05:10.028 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.028 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.031 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatSMRegions
Nov-06 09:05:10.031 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.031 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.039 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SMRegions` matches process SMRegions
Nov-06 09:05:10.040 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.040 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.048 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatCBaSE
Nov-06 09:05:10.048 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.048 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.052 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CBaSE` matches process CBaSE
Nov-06 09:05:10.053 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.054 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.062 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatMutPanning
Nov-06 09:05:10.062 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.063 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.064 [Actor Thread 23] INFO nextflow.processor.TaskProcessor - [aa/73446b] Cached process > LoadPlatform (Load sequencing platform CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.064 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [c4/d537a7] Cached process > LoadCancer (Load cancer type CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.064 [Actor Thread 16] INFO nextflow.processor.TaskProcessor - [71/a60cf5] Cached process > LoadGenome (Load reference genome CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.069 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MutPanning` matches process MutPanning
Nov-06 09:05:10.070 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.070 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.071 [Actor Thread 5] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=4; maxSize=4; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Nov-06 09:05:10.075 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatHotMAPS
Nov-06 09:05:10.076 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.076 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.087 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:HotMAPS` matches process HotMAPS
Nov-06 09:05:10.087 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.087 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.088 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [9a/971d79] Cached process > ProcessVariants (Process variants CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.098 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:Combination` matches process Combination
Nov-06 09:05:10.100 [Actor Thread 16] INFO nextflow.processor.TaskProcessor - [47/c5dca5] Cached process > FormatCLUSTL (Prepare for CLUSTL CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.100 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.100 [Actor Thread 22] INFO nextflow.processor.TaskProcessor - [73/de532b] Cached process > FormatDNDSCV (Prepare for DNDSCV CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.101 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.101 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [b1/dfdf98] Cached process > FormatSignature (Prepare for signatures CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.101 [Actor Thread 13] INFO nextflow.processor.TaskProcessor - [e1/a07fc4] Cached process > FormatFML (Prepare for FML CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.103 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [8a/5c2af4] Cached process > FormatVEP (Prepare for VEP CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.106 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FormatdeconstructSigs
Nov-06 09:05:10.106 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.106 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.109 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:deconstructSigs` matches process deconstructSigs
Nov-06 09:05:10.109 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.109 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.120 [Actor Thread 20] INFO nextflow.processor.TaskProcessor - [f2/f00b54] Cached process > dNdScv (dNdScv CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.126 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.126 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.137 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [60/769114] Cached process > VEP (VEP CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.138 [Actor Thread 11] INFO nextflow.processor.TaskProcessor - [7d/f21e06] Cached process > ComputeProfile (ComputeProfile CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.138 [Actor Thread 20] INFO nextflow.processor.TaskProcessor - [6f/f557e9] Cached process > CohortCounts (Count variants CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.143 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.144 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.159 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name MutationsSummary
Nov-06 09:05:10.160 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.160 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.163 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [14/68cab8] Cached process > ProcessVEPoutput (Process vep output CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.170 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name DriverDiscovery
Nov-06 09:05:10.171 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.171 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.177 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name DriverSummary
Nov-06 09:05:10.178 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.178 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.179 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [e9/71a8f6] Cached process > FormatMutPanning (Prepare for MutPanning CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.179 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [bd/a3a4b5] Cached process > FormatHotMAPS (Prepare for HotMAPS CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.179 [Actor Thread 1] INFO nextflow.processor.TaskProcessor - [ff/ac3e16] Cached process > FilterNonSynonymous (Filter non synonymus CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.179 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [89/381942] Cached process > CohortSummary (Count variants)
Nov-06 09:05:10.179 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [a5/c44d35] Cached process > MutationsSummary (Mutations)
Nov-06 09:05:10.182 [Actor Thread 24] INFO nextflow.processor.TaskProcessor - [d3/1ac642] Cached process > FormatdeconstructSigs (Prepare for deconstructSigs CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.182 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [99/efe815] Cached process > FormatCBaSE (Prepare for CBaSE CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.183 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name ParseProfile
Nov-06 09:05:10.183 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ParseProfile` matches process ParseProfile
Nov-06 09:05:10.184 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.184 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.190 [Actor Thread 11] INFO nextflow.processor.TaskProcessor - [d4/b7d268] Cached process > OncodriveCLUSTL (OncodriveCLUSTL CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.191 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name DriverSaturation
Nov-06 09:05:10.192 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.192 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.192 [Actor Thread 22] INFO nextflow.processor.TaskProcessor - [87/b0aba9] Cached process > OncodriveFML (OncodriveFML CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.196 [Actor Thread 8] INFO nextflow.processor.TaskProcessor - [44/794784] Cached process > FormatSMRegions (Prepare for SMRegions CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.196 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [ab/ee3e83] Cached process > ParseProfile (Parsing profile CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.200 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:core` matches labels `core` for process with name FilterMNVS
Nov-06 09:05:10.200 [Actor Thread 21] INFO nextflow.processor.TaskProcessor - [5b/692030] Cached process > deconstructSigs (deconstructSigs CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.200 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Nov-06 09:05:10.200 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-06 09:05:10.203 [Actor Thread 16] INFO nextflow.processor.TaskProcessor - [9f/ee5547] Cached process > CBaSE (CBaSE CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.205 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: VEP, FormatFML, CohortSummary, MutationsSummary, FormatCBaSE, OncodriveFML, FilterMNVS, FormatDNDSCV, ProcessVariants, ParseInput, dNdScv, FormatHotMAPS, CohortCounts, LoadPlatform, Combination, SMRegions, DriverDiscovery, FormatSignature, OncodriveCLUSTL, MutPanning, FormatVEP, DriverSaturation, DriverSummary, ComputeProfile, ParseProfile, FilterNonSynonymous, ProcessVEPoutput, FormatCLUSTL, HotMAPS, FormatdeconstructSigs, LoadGenome, FormatMutPanning, FormatSMRegions, CBaSE, deconstructSigs, LoadCancer
Nov-06 09:05:10.207 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [2a/534c1d] Cached process > FilterMNVS (MNVs filter)
Nov-06 09:05:10.207 [Actor Thread 26] INFO nextflow.processor.TaskProcessor - [df/ed4100] Cached process > HotMAPS (HotMAPS CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.208 [Actor Thread 28] INFO nextflow.processor.TaskProcessor - [11/e1384b] Cached process > MutPanning (MutPanning CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.221 [main] WARN nextflow.Session - There's no process matching config selector: Signature
Nov-06 09:05:10.222 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Nov-06 09:05:10.223 [main] DEBUG nextflow.Session - Session await
Nov-06 09:05:10.232 [Actor Thread 27] INFO nextflow.processor.TaskProcessor - [8c/fea8b0] Cached process > SMRegions (SMRegions CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.242 [Actor Thread 22] INFO nextflow.processor.TaskProcessor - [45/c3b85e] Cached process > Combination (Combination CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.255 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [7d/f92d51] Cached process > DriverDiscovery (Driver discovery CBIOP_WXS_PRAD_BROAD)
Nov-06 09:05:10.262 [Actor Thread 16] INFO nextflow.processor.TaskProcessor - [c1/bef0ff] Cached process > DriverSummary (Driver summary)
Nov-06 09:05:10.326 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-06 09:05:10.331 [Task submitter] INFO nextflow.Session - [51/b05421] Submitted process > DriverSaturation (Driver saturation)
Nov-06 09:05:28.116 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: DriverSaturation (Driver saturation); status: COMPLETED; exit: 0; error: -; workDir: /home/kairos/intogen-plus-2024/work/51/b05421972f21443417c0d8f7458c2c]
Nov-06 09:05:28.122 [main] DEBUG nextflow.Session - Session await > all process finished
Nov-06 09:05:28.127 [main] DEBUG nextflow.Session - Session await > all barriers passed
Nov-06 09:05:28.131 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=35; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=17.3s; failedDuration=0ms; cachedDuration=8h 42m 13s;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Nov-06 09:05:28.131 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Nov-06 09:05:28.132 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Nov-06 09:05:28.222 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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