oct-04 13:40:05.149 [main] DEBUG nextflow.cli.Launcher - $> nextflow run replikation/poreCov -profile local,docker -r 1.8.3 --fastq '/Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/catted_files/*.fastq.gz' --primerV V1200 --output /Users/agaliana/artic-ncov2019_poreCoV/CORONA_230928_NUEVO --cores 16 --memory 180 --update --rapid --medaka_model r1041_e82_400bps_fast_g632 --samples /Users/agaliana/artic-ncov2019_poreCoV/CORONA_230928_NUEVO/148_sec_pend.txt oct-04 13:40:05.218 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.3 oct-04 13:40:05.239 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/agaliana/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.4 oct-04 13:40:05.248 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] oct-04 13:40:05.249 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] oct-04 13:40:05.251 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode oct-04 13:40:05.259 [main] INFO org.pf4j.AbstractPluginManager - No plugins oct-04 13:40:05.275 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /Users/agaliana/.nextflow/scm oct-04 13:40:06.067 [main] DEBUG nextflow.scm.AssetManager - Git config: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/config; branch: master; remote: origin; url: https://github.com/replikation/poreCov.git oct-04 13:40:06.085 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] oct-04 13:40:06.092 [main] DEBUG nextflow.scm.AssetManager - Git config: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/config; branch: master; remote: origin; url: https://github.com/replikation/poreCov.git oct-04 13:40:07.007 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/agaliana/.nextflow/assets/replikation/poreCov/nextflow.config oct-04 13:40:07.008 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/agaliana/.nextflow/assets/replikation/poreCov/nextflow.config oct-04 13:40:07.016 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `local,docker` oct-04 13:40:07.238 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [test_fastq, test_fasta, slurm, ukj_cloud, nanozoo, test_fast5, stub, singularity, local, docker] oct-04 13:40:07.263 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion oct-04 13:40:07.264 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/replikation/poreCov` [crazy_miescher] DSL2 - revision: b86c57c384 [1.8.3] oct-04 13:40:07.264 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] oct-04 13:40:07.264 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] oct-04 13:40:07.267 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /Users/agaliana/.nextflow/secrets/store.json oct-04 13:40:07.269 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@c2df90e] - activable => nextflow.secret.LocalSecretsProvider@c2df90e oct-04 13:40:07.330 [main] DEBUG nextflow.Session - Session UUID: 7be3cfe0-fb3e-4804-90ec-73dc610afaf8 oct-04 13:40:07.330 [main] DEBUG nextflow.Session - Run name: crazy_miescher oct-04 13:40:07.330 [main] DEBUG nextflow.Session - Executor pool size: 32 oct-04 13:40:07.341 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false oct-04 13:40:07.503 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.3 build 5875 Created: 11-08-2023 18:37 UTC (20:37 CEST) System: Mac OS X 13.0.1 Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.8+7-LTS Encoding: UTF-8 (UTF-8) Process: 15252@Colossus.local [127.0.0.1] CPUs: 32 - Mem: 192 GB (30.3 MB) - Swap: 0 (0) oct-04 13:40:07.517 [main] DEBUG nextflow.Session - Work-dir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana [Mac OS X] oct-04 13:40:07.534 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] oct-04 13:40:07.543 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory oct-04 13:40:07.609 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory oct-04 13:40:07.619 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000 oct-04 13:40:07.685 [main] DEBUG nextflow.Session - Session start oct-04 13:40:08.572 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution oct-04 13:40:08.580 [main] INFO nextflow.Nextflow - ________________________________________________________________________________ poreCov | A Nextflow SARS-CoV-2 workflow for nanopore data oct-04 13:40:09.171 [main] INFO nextflow.script.BaseScript - oct-04 13:40:09.171 [main] INFO nextflow.script.BaseScript - Latest available poreCov release: 1.9.1 oct-04 13:40:09.171 [main] INFO nextflow.script.BaseScript - If neccessary update via: nextflow pull replikation/poreCov oct-04 13:40:09.171 [main] INFO nextflow.script.BaseScript - ________________________________________________________________________________ oct-04 13:40:09.172 [main] INFO nextflow.script.BaseScript -  Using 16/32 CPU threads per process for a local run [--max_cores] oct-04 13:40:09.172 [main] INFO nextflow.script.BaseScript - oct-04 13:40:09.689 [main] INFO nextflow.script.BaseScript - Warning: Running --update might not be poreCov compatible! oct-04 13:40:10.102 [main] INFO nextflow.script.BaseScript - Found latest pangolin container, using: nanozoo/pangolin-v4:4.3--1.22  oct-04 13:40:10.250 [main] INFO nextflow.script.BaseScript - Found latest nextclade2 container, using: nanozoo/nextclade2:2.14.0--2023-09-21  oct-04 13:40:10.252 [main] INFO nextflow.Nextflow - . Profile: local,docker Current User: agaliana Nextflow-version: 23.04.3 poreCov-version: 1.8.3  Pathing: Workdir location [-work-Dir]: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana Output dir [--output]: /Users/agaliana/artic-ncov2019_poreCoV/CORONA_230928_NUEVO Databases location [--databases]: databases Singularity cache dir [--cachedir]: singularity_images ______________________________________ Parameters: Medaka model: r1041_e82_400bps_fast_g632 [--medaka_model] Min depth nucleotide: 20 [--min_depth] Latest Pangolin/Nextclade?: true [--update] CPUs to use: 16 [--cores] Memory in GB: 180 [--memory] ______________________________________ oct-04 13:40:10.254 [main] INFO nextflow.Nextflow - Primerscheme: V1200 [--primerV] Min read-length set to: 400 [--minLength] Max read-length set to: 1500 [--maxLength] ______________________________________ oct-04 13:40:10.255 [main] INFO nextflow.Nextflow - RKI output for german DESH upload: Output stored at: /Users/agaliana/artic-ncov2019_poreCoV/CORONA_230928_NUEVO/4.RKI-summary Min Identity to NC_045512.2: 0.90 [--seq_threshold] Min Depth used: 20 [--min_depth] Min Depth should be 20 or more for RKI upload Proportion cutoff N: 0.05 [--n_threshold] ______________________________________ oct-04 13:40:12.132 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nanoplot` matches labels `nanoplot` for process with name read_qc_wf:nanoplot oct-04 13:40:12.136 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.136 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.140 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local oct-04 13:40:12.144 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=180 B; capacity=32; pollInterval=100ms; dumpInterval=5m oct-04 13:40:12.192 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:ubuntu` matches labels `ubuntu` for process with name filter_fastq_by_length oct-04 13:40:12.193 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.193 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.198 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:ubuntu` matches labels `ubuntu` for process with name read_classification_wf:download_database_kraken2 oct-04 13:40:12.199 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.199 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.202 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:kraken2` matches labels `kraken2` for process with name read_classification_wf:kraken2 oct-04 13:40:12.203 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.203 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.207 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:krona` matches labels `krona` for process with name read_classification_wf:krona oct-04 13:40:12.208 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.208 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.228 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:artic` matches labels `artic` for process with name artic_ncov_wf:artic_medaka oct-04 13:40:12.229 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.229 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.234 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:covarplot` matches labels `covarplot` for process with name artic_ncov_wf:covarplot oct-04 13:40:12.235 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.235 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.241 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:pangolin` matches labels `pangolin` for process with name determine_lineage_wf:pangolin oct-04 13:40:12.241 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.241 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.248 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:nextclade` matches labels `nextclade` for process with name determine_mutations_wf:nextclade oct-04 13:40:12.249 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.249 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.254 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:president` matches labels `president` for process with name genome_quality_wf:president oct-04 13:40:12.254 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.255 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.259 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:seqrs` matches labels `seqrs` for process with name genome_quality_wf:seqrs oct-04 13:40:12.260 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.260 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.269 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:ubuntu` matches labels `ubuntu` for process with name rki_report_wf:rki_report oct-04 13:40:12.269 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.269 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.285 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fastcov` matches labels `fastcov` for process with name create_json_entries_wf:json_report oct-04 13:40:12.286 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.286 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.290 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:minimap2` matches labels `minimap2` for process with name align_to_reference oct-04 13:40:12.290 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.290 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.293 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.293 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.320 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fastcov` matches labels `fastcov` for process with name create_summary_report_wf:plot_coverages oct-04 13:40:12.321 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.321 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.326 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:fastcov` matches labels `fastcov` for process with name create_summary_report_wf:summary_report oct-04 13:40:12.327 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local oct-04 13:40:12.327 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' oct-04 13:40:12.329 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: krona, get_variants_classification, summary_report_default, plot_coverages, summary_report, guppy_cpu, nanoplot, artic_medaka_custom_bed, guppy_gpu, read_classification_wf:kraken2, covarplot, summary_report_fasta, lcs_ucsc_markers_table, get_fast5, filter_fastq_by_length, genome_quality_wf:president, artic_medaka, artic_ncov_wf:covarplot, rki_report_wf:rki_report, json_report, collect_fastq, covarplot_custom_bed, get_nanopore_fastq, read_qc_wf:nanoplot, align_to_reference, artic_nanopolish, rki_report_extended, get_fasta, genome_quality_wf:seqrs, create_json_entries_wf:json_report, nextclade, lcs_plot, download_database_kraken2, artic_ncov_wf:artic_medaka, seqrs, rki_report, determine_mutations_wf:nextclade, lcs_sc2, create_summary_report_wf:get_variants_classification, read_classification_wf:download_database_kraken2, pycoqc, split_fasta, kraken2, read_classification_wf:krona, pangolin, artic_nanopolish_custom_bed, determine_lineage_wf:pangolin, create_summary_report_wf:summary_report, president, create_summary_report_wf:plot_coverages oct-04 13:40:12.330 [main] DEBUG nextflow.Session - Igniting dataflow network (30) oct-04 13:40:12.334 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > read_qc_wf:nanoplot oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > filter_fastq_by_length oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > read_classification_wf:download_database_kraken2 oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > read_classification_wf:kraken2 oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > read_classification_wf:krona oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > artic_ncov_wf:artic_medaka oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > artic_ncov_wf:covarplot oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > determine_lineage_wf:pangolin oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > determine_mutations_wf:nextclade oct-04 13:40:12.335 [PathVisitor-4] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/catted_files/; pattern: *.fastq.gz; options: [checkIfExists:true] oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > genome_quality_wf:president oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > genome_quality_wf:seqrs oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > rki_report_wf:rki_report oct-04 13:40:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > create_json_entries_wf:json_report oct-04 13:40:12.336 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > align_to_reference oct-04 13:40:12.336 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > create_summary_report_wf:get_variants_classification oct-04 13:40:12.336 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > create_summary_report_wf:plot_coverages oct-04 13:40:12.336 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > create_summary_report_wf:summary_report oct-04 13:40:12.336 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination oct-04 13:40:12.336 [main] DEBUG nextflow.Session - Session await oct-04 13:40:12.373 [Actor Thread 22] INFO nextflow.processor.TaskProcessor - [skipping] Stored process > read_classification_wf:download_database_kraken2 oct-04 13:40:12.409 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/LICENSE oct-04 13:40:12.413 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/summary_report.py oct-04 13:40:12.414 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/split.sh oct-04 13:40:12.415 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/create_references.sh oct-04 13:40:12.415 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/rki_report_parser_extended.sh oct-04 13:40:12.415 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/rki_report_parser.sh oct-04 13:40:12.415 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/split_fasta.py oct-04 13:40:12.416 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/mask_alignment.py oct-04 13:40:12.416 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/render_tree_circle.py oct-04 13:40:12.416 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/genome_integrity.sh oct-04 13:40:12.416 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/coverage_plot.R oct-04 13:40:12.416 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/render_tree.py oct-04 13:40:12.417 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/lcs_bar_plot.R oct-04 13:40:12.417 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/bin/json_parser.py oct-04 13:40:12.418 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/CITATION.cff oct-04 13:40:12.418 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/collect_fastq.nf oct-04 13:40:12.418 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/provide_rki.nf oct-04 13:40:12.418 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/read_qc.nf oct-04 13:40:12.418 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/genome_quality.nf oct-04 13:40:12.419 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/create_summary_report.nf oct-04 13:40:12.419 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/determine_lineage.nf oct-04 13:40:12.419 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/create_json_entries.nf oct-04 13:40:12.419 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/basecalling.nf oct-04 13:40:12.419 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/read_classification.nf oct-04 13:40:12.419 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/determine_mutations.nf oct-04 13:40:12.419 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/artic_nanopore_nCov19.nf oct-04 13:40:12.420 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/kraken2.nf oct-04 13:40:12.420 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/summary_report.nf oct-04 13:40:12.420 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/quality_genome_filter.nf oct-04 13:40:12.420 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/guppy.nf oct-04 13:40:12.421 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/nanoplot.nf oct-04 13:40:12.421 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/collect_fastq.nf oct-04 13:40:12.421 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/rki_report.nf oct-04 13:40:12.421 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/lcs_sc2.nf oct-04 13:40:12.421 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/president.nf oct-04 13:40:12.421 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/pycoqc.nf oct-04 13:40:12.421 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/nextclade.nf oct-04 13:40:12.422 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/artic.nf oct-04 13:40:12.422 [Actor Thread 13] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.01 s; total time: 0.011 s oct-04 13:40:12.422 [Actor Thread 11] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.01 s; total time: 0.011 s oct-04 13:40:12.422 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/json_report.nf oct-04 13:40:12.422 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/download_database_kraken2.nf oct-04 13:40:12.422 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/krona.nf oct-04 13:40:12.422 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/pangolin.nf oct-04 13:40:12.422 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/seqrs.nf oct-04 13:40:12.423 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/workflows/process/covarplot.nf oct-04 13:40:12.423 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/README.md oct-04 13:40:12.423 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/nextflow.config oct-04 13:40:12.423 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.gitignore oct-04 13:40:12.424 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/configs/container.config oct-04 13:40:12.424 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/configs/local.config oct-04 13:40:12.424 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/configs/nodes.config oct-04 13:40:12.424 [Actor Thread 11] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/collect-file/d09d21c5a4d1842c58bc37832c10d2fe oct-04 13:40:12.424 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/collect-file/18e6a0f4978b62d15c0e0130df90b6ef oct-04 13:40:12.424 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.github/workflows/DryRun.yml oct-04 13:40:12.425 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.github/ISSUE_TEMPLATE/error-or-bug-report.md oct-04 13:40:12.425 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.github/ISSUE_TEMPLATE/feature_request.md oct-04 13:40:12.425 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.gitattributes oct-04 13:40:12.425 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/poreCov.nf oct-04 13:40:12.426 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/config oct-04 13:40:12.426 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/objects/pack/pack-95ae801a10513f60ff45505e0841c8d4287c1944.idx oct-04 13:40:12.427 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/objects/pack/pack-95ae801a10513f60ff45505e0841c8d4287c1944.pack oct-04 13:40:12.431 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /var/folders/sy/4mzmjcq17txbv3vnznqk2v5c0000gn/T/nxf-11968787828233620608 oct-04 13:40:12.431 [Actor Thread 11] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /var/folders/sy/4mzmjcq17txbv3vnznqk2v5c0000gn/T/nxf-8848473078206627222 oct-04 13:40:12.446 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run oct-04 13:40:12.448 [Task submitter] INFO nextflow.Session - [b6/16d7b1] Submitted process > read_qc_wf:nanoplot (1) oct-04 13:40:12.454 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run oct-04 13:40:12.455 [Task submitter] INFO nextflow.Session - [d6/38d4f4] Submitted process > filter_fastq_by_length (1) oct-04 13:40:12.519 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/HEAD oct-04 13:40:12.520 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/HEAD oct-04 13:40:12.520 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/heads/master oct-04 13:40:12.520 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/README-update-published oct-04 13:40:12.521 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/hpc-guppy oct-04 13:40:12.521 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/dev_replikation oct-04 13:40:12.521 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/fix_nanopolish oct-04 13:40:12.522 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/nextclade_docker_update oct-04 13:40:12.522 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/slurm oct-04 13:40:12.522 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/up-medaka oct-04 13:40:12.522 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/fix_spaces_in_V4_1_primers oct-04 13:40:12.523 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/guppy oct-04 13:40:12.523 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/trimbam oct-04 13:40:12.523 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/bam oct-04 13:40:12.523 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/covarplot oct-04 13:40:12.524 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/AWSGCP oct-04 13:40:12.524 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/update_medaka oct-04 13:40:12.524 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/feature_param-artic-normalize oct-04 13:40:12.525 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/master oct-04 13:40:12.525 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/primer_help_update oct-04 13:40:12.525 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/pangolin_update oct-04 13:40:12.525 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/singularity oct-04 13:40:12.526 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/mutation_position_scan oct-04 13:40:12.526 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/update-medaka-in-artic oct-04 13:40:12.526 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/clean-up-unpacked-kraken2-db oct-04 13:40:12.527 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/mixed-samples oct-04 13:40:12.527 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/primer_bed_check oct-04 13:40:12.527 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/feature_more-N-info oct-04 13:40:12.527 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/MarieLataretu/issue238 oct-04 13:40:12.528 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/MarieLataretu/issue245 oct-04 13:40:12.528 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/MarieLataretu/issue256 oct-04 13:40:12.528 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/MarieLataretu/issue232 oct-04 13:40:12.528 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/rki_report_parser oct-04 13:40:12.529 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/up_pangolin oct-04 13:40:12.529 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/V1200_read_length oct-04 13:40:12.529 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/update_president oct-04 13:40:12.529 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/fix_nextclade_insertion_offset oct-04 13:40:12.529 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/fix134 oct-04 13:40:12.530 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/split_fasta_improvement oct-04 13:40:12.530 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/new_primervers oct-04 13:40:12.530 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/dev_martin oct-04 13:40:12.530 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/medaka_all_models oct-04 13:40:12.531 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/release1.5 oct-04 13:40:12.531 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/logs/refs/remotes/origin/auto_pangolin oct-04 13:40:12.531 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/refs/heads/master oct-04 13:40:12.532 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/index oct-04 13:40:12.532 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/packed-refs oct-04 13:40:12.533 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/.git/FETCH_HEAD oct-04 13:40:12.533 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/unused_modules/split_reference.nf oct-04 13:40:12.534 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/unused_modules/fasttree.nf oct-04 13:40:12.534 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/unused_modules/coverage_plot.nf oct-04 13:40:12.534 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/unused_modules/bwa_samtools.nf oct-04 13:40:12.535 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/unused_modules/snp_sites.nf oct-04 13:40:12.535 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/unused_modules/cat_fastq.nf oct-04 13:40:12.535 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/unused_modules/mafft.nf oct-04 13:40:12.535 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/unused_modules/treetime.nf oct-04 13:40:12.535 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/split_fasta.nf oct-04 13:40:12.536 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/get_fasta_test_data.nf oct-04 13:40:12.536 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/get_variants_classification.nf oct-04 13:40:12.536 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/filter_fastq_by_length.nf oct-04 13:40:12.536 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/get_fast5_test_data.nf oct-04 13:40:12.536 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/get_fastq_test_data.nf oct-04 13:40:12.536 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/align_to_reference.nf oct-04 13:40:12.536 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/modules/plot_coverages.nf oct-04 13:40:12.537 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/reference_nCov19/NC_045512.2.fasta.fai oct-04 13:40:12.537 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/reference_nCov19/NC_045512.2.fasta oct-04 13:40:12.538 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/reference_nCov19/MN908947.gb oct-04 13:40:12.538 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/variants_SARSCoV2/SARSCoV2_variants_fallback_2022-02-03--10-34-08.csv oct-04 13:40:12.539 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/variants_SARSCoV2/README.md oct-04 13:40:12.539 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/logo/mobile_logo.png oct-04 13:40:12.540 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/figures/index.html oct-04 13:40:12.547 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/figures/report_summary.png oct-04 13:40:12.549 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/figures/workflow.png oct-04 13:40:12.551 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1/nCoV-2019.bed oct-04 13:40:12.552 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1/nCoV-2019.reference.fasta.fai oct-04 13:40:12.552 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1/nCoV-2019.reference.fasta oct-04 13:40:12.553 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1/nCoV-2019.scheme.bed oct-04 13:40:12.553 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1/nCoV-2019.tsv oct-04 13:40:12.553 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1/nCoV-2019.insert.bed oct-04 13:40:12.553 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1/nCoV-2019.primer.bed oct-04 13:40:12.554 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV1a/nCoV-2019.reference.fasta.fai oct-04 13:40:12.554 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV1a/nCoV-2019.reference.fasta oct-04 13:40:12.555 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV1a/nCoV-2019.scheme.bed oct-04 13:40:12.555 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV1a/Readme.md oct-04 13:40:12.556 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.1/nCoV-2019.reference.fasta.fai oct-04 13:40:12.556 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.1/nCoV-2019.reference.fasta oct-04 13:40:12.557 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.1/nCoV-2019.scheme.bed oct-04 13:40:12.557 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.1/README.md oct-04 13:40:12.557 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.1/nCoV-2019.primer.bed oct-04 13:40:12.558 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V_custom/nCoV-2019.reference.fasta.fai oct-04 13:40:12.558 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V_custom/nCoV-2019.reference.fasta oct-04 13:40:12.558 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V_custom/Readme.md oct-04 13:40:12.559 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V2/nCoV-2019.bed oct-04 13:40:12.559 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta.fai oct-04 13:40:12.559 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta oct-04 13:40:12.560 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V2/nCoV-2019.scheme.bed oct-04 13:40:12.561 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V2/nCoV-2019.tsv oct-04 13:40:12.561 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V2/nCoV-2019.insert.bed oct-04 13:40:12.561 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V2/nCoV-2019.primer.bed oct-04 13:40:12.562 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5/nCoV-2019.reference.fasta.fai oct-04 13:40:12.562 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5/nCoV-2019.reference.fasta oct-04 13:40:12.563 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5/nCoV-2019.scheme.bed oct-04 13:40:12.563 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5/README.md oct-04 13:40:12.563 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5/nCoV-2019.primer.bed oct-04 13:40:12.564 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1200/nCoV-2019.bed oct-04 13:40:12.564 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta.fai oct-04 13:40:12.564 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta oct-04 13:40:12.564 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed oct-04 13:40:12.565 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1200/nCoV-2019.tsv oct-04 13:40:12.565 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V1200/Readme.md oct-04 13:40:12.565 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2b/nCoV-2019.reference.fasta.fai oct-04 13:40:12.566 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2b/nCoV-2019.reference.fasta oct-04 13:40:12.566 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2b/nCoV-2019.scheme.bed oct-04 13:40:12.566 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2b/nCoV-2019.tsv oct-04 13:40:12.567 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2b/Readme.md oct-04 13:40:12.567 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4/nCoV-2019.reference.fasta.fai oct-04 13:40:12.567 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4/nCoV-2019.reference.fasta oct-04 13:40:12.568 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4/nCoV-2019.scheme.bed oct-04 13:40:12.568 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4/Readme.me oct-04 13:40:12.568 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4/nCoV-2019.insert.bed oct-04 13:40:12.569 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4/nCoV-2019.design.fasta oct-04 13:40:12.570 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4/nCoV-2019.primer.bed oct-04 13:40:12.571 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.bed oct-04 13:40:12.571 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta.fai oct-04 13:40:12.571 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta oct-04 13:40:12.572 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.scheme.bed oct-04 13:40:12.572 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.tsv oct-04 13:40:12.572 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.insert.bed oct-04 13:40:12.573 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed oct-04 13:40:12.573 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2/nCoV-2019.reference.fasta.fai oct-04 13:40:12.573 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2/nCoV-2019.reference.fasta oct-04 13:40:12.574 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2/nCoV-2019.scheme.bed oct-04 13:40:12.574 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2/nCoV-2019.tsv oct-04 13:40:12.575 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/VarSkipV2/Readme.md oct-04 13:40:12.575 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4.1/nCoV-2019.reference.fasta.fai oct-04 13:40:12.575 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4.1/nCoV-2019.reference.fasta oct-04 13:40:12.576 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4.1/nCoV-2019.scheme.bed oct-04 13:40:12.576 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4.1/README.md oct-04 13:40:12.576 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V4.1/nCoV-2019.primer.bed oct-04 13:40:12.577 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.3.2_400/nCoV-2019.reference.fasta.fai oct-04 13:40:12.577 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.3.2_400/nCoV-2019.reference.fasta oct-04 13:40:12.577 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.3.2_400/nCoV-2019.scheme.bed oct-04 13:40:12.578 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.3.2_400/README.md oct-04 13:40:12.578 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/nCoV-2019/V5.3.2_400/nCoV-2019.primer.bed oct-04 13:40:12.578 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/external_primer_schemes/Readme.md oct-04 13:40:12.579 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/rki_report/Readme.md oct-04 13:40:12.579 [Actor Thread 28] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /Users/agaliana/.nextflow/assets/replikation/poreCov/data/rki_report/Readme.pdf oct-04 13:40:12.585 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run oct-04 13:40:12.586 [Task submitter] INFO nextflow.Session - [3c/532340] Submitted process > create_summary_report_wf:get_variants_classification oct-04 13:40:14.736 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: create_summary_report_wf:get_variants_classification; status: COMPLETED; exit: 0; error: -; workDir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/3c/532340610649ce4abe63a28e88324d] oct-04 13:40:14.747 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false oct-04 13:40:15.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: filter_fastq_by_length (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/d6/38d4f426a7db0baf6ca6f576524537] oct-04 13:40:15.069 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run oct-04 13:40:15.070 [Task submitter] INFO nextflow.Session - [fa/4629b3] Submitted process > read_classification_wf:kraken2 (1) oct-04 13:40:30.029 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: read_qc_wf:nanoplot (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/b6/16d7b141228ad1118b011c703be484] oct-04 13:40:30.033 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run oct-04 13:40:30.034 [Task submitter] INFO nextflow.Session - [db/20aae1] Submitted process > align_to_reference (1) oct-04 13:40:32.003 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: align_to_reference (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/db/20aae1926ea012c4f3b15ac37bd29d] oct-04 13:40:32.008 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run oct-04 13:40:32.008 [Task submitter] INFO nextflow.Session - [26/6c36bd] Submitted process > artic_ncov_wf:artic_medaka (1) oct-04 13:41:42.060 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: artic_ncov_wf:artic_medaka (1); status: COMPLETED; exit: 4; error: -; workDir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/26/6c36bd465ccb708ebed5e778c4cde4] oct-04 13:41:42.063 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=artic_ncov_wf:artic_medaka (1); work-dir=/Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/26/6c36bd465ccb708ebed5e778c4cde4 error [nextflow.exception.ProcessFailedException]: Process `artic_ncov_wf:artic_medaka (1)` terminated with an error exit status (4) oct-04 13:41:42.065 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run oct-04 13:41:42.065 [Task monitor] INFO nextflow.processor.TaskProcessor - [26/6c36bd] NOTE: Process `artic_ncov_wf:artic_medaka (1)` terminated with an error exit status (4) -- Error is ignored oct-04 13:41:42.066 [Task submitter] INFO nextflow.Session - [f6/6b3d50] Submitted process > create_summary_report_wf:plot_coverages (1) oct-04 13:41:42.066 [Actor Thread 31] INFO nextflow.Nextflow - Could not generate any genomes, please check your reads /Users/agaliana/artic-ncov2019_poreCoV/CORONA_230928_NUEVO/1.Read_quality oct-04 13:41:42.066 [Actor Thread 22] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null oct-04 13:41:42.066 [Actor Thread 14] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null oct-04 13:41:42.066 [Actor Thread 30] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null oct-04 13:41:42.066 [Actor Thread 1] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null oct-04 13:41:42.066 [Actor Thread 26] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null oct-04 13:41:42.066 [Actor Thread 3] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null oct-04 13:41:42.066 [Actor Thread 16] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null oct-04 13:41:42.067 [Actor Thread 34] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null oct-04 13:41:52.506 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: create_summary_report_wf:plot_coverages (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/f6/6b3d50009921e7df0b5710aa4f609a] oct-04 13:44:09.404 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: read_classification_wf:kraken2 (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/fa/4629b3ac0ef8ef5e6d3046336c5b53] oct-04 13:44:09.416 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run oct-04 13:44:09.416 [Task submitter] INFO nextflow.Session - [b2/194e57] Submitted process > read_classification_wf:krona (1) oct-04 13:44:13.387 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: read_classification_wf:krona (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass_test/work/nextflow-poreCov-agaliana/b2/194e57b947e14a7e42e255eb5e44a4] oct-04 13:44:13.389 [main] DEBUG nextflow.Session - Session await > all processes finished oct-04 13:44:13.391 [main] DEBUG nextflow.Session - Session await > all barriers passed oct-04 13:44:13.395 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) oct-04 13:44:13.400 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=7; failedCount=1; ignoredCount=1; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=1h 9m 26s; failedDuration=18m 39s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=32; peakMemory=0; ] oct-04 13:44:13.400 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report oct-04 13:44:13.451 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":{"mean":3.9,"min":3.9,"q1":3.9,"q2":3.9,"q3":3.9,"max":3.9,"minLabel":"create_summary_report_wf:get_variants_classification","maxLabel":"create_summary_report_wf:get_variants_classification","q1Label":"create_summary_report_wf:get_variants_classification","q2Label":"create_summary_report_wf:get_variants_classification","q3Label":"create_summary_report_wf:get_variants_classification"},"process":"get_variants_classification","mem":{"mean":6758400,"min":6758400,"q1":6758400,"q2":6758400,"q3":6758400,"max":6758400,"minLabel":"create_summary_report_wf:get_variants_classification","maxLabel":"create_summary_report_wf:get_variants_classification","q1Label":"create_summary_report_wf:get_variants_classification","q2Label":"create_summary_report_wf:get_variants_classification","q3Label":"create_summary_report_wf:get_variants_classification"},"memUsage":null,"timeUsage":null,"vmem":{"mean":21241856,"min":21241856,"q1":21241856,"q2":21241856,"q3":21241856,"max":21241856,"minLabel":"create_summary_report_wf:get_variants_classification","maxLabel":"create_summary_report_wf:get_variants_classification","q1Label":"create_summary_report_wf:get_variants_classification","q2Label":"create_summary_report_wf:get_variants_classification","q3Label":"create_summary_report_wf:get_variants_classification"},"reads":{"mean":269852,"min":269852,"q1":269852,"q2":269852,"q3":269852,"max":269852,"minLabel":"create_summary_report_wf:get_variants_classification","maxLabel":"create_summary_report_wf:get_variants_classification","q1Label":"create_summary_report_wf:get_variants_classification","q2Label":"create_summary_report_wf:get_variants_classification","q3Label":"create_summary_report_wf:get_variants_classification"},"cpu":{"mean":3.9,"min":3.9,"q1":3.9,"q2":3.9,"q3":3.9,"max":3.9,"minLabel":"create_summary_report_wf:get_variants_classification","maxLabel":"create_summary_report_wf:get_variants_classification","q1Label":"create_summary_report_wf:get_variants_classification","q2Label":"create_summary_report_wf:get_variants_classification","q3Label":"create_summary_report_wf:get_variants_classification"},"time":{"mean":1030,"min":1030,"q1":1030,"q2":1030,"q3":1030,"max":1030,"minLabel":"create_summary_report_wf:get_variants_classification","maxLabel":"create_summary_report_wf:get_variants_classification","q1Label":"create_summary_report_wf:get_variants_classification","q2Label":"create_summary_report_wf:get_variants_classification","q3Label":"create_summary_report_wf:get_variants_classification"},"writes":{"mean":94385,"min":94385,"q1":94385,"q2":94385,"q3":94385,"max":94385,"minLabel":"create_summary_report_wf:get_variants_classification","maxLabel":"create_summary_report_wf:get_variants_classification","q1Label":"create_summary_report_wf:get_variants_classification","q2Label":"create_summary_report_wf:get_variants_classification","q3Label":"create_summary_report_wf:get_variants_classification"}},{"cpuUsage":{"mean":125.9,"min":125.9,"q1":125.9,"q2":125.9,"q3":125.9,"max":125.9,"minLabel":"filter_fastq_by_length (1)","maxLabel":"filter_fastq_by_length (1)","q1Label":"filter_fastq_by_length (1)","q2Label":"filter_fastq_by_length (1)","q3Label":"filter_fastq_by_length (1)"},"process":"filter_fastq_by_length","mem":{"mean":12165120,"min":12165120,"q1":12165120,"q2":12165120,"q3":12165120,"max":12165120,"minLabel":"filter_fastq_by_length (1)","maxLabel":"filter_fastq_by_length (1)","q1Label":"filter_fastq_by_length (1)","q2Label":"filter_fastq_by_length (1)","q3Label":"filter_fastq_by_length (1)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":30760960,"min":30760960,"q1":30760960,"q2":30760960,"q3":30760960,"max":30760960,"minLabel":"filter_fastq_by_length (1)","maxLabel":"filter_fastq_by_length (1)","q1Label":"filter_fastq_by_length (1)","q2Label":"filter_fastq_by_length (1)","q3Label":"filter_fastq_by_length (1)"},"reads":{"mean":108138350,"min":108138350,"q1":108138350,"q2":108138350,"q3":108138350,"max":108138350,"minLabel":"filter_fastq_by_length (1)","maxLabel":"filter_fastq_by_length (1)","q1Label":"filter_fastq_by_length (1)","q2Label":"filter_fastq_by_length (1)","q3Label":"filter_fastq_by_length (1)"},"cpu":{"mean":125.9,"min":125.9,"q1":125.9,"q2":125.9,"q3":125.9,"max":125.9,"minLabel":"filter_fastq_by_length (1)","maxLabel":"filter_fastq_by_length (1)","q1Label":"filter_fastq_by_length (1)","q2Label":"filter_fastq_by_length (1)","q3Label":"filter_fastq_by_length (1)"},"time":{"mean":1363,"min":1363,"q1":1363,"q2":1363,"q3":1363,"max":1363,"minLabel":"filter_fastq_by_length (1)","maxLabel":"filter_fastq_by_length (1)","q1Label":"filter_fastq_by_length (1)","q2Label":"filter_fastq_by_length (1)","q3Label":"filter_fastq_by_length (1)"},"writes":{"mean":104824798,"min":104824798,"q1":104824798,"q2":104824798,"q3":104824798,"max":104824798,"minLabel":"filter_fastq_by_length (1)","maxLabel":"filter_fastq_by_length (1)","q1Label":"filter_fastq_by_length (1)","q2Label":"filter_fastq_by_length (1)","q3Label":"filter_fastq_by_length (1)"}},{"cpuUsage":{"mean":9.88,"min":9.88,"q1":9.88,"q2":9.88,"q3":9.88,"max":9.88,"minLabel":"read_qc_wf:nanoplot (1)","maxLabel":"read_qc_wf:nanoplot (1)","q1Label":"read_qc_wf:nanoplot (1)","q2Label":"read_qc_wf:nanoplot (1)","q3Label":"read_qc_wf:nanoplot (1)"},"process":"nanoplot","mem":{"mean":205627392,"min":205627392,"q1":205627392,"q2":205627392,"q3":205627392,"max":205627392,"minLabel":"read_qc_wf:nanoplot (1)","maxLabel":"read_qc_wf:nanoplot (1)","q1Label":"read_qc_wf:nanoplot (1)","q2Label":"read_qc_wf:nanoplot (1)","q3Label":"read_qc_wf:nanoplot (1)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":9190227968,"min":9190227968,"q1":9190227968,"q2":9190227968,"q3":9190227968,"max":9190227968,"minLabel":"read_qc_wf:nanoplot (1)","maxLabel":"read_qc_wf:nanoplot (1)","q1Label":"read_qc_wf:nanoplot (1)","q2Label":"read_qc_wf:nanoplot (1)","q3Label":"read_qc_wf:nanoplot (1)"},"reads":{"mean":249719828,"min":249719828,"q1":249719828,"q2":249719828,"q3":249719828,"max":249719828,"minLabel":"read_qc_wf:nanoplot (1)","maxLabel":"read_qc_wf:nanoplot (1)","q1Label":"read_qc_wf:nanoplot (1)","q2Label":"read_qc_wf:nanoplot (1)","q3Label":"read_qc_wf:nanoplot (1)"},"cpu":{"mean":158,"min":158,"q1":158,"q2":158,"q3":158,"max":158,"minLabel":"read_qc_wf:nanoplot (1)","maxLabel":"read_qc_wf:nanoplot (1)","q1Label":"read_qc_wf:nanoplot (1)","q2Label":"read_qc_wf:nanoplot (1)","q3Label":"read_qc_wf:nanoplot (1)"},"time":{"mean":16266,"min":16266,"q1":16266,"q2":16266,"q3":16266,"max":16266,"minLabel":"read_qc_wf:nanoplot (1)","maxLabel":"read_qc_wf:nanoplot (1)","q1Label":"read_qc_wf:nanoplot (1)","q2Label":"read_qc_wf:nanoplot (1)","q3Label":"read_qc_wf:nanoplot (1)"},"writes":{"mean":15092760,"min":15092760,"q1":15092760,"q2":15092760,"q3":15092760,"max":15092760,"minLabel":"read_qc_wf:nanoplot (1)","maxLabel":"read_qc_wf:nanoplot (1)","q1Label":"read_qc_wf:nanoplot (1)","q2Label":"read_qc_wf:nanoplot (1)","q3Label":"read_qc_wf:nanoplot (1)"}},{"cpuUsage":{"mean":30.5,"min":30.5,"q1":30.5,"q2":30.5,"q3":30.5,"max":30.5,"minLabel":"align_to_reference (1)","maxLabel":"align_to_reference (1)","q1Label":"align_to_reference (1)","q2Label":"align_to_reference (1)","q3Label":"align_to_reference (1)"},"process":"align_to_reference","mem":{"mean":13516800,"min":13516800,"q1":13516800,"q2":13516800,"q3":13516800,"max":13516800,"minLabel":"align_to_reference (1)","maxLabel":"align_to_reference (1)","q1Label":"align_to_reference (1)","q2Label":"align_to_reference (1)","q3Label":"align_to_reference (1)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":870862848,"min":870862848,"q1":870862848,"q2":870862848,"q3":870862848,"max":870862848,"minLabel":"align_to_reference (1)","maxLabel":"align_to_reference (1)","q1Label":"align_to_reference (1)","q2Label":"align_to_reference (1)","q3Label":"align_to_reference (1)"},"reads":{"mean":44697107,"min":44697107,"q1":44697107,"q2":44697107,"q3":44697107,"max":44697107,"minLabel":"align_to_reference (1)","maxLabel":"align_to_reference (1)","q1Label":"align_to_reference (1)","q2Label":"align_to_reference (1)","q3Label":"align_to_reference (1)"},"cpu":{"mean":488,"min":488,"q1":488,"q2":488,"q3":488,"max":488,"minLabel":"align_to_reference (1)","maxLabel":"align_to_reference (1)","q1Label":"align_to_reference (1)","q2Label":"align_to_reference (1)","q3Label":"align_to_reference (1)"},"time":{"mean":1093,"min":1093,"q1":1093,"q2":1093,"q3":1093,"max":1093,"minLabel":"align_to_reference (1)","maxLabel":"align_to_reference (1)","q1Label":"align_to_reference (1)","q2Label":"align_to_reference (1)","q3Label":"align_to_reference (1)"},"writes":{"mean":36006078,"min":36006078,"q1":36006078,"q2":36006078,"q3":36006078,"max":36006078,"minLabel":"align_to_reference (1)","maxLabel":"align_to_reference (1)","q1Label":"align_to_reference (1)","q2Label":"align_to_reference (1)","q3Label":"align_to_reference (1)"}},{"cpuUsage":null,"process":"artic_medaka","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":69954,"min":69954,"q1":69954,"q2":69954,"q3":69954,"max":69954,"minLabel":"artic_ncov_wf:artic_medaka (1)","maxLabel":"artic_ncov_wf:artic_medaka (1)","q1Label":"artic_ncov_wf:artic_medaka (1)","q2Label":"artic_ncov_wf:artic_medaka (1)","q3Label":"artic_ncov_wf:artic_medaka (1)"},"writes":null},{"cpuUsage":{"mean":9.27,"min":9.27,"q1":9.27,"q2":9.27,"q3":9.27,"max":9.27,"minLabel":"create_summary_report_wf:plot_coverages (1)","maxLabel":"create_summary_report_wf:plot_coverages (1)","q1Label":"create_summary_report_wf:plot_coverages (1)","q2Label":"create_summary_report_wf:plot_coverages (1)","q3Label":"create_summary_report_wf:plot_coverages (1)"},"process":"plot_coverages","mem":{"mean":222109696,"min":222109696,"q1":222109696,"q2":222109696,"q3":222109696,"max":222109696,"minLabel":"create_summary_report_wf:plot_coverages (1)","maxLabel":"create_summary_report_wf:plot_coverages (1)","q1Label":"create_summary_report_wf:plot_coverages (1)","q2Label":"create_summary_report_wf:plot_coverages (1)","q3Label":"create_summary_report_wf:plot_coverages (1)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":9038143488,"min":9038143488,"q1":9038143488,"q2":9038143488,"q3":9038143488,"max":9038143488,"minLabel":"create_summary_report_wf:plot_coverages (1)","maxLabel":"create_summary_report_wf:plot_coverages (1)","q1Label":"create_summary_report_wf:plot_coverages (1)","q2Label":"create_summary_report_wf:plot_coverages (1)","q3Label":"create_summary_report_wf:plot_coverages (1)"},"reads":{"mean":67761729,"min":67761729,"q1":67761729,"q2":67761729,"q3":67761729,"max":67761729,"minLabel":"create_summary_report_wf:plot_coverages (1)","maxLabel":"create_summary_report_wf:plot_coverages (1)","q1Label":"create_summary_report_wf:plot_coverages (1)","q2Label":"create_summary_report_wf:plot_coverages (1)","q3Label":"create_summary_report_wf:plot_coverages (1)"},"cpu":{"mean":148.3,"min":148.3,"q1":148.3,"q2":148.3,"q3":148.3,"max":148.3,"minLabel":"create_summary_report_wf:plot_coverages (1)","maxLabel":"create_summary_report_wf:plot_coverages (1)","q1Label":"create_summary_report_wf:plot_coverages (1)","q2Label":"create_summary_report_wf:plot_coverages (1)","q3Label":"create_summary_report_wf:plot_coverages (1)"},"time":{"mean":9225,"min":9225,"q1":9225,"q2":9225,"q3":9225,"max":9225,"minLabel":"create_summary_report_wf:plot_coverages (1)","maxLabel":"create_summary_report_wf:plot_coverages (1)","q1Label":"create_summary_report_wf:plot_coverages (1)","q2Label":"create_summary_report_wf:plot_coverages (1)","q3Label":"create_summary_report_wf:plot_coverages (1)"},"writes":{"mean":429701,"min":429701,"q1":429701,"q2":429701,"q3":429701,"max":429701,"minLabel":"create_summary_report_wf:plot_coverages (1)","maxLabel":"create_summary_report_wf:plot_coverages (1)","q1Label":"create_summary_report_wf:plot_coverages (1)","q2Label":"create_summary_report_wf:plot_coverages (1)","q3Label":"create_summary_report_wf:plot_coverages (1)"}},{"cpuUsage":{"mean":3.29,"min":3.29,"q1":3.29,"q2":3.29,"q3":3.29,"max":3.29,"minLabel":"read_classification_wf:kraken2 (1)","maxLabel":"read_classification_wf:kraken2 (1)","q1Label":"read_classification_wf:kraken2 (1)","q2Label":"read_classification_wf:kraken2 (1)","q3Label":"read_classification_wf:kraken2 (1)"},"process":"kraken2","mem":{"mean":3603849216,"min":3603849216,"q1":3603849216,"q2":3603849216,"q3":3603849216,"max":3603849216,"minLabel":"read_classification_wf:kraken2 (1)","maxLabel":"read_classification_wf:kraken2 (1)","q1Label":"read_classification_wf:kraken2 (1)","q2Label":"read_classification_wf:kraken2 (1)","q3Label":"read_classification_wf:kraken2 (1)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":4146896896,"min":4146896896,"q1":4146896896,"q2":4146896896,"q3":4146896896,"max":4146896896,"minLabel":"read_classification_wf:kraken2 (1)","maxLabel":"read_classification_wf:kraken2 (1)","q1Label":"read_classification_wf:kraken2 (1)","q2Label":"read_classification_wf:kraken2 (1)","q3Label":"read_classification_wf:kraken2 (1)"},"reads":{"mean":11378120203,"min":11378120203,"q1":11378120203,"q2":11378120203,"q3":11378120203,"max":11378120203,"minLabel":"read_classification_wf:kraken2 (1)","maxLabel":"read_classification_wf:kraken2 (1)","q1Label":"read_classification_wf:kraken2 (1)","q2Label":"read_classification_wf:kraken2 (1)","q3Label":"read_classification_wf:kraken2 (1)"},"cpu":{"mean":52.6,"min":52.6,"q1":52.6,"q2":52.6,"q3":52.6,"max":52.6,"minLabel":"read_classification_wf:kraken2 (1)","maxLabel":"read_classification_wf:kraken2 (1)","q1Label":"read_classification_wf:kraken2 (1)","q2Label":"read_classification_wf:kraken2 (1)","q3Label":"read_classification_wf:kraken2 (1)"},"time":{"mean":233495,"min":233495,"q1":233495,"q2":233495,"q3":233495,"max":233495,"minLabel":"read_classification_wf:kraken2 (1)","maxLabel":"read_classification_wf:kraken2 (1)","q1Label":"read_classification_wf:kraken2 (1)","q2Label":"read_classification_wf:kraken2 (1)","q3Label":"read_classification_wf:kraken2 (1)"},"writes":{"mean":8530517478,"min":8530517478,"q1":8530517478,"q2":8530517478,"q3":8530517478,"max":8530517478,"minLabel":"read_classification_wf:kraken2 (1)","maxLabel":"read_classification_wf:kraken2 (1)","q1Label":"read_classification_wf:kraken2 (1)","q2Label":"read_classification_wf:kraken2 (1)","q3Label":"read_classification_wf:kraken2 (1)"}},{"cpuUsage":{"mean":98.5,"min":98.5,"q1":98.5,"q2":98.5,"q3":98.5,"max":98.5,"minLabel":"read_classification_wf:krona (1)","maxLabel":"read_classification_wf:krona (1)","q1Label":"read_classification_wf:krona (1)","q2Label":"read_classification_wf:krona (1)","q3Label":"read_classification_wf:krona (1)"},"process":"krona","mem":{"mean":643940352,"min":643940352,"q1":643940352,"q2":643940352,"q3":643940352,"max":643940352,"minLabel":"read_classification_wf:krona (1)","maxLabel":"read_classification_wf:krona (1)","q1Label":"read_classification_wf:krona (1)","q2Label":"read_classification_wf:krona (1)","q3Label":"read_classification_wf:krona (1)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":650539008,"min":650539008,"q1":650539008,"q2":650539008,"q3":650539008,"max":650539008,"minLabel":"read_classification_wf:krona (1)","maxLabel":"read_classification_wf:krona (1)","q1Label":"read_classification_wf:krona (1)","q2Label":"read_classification_wf:krona (1)","q3Label":"read_classification_wf:krona (1)"},"reads":{"mean":122229979,"min":122229979,"q1":122229979,"q2":122229979,"q3":122229979,"max":122229979,"minLabel":"read_classification_wf:krona (1)","maxLabel":"read_classification_wf:krona (1)","q1Label":"read_classification_wf:krona (1)","q2Label":"read_classification_wf:krona (1)","q3Label":"read_classification_wf:krona (1)"},"cpu":{"mean":98.5,"min":98.5,"q1":98.5,"q2":98.5,"q3":98.5,"max":98.5,"minLabel":"read_classification_wf:krona (1)","maxLabel":"read_classification_wf:krona (1)","q1Label":"read_classification_wf:krona (1)","q2Label":"read_classification_wf:krona (1)","q3Label":"read_classification_wf:krona (1)"},"time":{"mean":2816,"min":2816,"q1":2816,"q2":2816,"q3":2816,"max":2816,"minLabel":"read_classification_wf:krona (1)","maxLabel":"read_classification_wf:krona (1)","q1Label":"read_classification_wf:krona (1)","q2Label":"read_classification_wf:krona (1)","q3Label":"read_classification_wf:krona (1)"},"writes":{"mean":231211,"min":231211,"q1":231211,"q2":231211,"q3":231211,"max":231211,"minLabel":"read_classification_wf:krona (1)","maxLabel":"read_classification_wf:krona (1)","q1Label":"read_classification_wf:krona (1)","q2Label":"read_classification_wf:krona (1)","q3Label":"read_classification_wf:krona (1)"}}] oct-04 13:44:13.943 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline oct-04 13:44:14.140 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done oct-04 13:44:14.212 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) oct-04 13:44:14.213 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye