Dec-03 09:24:00.690 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: ProxyConfig[protocol=http; host=klone-dip1; port=3128]
Dec-03 09:24:00.743 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/fetchngs -resume -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config --input /gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/ids.csv --outdir /gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest --download_method sratools
Dec-03 09:24:00.854 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.1
Dec-03 09:24:00.963 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/mmfs1/gscratch/srlab/strigg/bin/plugins; core-plugins: nf-amazon@2.9.1,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.3
Dec-03 09:24:01.008 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Dec-03 09:24:01.009 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Dec-03 09:24:01.011 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Dec-03 09:24:01.025 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Dec-03 09:24:01.033 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /mmfs1/gscratch/srlab/strigg/bin/scm
Dec-03 09:24:01.088 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Dec-03 09:24:01.108 [main] INFO nextflow.cli.CmdRun - Pulling nf-core/fetchngs ...
Dec-03 09:24:01.139 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/fetchngs/contents/nextflow.config
Dec-03 09:24:03.333 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/fetchngs/contents/main.nf
Dec-03 09:24:03.482 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/fetchngs
Dec-03 09:24:03.656 [main] DEBUG nextflow.scm.AssetManager - Pulling nf-core/fetchngs -- Using remote clone url: https://github.com/nf-core/fetchngs.git
Dec-03 09:24:05.745 [main] INFO nextflow.cli.CmdRun - downloaded from https://github.com/nf-core/fetchngs.git
Dec-03 09:24:05.775 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/nextflow.config
Dec-03 09:24:05.777 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /gscratch/srlab/strigg/bin/uw_hyak_srlab.config
Dec-03 09:24:05.778 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/nextflow.config
Dec-03 09:24:05.778 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /gscratch/srlab/strigg/bin/uw_hyak_srlab.config
Dec-03 09:24:05.811 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /mmfs1/gscratch/srlab/strigg/bin/secrets/store.json
Dec-03 09:24:05.813 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@45c80312] - activable => nextflow.secret.LocalSecretsProvider@45c80312
Dec-03 09:24:05.849 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Dec-03 09:24:07.442 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Dec-03 09:24:07.616 [main] WARN nextflow.config.ConfigBuilder - It appears you have never run this project before -- Option `-resume` is ignored
Dec-03 09:24:07.673 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Dec-03 09:24:07.673 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/fetchngs` [nauseous_planck] DSL2 - revision: 8ec2d934f9 [master]
Dec-03 09:24:07.674 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation@1.1.3]
Dec-03 09:24:07.675 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Dec-03 09:24:07.675 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation@1.1.3]
Dec-03 09:24:07.675 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3
Dec-03 09:24:07.709 [main] INFO nextflow.plugin.PluginUpdater - Downloading plugin nf-validation@1.1.3
Dec-03 09:24:08.839 [main] INFO org.pf4j.util.FileUtils - Expanded plugin zip 'nf-validation-1.1.3.zip' in 'nf-validation-1.1.3'
Dec-03 09:24:08.845 [main] DEBUG nextflow.plugin.PluginUpdater - Failed atomic move for plugin /gscratch/scrubbed/strigg/bin/pf4j-update-downloader7221878700602022803/nf-validation-1.1.3 -> /mmfs1/gscratch/srlab/strigg/bin/plugins/nf-validation-1.1.3 - Reason: /gscratch/scrubbed/strigg/bin/pf4j-update-downloader7221878700602022803/nf-validation-1.1.3 -> /mmfs1/gscratch/srlab/strigg/bin/plugins/nf-validation-1.1.3: Invalid cross-device link - Fallback on safe move
Dec-03 09:24:08.934 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved
Dec-03 09:24:08.935 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3'
Dec-03 09:24:08.953 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3
Dec-03 09:24:09.037 [main] DEBUG nextflow.Session - Session UUID: 8be703f5-2445-4ba5-b61a-7f0425284416
Dec-03 09:24:09.038 [main] DEBUG nextflow.Session - Run name: nauseous_planck
Dec-03 09:24:09.038 [main] DEBUG nextflow.Session - Executor pool size: 2
Dec-03 09:24:09.054 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Dec-03 09:24:09.058 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Dec-03 09:24:09.170 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.10.1 build 5930
Created: 18-11-2024 12:21 UTC (04:21 PDT)
System: Linux 4.18.0-513.18.1.el8_9.x86_64
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.13-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)
Process: 82428@n3439 [10.64.66.183]
CPUs: 1 - Mem: 16 GB (15.7 GB) - Swap: 74.5 GB (74.5 GB)
Dec-03 09:24:09.309 [main] DEBUG nextflow.Session - Work-dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work [gpfs]
Dec-03 09:24:09.362 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Dec-03 09:24:09.384 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Dec-03 09:24:09.464 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Dec-03 09:24:09.471 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 2; maxThreads: 1000
Dec-03 09:24:09.705 [main] DEBUG nextflow.Session - Session start
Dec-03 09:24:09.707 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/pipeline_trace.txt
Dec-03 09:24:10.038 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Dec-03 09:24:13.824 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation
Dec-03 09:24:13.902 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation
Dec-03 09:24:13.902 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation
Dec-03 09:24:13.904 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation
Dec-03 09:24:13.905 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
Dec-03 09:24:14.502 [main] DEBUG nextflow.Nextflow - Using schema file: nextflow_schema.json
Dec-03 09:24:14.503 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
Dec-03 09:24:14.522 [main] INFO nextflow.Nextflow -
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/fetchngs v1.12.0-g8ec2d93[0m
-[2m----------------------------------------------------[0m-
[1mCore Nextflow options[0m
[0;34mrevision : [0;32mmaster[0m
[0;34mrunName : [0;32mnauseous_planck[0m
[0;34mcontainerEngine : [0;32msingularity[0m
[0;34mlaunchDir : [0;32m/mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest[0m
[0;34mworkDir : [0;32m/mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work[0m
[0;34mprojectDir : [0;32m/mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs[0m
[0;34muserName : [0;32mstrigg[0m
[0;34mprofile : [0;32mstandard[0m
[0;34mconfigFiles : [0;32m[0m
[1mInput/output options[0m
[0;34minput : [0;32m/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/ids.csv[0m
[0;34mdownload_method : [0;32msratools[0m
[0;34moutdir : [0;32m/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_description: [0;32mUW Hyak Roberts labs cluster profile provided by nf-core/configs.[0m
[0;34mconfig_profile_contact : [0;32mShelly A. Wanamaker @shellywanamaker[0m
[0;34mconfig_profile_url : [0;32mhttps://faculty.washington.edu/sr320/[0m
[1mMax job request options[0m
[0;34mmax_cpus : [0;32m40[0m
[0;34mmax_memory : [0;32m742 GB[0m
[0;34mmax_time : [0;32m3d[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
If you use nf-core/fetchngs for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.5070524
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
-[2m----------------------------------------------------[0m-
Dec-03 09:24:14.525 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation
Dec-03 09:24:14.672 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/ids.csv' with '/mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/assets/schema_input.json'
Dec-03 09:24:14.725 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/ids.csv' with '/mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/assets/schema_input.json'
Dec-03 09:24:14.725 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation
Dec-03 09:24:14.932 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `error_retry` for process with name NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO
Dec-03 09:24:14.934 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SRA_IDS_TO_RUNINFO` matches process NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO
Dec-03 09:24:14.939 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Dec-03 09:24:14.939 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Dec-03 09:24:14.959 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm
Dec-03 09:24:14.963 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
Dec-03 09:24:14.964 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm)
Dec-03 09:24:14.979 [main] DEBUG n.processor.TaskPollingMonitor - Creating submit rate limit of 1 submissions per 1 seconds
Dec-03 09:24:15.007 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
Dec-03 09:24:15.071 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SRA_RUNINFO_TO_FTP` matches process NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP
Dec-03 09:24:15.074 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Dec-03 09:24:15.074 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Dec-03 09:24:15.111 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,error_retry` for process with name NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP
Dec-03 09:24:15.111 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_low,error_retry` for process with name NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP
Dec-03 09:24:15.132 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SRA_FASTQ_FTP` matches process NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP
Dec-03 09:24:15.136 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Dec-03 09:24:15.136 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Dec-03 09:24:15.171 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS
Dec-03 09:24:15.173 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Dec-03 09:24:15.173 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Dec-03 09:24:15.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH
Dec-03 09:24:15.185 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SRATOOLS_PREFETCH` matches process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH
Dec-03 09:24:15.194 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Dec-03 09:24:15.194 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Dec-03 09:24:15.202 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP
Dec-03 09:24:15.203 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SRATOOLS_FASTERQDUMP` matches process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP
Dec-03 09:24:15.204 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Dec-03 09:24:15.204 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Dec-03 09:24:15.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_FETCHNGS:SRA:ASPERA_CLI
Dec-03 09:24:15.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ASPERA_CLI` matches process NFCORE_FETCHNGS:SRA:ASPERA_CLI
Dec-03 09:24:15.238 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Dec-03 09:24:15.238 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Dec-03 09:24:15.312 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SRA_TO_SAMPLESHEET` matches process NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET
Dec-03 09:24:15.314 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Dec-03 09:24:15.314 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Dec-03 09:24:15.316 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Dec-03 09:24:15.321 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=1; memory=16 GB; capacity=1; pollInterval=100ms; dumpInterval=5m
Dec-03 09:24:15.322 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Dec-03 09:24:15.322 [main] DEBUG n.processor.TaskPollingMonitor - Creating submit rate limit of 1 submissions per 1 seconds
Dec-03 09:24:15.390 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_MAPPINGS_CONFIG` matches process NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG
Dec-03 09:24:15.391 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Dec-03 09:24:15.391 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Dec-03 09:24:15.420 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
Dec-03 09:24:15.440 [main] DEBUG nextflow.Session - Igniting dataflow network (14)
Dec-03 09:24:15.441 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO
Dec-03 09:24:15.441 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP
Dec-03 09:24:15.441 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP
Dec-03 09:24:15.441 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS
Dec-03 09:24:15.463 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH
Dec-03 09:24:15.463 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP
Dec-03 09:24:15.463 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:ASPERA_CLI
Dec-03 09:24:15.463 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET
Dec-03 09:24:15.463 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG
Dec-03 09:24:15.483 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_acdf5c75414b64a7: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../modules/local/multiqc_mappings_config/main.nf
Script_0b19867a805793b5: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/../../../modules/nf-core/custom/sratoolsncbisettings/main.nf
Script_ce0dbbb175f3fbb3: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf
Script_ecccbd2ace139150: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/main.nf
Script_021e0c2a2b0acb95: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/../../../modules/nf-core/sratools/fasterqdump/main.nf
Script_13a134c588d4965b: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main.nf
Script_2e98d68d92094a51: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../modules/local/aspera_cli/main.nf
Script_34a6e65ee7dbdbe0: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./subworkflows/local/utils_nfcore_fetchngs_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf
Script_a7d371fe23db7aab: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./subworkflows/local/utils_nfcore_fetchngs_pipeline/../../nf-core/utils_nfvalidation_plugin/main.nf
Script_be0adedc591c66cc: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./subworkflows/local/utils_nfcore_fetchngs_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf
Script_8e47246e1eaac81c: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../modules/local/sra_to_samplesheet/main.nf
Script_7fead60763b2b030: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../modules/local/sra_ids_to_runinfo/main.nf
Script_ba8dd5d95260fdf7: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/../../../modules/nf-core/sratools/prefetch/main.nf
Script_3c69d3862c8e77dc: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../modules/local/sra_fastq_ftp/main.nf
Script_907f29c748a0f2e5: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/main.nf
Script_a9ea706fbcc7c682: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/./workflows/sra/../../modules/local/sra_runinfo_to_ftp/main.nf
Dec-03 09:24:15.483 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Dec-03 09:24:15.483 [main] DEBUG nextflow.Session - Session await
Dec-03 09:24:15.589 [Actor Thread 4] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/python:3.9--1; path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-python-3.9--1.img
Dec-03 09:24:15.599 [Actor Thread 1] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/bin/sra_ids_to_runinfo.py
Dec-03 09:24:16.023 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR8856650) > jobId: 22689617; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/18/93da4d773342d11f93863f3ce1b935
Dec-03 09:24:16.024 [Task submitter] INFO nextflow.Session - [18/93da4d] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR8856650)
Dec-03 09:24:16.160 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR8856651) > jobId: 22689618; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/8a/a879edcb66a000131243d8ea16ab54
Dec-03 09:24:16.161 [Task submitter] INFO nextflow.Session - [8a/a879ed] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR8856651)
Dec-03 09:27:15.010 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689617; id: 1; name: NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR8856650); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/18/93da4d773342d11f93863f3ce1b935 started: 1733246830003; exited: 2024-12-03T17:27:13.269030383Z; ]
Dec-03 09:27:15.036 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Dec-03 09:27:15.105 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689618; id: 2; name: NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR8856651); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/8a/a879edcb66a000131243d8ea16ab54 started: 1733246830032; exited: 2024-12-03T17:27:13.271095151Z; ]
Dec-03 09:27:15.256 [Actor Thread 14] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/bin/sra_runinfo_to_ftp.py
Dec-03 09:27:15.553 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1) > jobId: 22689652; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/a0/05e3d550e30d915b32e83971a6e756
Dec-03 09:27:15.554 [Task submitter] INFO nextflow.Session - [a0/05e3d5] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)
Dec-03 09:27:15.724 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (2) > jobId: 22689653; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/f7/cdc285d2414a88284282a49fb3d812
Dec-03 09:27:15.728 [Task submitter] INFO nextflow.Session - [f7/cdc285] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (2)
Dec-03 09:28:10.017 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689653; id: 4; name: NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (2); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/f7/cdc285d2414a88284282a49fb3d812 started: 1733246890009; exited: 2024-12-03T17:28:09.367796562Z; ]
Dec-03 09:28:10.078 [TaskFinalizer-3] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Dec-03 09:28:15.036 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689652; id: 3; name: NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/a0/05e3d550e30d915b32e83971a6e756 started: 1733246895005; exited: 2024-12-03T17:28:13.335603272Z; ]
Dec-03 09:28:15.229 [Actor Thread 18] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/sra-tools:3.0.8--h9f5acd7_0; path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-sra-tools-3.0.8--h9f5acd7_0.img
Dec-03 09:28:15.400 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings) > jobId: 22689658; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/18/41ca2b09f09171c534b74720cc9d7c
Dec-03 09:28:15.401 [Task submitter] INFO nextflow.Session - [18/41ca2b] Submitted process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)
Dec-03 09:29:15.490 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > No more task to compute -- The following nodes are still active:
[process] NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) OPEN ; channel: ncbi_settings
port 2: (value) bound ; channel: certificate
port 3: (cntrl) - ; channel: $
[process] NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) OPEN ; channel: ncbi_settings
port 2: (value) bound ; channel: certificate
port 3: (cntrl) - ; channel: $
[process] NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET
status=ACTIVE
port 0: (queue) OPEN ; channel: meta
port 1: (value) bound ; channel: pipeline
port 2: (value) bound ; channel: strandedness
port 3: (value) bound ; channel: mapping_fields
port 4: (cntrl) - ; channel: $
[process] NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG
status=ACTIVE
port 0: (queue) OPEN ; channel: csv
port 1: (cntrl) - ; channel: $
Dec-03 09:29:20.001 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[jobId: 22689658; id: 5; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings); status: SUBMITTED; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/18/41ca2b09f09171c534b74720cc9d7c started: -; exited: -; ]
Dec-03 09:29:45.016 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689658; id: 5; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/18/41ca2b09f09171c534b74720cc9d7c started: 1733246985010; exited: 2024-12-03T17:29:44.420321318Z; ]
Dec-03 09:29:45.692 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR8856651) > jobId: 22689661; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/00/68c91a31c863163fe002c6975215b7
Dec-03 09:29:45.692 [Task submitter] INFO nextflow.Session - [00/68c91a] Submitted process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR8856651)
Dec-03 09:29:45.848 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR8856650) > jobId: 22689662; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/2d/cd759e199dcc953651ff5e0131a0f2
Dec-03 09:29:45.848 [Task submitter] INFO nextflow.Session - [2d/cd759e] Submitted process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR8856650)
Dec-03 09:33:25.015 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689662; id: 7; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR8856650); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/2d/cd759e199dcc953651ff5e0131a0f2 started: 1733247080013; exited: 2024-12-03T17:33:21.182860824Z; ]
Dec-03 09:33:25.100 [Actor Thread 17] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0; path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a-6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0.img
Dec-03 09:33:25.316 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX5644339_SRR8856650) > jobId: 22689670; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/17/9d377589c96e30e237974db3f58dc6
Dec-03 09:33:25.317 [Task submitter] INFO nextflow.Session - [17/9d3775] Submitted process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX5644339_SRR8856650)
Dec-03 09:34:15.556 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > No more task to compute -- The following nodes are still active:
[process] NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: ncbi_settings
port 2: (value) bound ; channel: certificate
port 3: (cntrl) - ; channel: $
[process] NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET
status=ACTIVE
port 0: (queue) OPEN ; channel: meta
port 1: (value) bound ; channel: pipeline
port 2: (value) bound ; channel: strandedness
port 3: (value) bound ; channel: mapping_fields
port 4: (cntrl) - ; channel: $
[process] NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG
status=ACTIVE
port 0: (queue) OPEN ; channel: csv
port 1: (cntrl) - ; channel: $
Dec-03 09:34:20.008 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[jobId: 22689661; id: 6; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR8856651); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/00/68c91a31c863163fe002c6975215b7 started: 1733247085012; exited: -; ]
~> TaskHandler[jobId: 22689670; id: 8; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX5644339_SRR8856650); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/17/9d377589c96e30e237974db3f58dc6 started: 1733247240013; exited: -; ]
Dec-03 09:36:50.053 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689670; id: 8; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX5644339_SRR8856650); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/17/9d377589c96e30e237974db3f58dc6 started: 1733247240013; exited: 2024-12-03T17:36:45.951445476Z; ]
Dec-03 09:36:50.179 [Task submitter] INFO nextflow.Session - [50/760d7d] Submitted process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX5644339_SRR8856650)
Dec-03 09:36:50.233 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX5644339_SRR8856650); status: COMPLETED; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/50/760d7d9f717f6f14e61686bc831d68]
Dec-03 09:37:15.053 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689661; id: 6; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR8856651); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/00/68c91a31c863163fe002c6975215b7 started: 1733247085012; exited: 2024-12-03T17:37:14.861537635Z; ]
Dec-03 09:37:15.306 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX5644338_SRR8856651) > jobId: 22689677; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/66/13bdfc037e2c60fb3add79fa413d39
Dec-03 09:37:15.307 [Task submitter] INFO nextflow.Session - [66/13bdfc] Submitted process > NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX5644338_SRR8856651)
Dec-03 09:39:15.586 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > No more task to compute -- The following nodes are still active:
[process] NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET
status=ACTIVE
port 0: (queue) OPEN ; channel: meta
port 1: (value) bound ; channel: pipeline
port 2: (value) bound ; channel: strandedness
port 3: (value) bound ; channel: mapping_fields
port 4: (cntrl) - ; channel: $
[process] NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG
status=ACTIVE
port 0: (queue) OPEN ; channel: csv
port 1: (cntrl) - ; channel: $
Dec-03 09:39:20.050 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[jobId: 22689677; id: 10; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX5644338_SRR8856651); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/66/13bdfc037e2c60fb3add79fa413d39 started: 1733247460055; exited: -; ]
Dec-03 09:40:45.061 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689677; id: 10; name: NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX5644338_SRR8856651); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/66/13bdfc037e2c60fb3add79fa413d39 started: 1733247460055; exited: 2024-12-03T17:40:43.347538956Z; ]
Dec-03 09:40:45.247 [Task submitter] INFO nextflow.Session - [93/2a7ee3] Submitted process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX5644338_SRR8856651)
Dec-03 09:40:45.303 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX5644338_SRR8856651); status: COMPLETED; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/93/2a7ee36b074f341d75cb8f939a0190]
Dec-03 09:40:45.346 [Actor Thread 34] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.008 s; external sort time: 0.002 s; total time: 0.01 s
Dec-03 09:40:45.346 [Actor Thread 35] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.001 s; external sort time: 0.001 s; total time: 0.002 s
Dec-03 09:40:45.383 [Actor Thread 34] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/collect-file/216a9c8563b882ea54cfc7da8d4296db
Dec-03 09:40:45.388 [Actor Thread 35] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/collect-file/f68aff03390f4cc5c762d43a476fa156
Dec-03 09:40:45.435 [Actor Thread 35] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /gscratch/scrubbed/strigg/bin/nxf-16439868557801153190
Dec-03 09:40:45.439 [Actor Thread 34] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /gscratch/scrubbed/strigg/bin/nxf-5377050120786790136
Dec-03 09:40:45.663 [Actor Thread 32] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.004 s; external sort time: 0.003 s; total time: 0.007 s
Dec-03 09:40:45.887 [Actor Thread 37] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.022 s; external sort time: 0.001 s; total time: 0.023 s
Dec-03 09:40:45.966 [Actor Thread 32] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/collect-file/0749ba8b32bbb36034f6728b7f69abc3
Dec-03 09:40:45.967 [Actor Thread 37] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/collect-file/ea6cc9db05edf898d3037c8717028d3c
Dec-03 09:40:45.970 [Actor Thread 36] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /mmfs1/gscratch/srlab/strigg/bin/assets/nf-core/fetchngs/bin/multiqc_mappings_config.py
Dec-03 09:40:46.016 [Actor Thread 37] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /gscratch/scrubbed/strigg/bin/nxf-17702090539189268034
Dec-03 09:40:46.024 [Actor Thread 32] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /gscratch/scrubbed/strigg/bin/nxf-17478602677182397163
Dec-03 09:40:47.227 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG (1) > jobId: 22689692; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/47/15e22a727a6f51e273261fb3e0e160
Dec-03 09:40:47.227 [Task submitter] INFO nextflow.Session - [47/15e22a] Submitted process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG (1)
Dec-03 09:42:30.068 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 22689692; id: 12; name: NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG (1); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/47/15e22a727a6f51e273261fb3e0e160 started: 1733247745063; exited: 2024-12-03T17:42:26.013598688Z; ]
Dec-03 09:42:30.128 [main] DEBUG nextflow.Session - Session await > all processes finished
Dec-03 09:42:30.157 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Dec-03 09:42:30.158 [Actor Thread 37] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 5; slices: 1; internal sort time: 0.006 s; external sort time: 0.001 s; total time: 0.007 s
Dec-03 09:42:30.162 [Actor Thread 37] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mmfs1/gscratch/scrubbed/strigg/analyses/20241203_FetchNGStest/work/collect-file/5845ca71cb3bdc423ebec94273f5941f
Dec-03 09:42:30.282 [Actor Thread 37] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /gscratch/scrubbed/strigg/bin/nxf-6414059020264382739
Dec-03 09:42:35.058 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop
Dec-03 09:42:35.059 [main] DEBUG nextflow.Session - Session await > all barriers passed
Dec-03 09:42:35.065 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Dec-03 09:42:35.066 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Dec-03 09:42:35.068 [main] INFO nextflow.Nextflow - -[0;35m[nf-core/fetchngs][0;32m Pipeline completed successfully[0m-
Dec-03 09:42:35.069 [main] WARN nextflow.Nextflow - =============================================================================
Please double-check the samplesheet that has been auto-created by the pipeline.
Public databases don't reliably hold information such as strandedness
information, controls etc
All of the sample metadata obtained from the ENA has been appended
as additional columns to help you manually curate the samplesheet before
running nf-core/other pipelines.
===================================================================================
Dec-03 09:42:35.072 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=12; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=50m 54s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=8; peakMemory=48 GB; ]
Dec-03 09:42:35.072 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Dec-03 09:42:35.075 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Dec-03 09:42:35.721 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Dec-03 09:42:36.038 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Dec-03 09:42:36.141 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-validation@1.1.3'
Dec-03 09:42:36.141 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation
Dec-03 09:42:36.142 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Dec-03 09:42:36.142 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye