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nf-core / smrnaseq

A small-RNA sequencing analysis pipeline
https://nf-co.re/smrnaseq
MIT License
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ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN (1) #298

Closed sameet closed 10 months ago

sameet commented 11 months ago

Description of the bug

I am trying to run nf-core/smrnaseq pipeline. I get the following error:

ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN (1)'

Caused by:
 Not a valid path value type: java.util.ArrayList ([/vast/palmer/scratch/mane/sm2556/raw_data/p7_3_48_Dec_S3_L003_R1_001.fastq.gz])

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

Command used and terminal output

nextflow run nf-core/smrnaseq -r 2.2.3 -params-file nf-params.json -profile singularity --max_cpus 20 -resume

Relevant files

Nov-27 10:27:49.252 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/smrnaseq -r 2.2.3 -params-file nf-params.json -profile singularity --max_cpus 20 -resume
Nov-27 10:27:49.334 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.04.1
Nov-27 10:27:49.348 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/sm2556/.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-googl
e@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2
Nov-27 10:27:49.357 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Nov-27 10:27:49.358 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Nov-27 10:27:49.360 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Nov-27 10:27:49.368 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Nov-27 10:27:49.378 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/sm2556/.nextflow/scm
Nov-27 10:27:49.990 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/sm2556/.nextflow/assets/nf-core/smrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/smrnaseq.git
Nov-27 10:27:50.004 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Nov-27 10:27:50.010 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/sm2556/.nextflow/assets/nf-core/smrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/smrnaseq.git
Nov-27 10:27:50.618 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/sm2556/.nextflow/assets/nf-core/smrnaseq/nextflow.config
Nov-27 10:27:50.619 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/sm2556/.nextflow/assets/nf-core/smrnaseq/nextflow.config
Nov-27 10:27:50.633 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Nov-27 10:27:51.382 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, test_no_genome, tigem
, tubingen_apg, google, apollo, ipop_up, pdc_kth, googlels, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh
, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, unc_lccc, wehi, awsbatch, wustl_htcf, imperial, maestro, software_license, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc
_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, test, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, ethz_euler, test_full, imb, tuos_stanage, azurebatch, hki, crukmi, docker, engaging, gis, hypatia, psmn, eva, fgcz, conda, crg, singu
larity, uw_hyak_pedslabs, prince, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac]
Nov-27 10:27:51.411 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Nov-27 10:27:51.411 [main] INFO  nextflow.cli.CmdRun - Launching `https://github.com/nf-core/smrnaseq` [tiny_euclid] DSL2 - revision: 18d6c84926 [2.2.3]
Nov-27 10:27:51.412 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation]
Nov-27 10:27:51.412 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Nov-27 10:27:51.412 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation]
Nov-27 10:27:51.412 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: latest
Nov-27 10:27:51.617 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved
Nov-27 10:27:51.617 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3'
Nov-27 10:27:51.633 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3
Nov-27 10:27:51.638 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/sm2556/.nextflow/secrets/store.json
Nov-27 10:27:51.641 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@7f93f4c] - activable => nextflow.secret.LocalSecretsProvider@7f93f4c
Nov-27 10:27:51.711 [main] DEBUG nextflow.Session - Session UUID: ac779a06-c1de-4597-b5f1-987aa31cfb61
Nov-27 10:27:51.711 [main] DEBUG nextflow.Session - Run name: tiny_euclid
Nov-27 10:27:51.712 [main] DEBUG nextflow.Session - Executor pool size: 10
Nov-27 10:27:51.719 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=30; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Nov-27 10:27:51.733 [main] DEBUG nextflow.cli.CmdRun -
  Version: 23.04.1 build 5866
  Created: 15-04-2023 06:51 UTC (02:51 EDT)
  System: Linux 4.18.0-477.27.1.el8_8.x86_64
  Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 20-internal-adhoc..src
  Encoding: UTF-8 (UTF-8)
  Process: 3097925@r814u03n03.mccleary.ycrc.yale.edu [10.178.138.7]
  CPUs: 10 - Mem: 59 GB (22.2 GB) - Swap: 0 (0)
Nov-27 10:27:51.760 [main] DEBUG nextflow.Session - Work-dir: /vast/palmer/scratch/mane/sm2556/raw_data/work [nfs]
Nov-27 10:27:51.777 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Nov-27 10:27:51.784 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Nov-27 10:27:51.852 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Nov-27 10:27:51.858 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 11; maxThreads: 1000
Nov-27 10:27:51.947 [main] DEBUG nextflow.Session - Session start
Nov-27 10:27:51.951 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /vast/palmer/scratch/mane/sm2556/raw_data/smrna_nflow_nov272023/pipeline_info/execution_trace_2023-11-27_10-27-51.txt
Nov-27 10:27:51.959 [main] DEBUG nextflow.Session - Using default localLib path: /home/sm2556/.nextflow/assets/nf-core/smrnaseq/lib
Nov-27 10:27:51.963 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/sm2556/.nextflow/assets/nf-core/smrnaseq/lib
Nov-27 10:27:51.963 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/sm2556/.nextflow/assets/nf-core/smrnaseq/lib/nfcore_external_java_deps.jar
Nov-27 10:27:52.237 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Nov-27 10:27:52.248 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsHelp:paramsHelp]; plugin Id: nf-validation
Nov-27 10:27:52.271 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation
Nov-27 10:27:52.358 [main] DEBUG n.validation.DirectoryPathValidator - S3 paths are not supported by 'DirectoryPathValidator': 's3://ngi-igenomes/igenomes'
Nov-27 10:27:52.359 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation
Nov-27 10:27:52.361 [main] WARN  nextflow.Nextflow - Running with Protocol illumina
Nov-27 10:27:52.362 [main] WARN  nextflow.Nextflow - Therefore using Adapter: TGGAATTCTCGGGTGCCAAGG
Nov-27 10:27:52.362 [main] WARN  nextflow.Nextflow - Clipping 0 bases from R1
Nov-27 10:27:52.362 [main] WARN  nextflow.Nextflow - And clipping 0 bases from 3' end
Nov-27 10:27:52.538 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
Nov-27 10:27:52.548 [main] INFO  nextflow.Nextflow -
------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/smrnaseq v2.2.3-g18d6c84
------------------------------------------------------
Core Nextflow options
  revision           : 2.2.3
  runName            : tiny_euclid
  containerEngine    : singularity
  launchDir          : /vast/palmer/scratch/mane/sm2556/raw_data
  workDir            : /vast/palmer/scratch/mane/sm2556/raw_data/work
  projectDir         : /home/sm2556/.nextflow/assets/nf-core/smrnaseq
  userName           : sm2556
  profile            : singularity
  configFiles        :

Input/output options
  input              : sample-sheet.csv
  outdir             : smrna_nflow_nov272023

Reference genome options
  genome             : GRCh38
  mirtrace_species   : hsa
  fasta              : /gpfs/gibbs/data/genomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa

Trimming options
  clip_r1            : 0
  three_prime_clip_r1: 0

Skipping pipeline steps
  skip_fastqc        : true
  skip_fastp         : true

Max job request options
  max_cpus           : 20

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/smrnaseq for your analysis please cite:

* The pipeline
  https://zenodo.org/badge/latestdoi/140590861

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/smrnaseq/blob/master/CITATIONS.md

Nov-27 10:27:55.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Nov-27 10:27:55.265 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK` matches process NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Nov-27 10:27:55.269 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.269 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.274 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Nov-27 10:27:55.278 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=10; memory=59 GB; capacity=10; pollInterval=100ms; dumpInterval=5m
Nov-27 10:27:55.348 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:CAT_FASTQ
Nov-27 10:27:55.348 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SMRNASEQ:SMRNASEQ:CAT_FASTQ
Nov-27 10:27:55.349 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.350 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.369 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN
Nov-27 10:27:55.369 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MIRTRACE_RUN` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN
Nov-27 10:27:55.369 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.369 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.373 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_MATURE
Nov-27 10:27:55.373 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_MATURE
Nov-27 10:27:55.374 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.374 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.377 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_MATURE
Nov-27 10:27:55.378 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_MATURE
Nov-27 10:27:55.378 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.378 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.380 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_HAIRPIN
Nov-27 10:27:55.381 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_HAIRPIN
Nov-27 10:27:55.381 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.381 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.383 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_HAIRPIN
Nov-27 10:27:55.384 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_HAIRPIN
Nov-27 10:27:55.384 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.384 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.386 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE
Nov-27 10:27:55.387 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.387 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.389 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_HAIRPIN
Nov-27 10:27:55.390 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.390 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.394 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE
Nov-27 10:27:55.394 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE
Nov-27 10:27:55.394 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.394 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.397 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN
Nov-27 10:27:55.398 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN
Nov-27 10:27:55.398 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.398 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.403 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_SORT
Nov-27 10:27:55.403 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:SAMTOOLS_SORT` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_SORT
Nov-27 10:27:55.404 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.404 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.408 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_INDEX
Nov-27 10:27:55.408 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.408 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.414 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Nov-27 10:27:55.415 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Nov-27 10:27:55.415 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.415 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Nov-27 10:27:55.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Nov-27 10:27:55.419 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.419 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.422 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Nov-27 10:27:55.422 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Nov-27 10:27:55.423 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.423 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.426 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:SAMTOOLS_SORT
Nov-27 10:27:55.426 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:SAMTOOLS_SORT` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:SAMTOOLS_SORT
Nov-27 10:27:55.427 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.427 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.429 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:SAMTOOLS_INDEX
Nov-27 10:27:55.430 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.430 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Nov-27 10:27:55.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Nov-27 10:27:55.434 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.434 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.437 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Nov-27 10:27:55.437 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTA
T
Nov-27 10:27:55.438 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.438 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.440 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Nov-27 10:27:55.440 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTAT
S
Nov-27 10:27:55.441 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.441 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.448 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:EDGER_QC
Nov-27 10:27:55.448 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:EDGER_QC` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:EDGER_QC
Nov-27 10:27:55.449 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.449 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.452 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:SEQCLUSTER_SEQUENCES
Nov-27 10:27:55.452 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SEQCLUSTER_SEQUENCES` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:SEQCLUSTER_SEQUENCES
Nov-27 10:27:55.452 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.452 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.455 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER
Nov-27 10:27:55.455 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER
Nov-27 10:27:55.455 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.455 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.460 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT
Nov-27 10:27:55.460 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MIRTOP_QUANT` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT
Nov-27 10:27:55.460 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.460 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.463 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:TABLE_MERGE
Nov-27 10:27:55.464 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:TABLE_MERGE` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:TABLE_MERGE
Nov-27 10:27:55.464 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.464 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.469 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME
Nov-27 10:27:55.469 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:INDEX_GENOME` matches process NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME
Nov-27 10:27:55.470 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.470 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.473 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME
Nov-27 10:27:55.473 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME
Nov-27 10:27:55.474 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.474 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.478 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Nov-27 10:27:55.479 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Nov-27 10:27:55.479 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.479 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.483 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Nov-27 10:27:55.484 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Nov-27 10:27:55.484 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.484 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.490 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Nov-27 10:27:55.490 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOO
LS:SAMTOOLS_STATS
Nov-27 10:27:55.491 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.491 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.494 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Nov-27 10:27:55.494 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOO
LS:SAMTOOLS_FLAGSTAT
Nov-27 10:27:55.494 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.494 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.497 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Nov-27 10:27:55.498 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOO
LS:SAMTOOLS_IDXSTATS
Nov-27 10:27:55.498 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.498 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.503 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_PIGZ
Nov-27 10:27:55.504 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.504 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER
Nov-27 10:27:55.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MIRDEEP2_MAPPER` matches process NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER
Nov-27 10:27:55.508 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.508 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.512 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN
Nov-27 10:27:55.513 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.513 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.534 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Nov-27 10:27:55.534 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_SMRNASEQ:SMRNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Nov-27 10:27:55.534 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.534 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.571 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SMRNASEQ:SMRNASEQ:MULTIQC
Nov-27 10:27:55.572 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SMRNASEQ:SMRNASEQ:MULTIQC
Nov-27 10:27:55.572 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 10:27:55.572 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 10:27:55.576 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: BOWTIE_MAP_SEQCLUSTER, FORMAT_MATURE, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, MAP_RRNA, FASTQC_TRIM, SEQCLUSTER_SEQUENCES, INDEX_MIRNA
, FASTP, NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:TABLE_MERGE, BLAT_NCRNA, BOWTIE_MAP_GENOME, INDEX_OTHER, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_HAIRPIN, NFCORE_SMRNASEQ
:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER, CAT_FASTQ, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, SAMTOOLS_STATS, INDEX_GENOME, FA
STQC_RAW, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_HAIRPIN, NFCORE_SMRNASEQ:SMRNASEQ:MULTIQC, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:SEQCLUSTER_SEQUENCES, NFCORE_SMRNASEQ:SMRNAS
EQ:MIRDEEP2:MIRDEEP2_PIGZ, MIRDEEP2_PIGZ, NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_SORT, FILTER_STATS, INDEX_TRNA, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN, NFCORE_SMRNASEQ:SMRN
ASEQ:GENOME_QUANT:INDEX_GENOME, EDGER_QC, NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN, INDEX_HAIRPIN, FORMAT_FASTA_MIRNA, NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, INDEX_CONTAMINANTS, BLAT_PIRNA, NFCORE_SMRNAS
EQ:SMRNASEQ:MIRNA_QUANT:INDEX_HAIRPIN, PARSE_MATURE, BLAT_OTHER, BOWTIE_MAP_SEQ, NFCORE_SMRNASEQ:SMRNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS, SAMTOOLS_INDEX, NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_MATURE, FASTQC, MAP_TRNA,
 INDEX_NCRNA, NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:EDGER_QC, MULTIQC, BOWTIE_MAP_CONTAMINANTS, NFCORE_SMRNASEQ:SMRNAS
EQ:MIRNA_QUANT:MIRTOP_QUANT, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_INDEX, FORMAT_HAIRPIN, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, SAMTOOLS_SORT, NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_S
TATS_SAMTOOLS:SAMTOOLS_SORT, MIRDEEP2_MAPPER, PARSE_HAIRPIN, NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN, INDEX_RRNA, BLAT_MIRNA, MAP_NCRNA, MIRTRACE_RUN, BOWTIE_MAP_HAIRPIN, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_MATURE, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM
_STATS_HAIRPIN:SAMTOOLS_INDEX, PARSE_FASTA_MIRNA, NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX, INDEX_PIRNA, SAMTOOLS_FLAGSTAT, SAMPLESHEET_CHECK, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE, MIRTOP_QUANT, INDEX_CDNA, BOWTIE_MAP_MAT
URE, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME, TABLE_MERGE, BLAT_CDNA, MAP_PIRNA, MIRDEEP2_RUN, INDEX_MATURE, SAMTOOLS_IDXSTATS, CUSTOM_DUMPSOFTWAREVERSIONS, MAP_CDN
A, MAP_OTHER, NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:SAMTOOLS_SORT, NFCORE_SMRNASEQ:SMRNASEQ:CAT_FASTQ
Nov-27 10:27:55.578 [main] DEBUG nextflow.Session - Igniting dataflow network (69)
Nov-27 10:27:55.582 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:CAT_FASTQ
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_MATURE
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_MATURE
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_HAIRPIN
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_HAIRPIN
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_HAIRPIN
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE
Nov-27 10:27:55.583 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN
Nov-27 10:27:55.584 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_SORT
Nov-27 10:27:55.585 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:SAMTOOLS_INDEX
Nov-27 10:27:55.585 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Nov-27 10:27:55.585 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Nov-27 10:27:55.585 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Nov-27 10:27:55.585 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:SAMTOOLS_SORT
Nov-27 10:27:55.585 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:SAMTOOLS_INDEX
Nov-27 10:27:55.588 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:EDGER_QC
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:SEQCLUSTER_SEQUENCES
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:TABLE_MERGE
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_PIGZ
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Nov-27 10:27:55.589 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SMRNASEQ:SMRNASEQ:MULTIQC
Nov-27 10:27:55.589 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Nov-27 10:27:55.589 [main] DEBUG nextflow.Session - Session await
Nov-27 10:27:55.634 [Actor Thread 2] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/python:3.8.3; path=/home/sm2556/project_ycga/resources/singularity/smrnaseq/depot.galaxyproject.org-singu
larity-python-3.8.3.img
Nov-27 10:27:55.634 [Actor Thread 7] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/bowtie%3A1.3.1--py39hd400a0c_2; path=/home/sm2556/project_ycga/resources/singularity/smrnaseq/depot.galax
yproject.org-singularity-bowtie%3A1.3.1--py39hd400a0c_2.img
Nov-27 10:27:55.644 [Actor Thread 17] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/sm2556/.nextflow/assets/nf-core/smrnaseq/bin/check_samplesheet.py
Nov-27 10:27:55.648 [Actor Thread 23] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.009 s; total time: 0.01 s
Nov-27 10:27:55.649 [Actor Thread 23] DEBUG nextflow.file.FileCollector - >> temp file exists? false
Nov-27 10:27:55.649 [Actor Thread 23] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /vast/palmer/scratch/mane/sm2556/raw_data/work/collect-file/ecd0176de20acfa78c50f70ea420a702
Nov-27 10:27:55.657 [Actor Thread 23] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /vast/palmer/scratch/mane/sm2556/raw_data/work/collect-file/ecd0176de20acfa78c50f70ea420a702
Nov-27 10:27:55.662 [Actor Thread 23] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-14202704766962185653
Nov-27 10:27:55.672 [Actor Thread 17] INFO  nextflow.processor.TaskProcessor - [76/8a187d] Cached process > NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)
Nov-27 10:27:55.672 [Actor Thread 12] INFO  nextflow.processor.TaskProcessor - [e5/266aad] Cached process > NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)
Nov-27 10:27:55.689 [Actor Thread 7] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/seqcluster:1.2.9--pyh5e36f6f_0; path=/home/sm2556/project_ycga/resources/singularity/smrnaseq/depot.galax
yproject.org-singularity-seqcluster-1.2.9--pyh5e36f6f_0.img
Nov-27 10:27:55.691 [Actor Thread 2] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/bioconvert:0.4.3--py_0; path=/home/sm2556/project_ycga/resources/singularity/smrnaseq/depot.galaxyproject
.org-singularity-bioconvert-0.4.3--py_0.img
Nov-27 10:27:55.693 [Actor Thread 12] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=30; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Nov-27 10:27:55.701 [Actor Thread 5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN (1); work-dir=null
  error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value type: java.util.ArrayList ([/vast/palmer/scratch/mane/sm2556/raw_data/p7_3_48_Dec_S3_L003_R1_001.fastq.gz])
Nov-27 10:27:55.710 [Actor Thread 5] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN (1)'

Caused by:
  Not a valid path value type: java.util.ArrayList ([/vast/palmer/scratch/mane/sm2556/raw_data/p7_3_48_Dec_S3_L003_R1_001.fastq.gz])

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Nov-27 10:27:55.712 [Actor Thread 5] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Nov-27 10:27:55.717 [main] DEBUG nextflow.Session - Session await > all processes finished
Nov-27 10:27:55.718 [main] DEBUG nextflow.Session - Session await > all barriers passed
Nov-27 10:27:55.718 [Actor Thread 10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_MATURE; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-27 10:27:55.719 [Actor Thread 22] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-27 10:27:55.719 [Actor Thread 14] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_HAIRPIN; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-27 10:27:55.726 [Actor Thread 25] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:SEQCLUSTER_SEQUENCES; work-dir=null
  error [java.lang.IllegalStateException]: Cannot obtain the semaphore to fork operator's body.
Nov-27 10:27:55.726 [Actor Thread 22] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-27 10:27:55.726 [Actor Thread 3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_PIGZ; work-dir=null
  error [java.lang.IllegalStateException]: Cannot obtain the semaphore to fork operator's body.
Nov-27 10:27:55.727 [Actor Thread 17] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SMRNASEQ:SMRNASEQ:MIRTRACE:MIRTRACE_RUN; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-27 10:27:55.728 [Actor Thread 28] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.001 s; external sort time: 0.0 s; total time: 0.001 s
Nov-27 10:27:55.729 [Actor Thread 28] DEBUG nextflow.file.FileCollector - >> temp file exists? false
Nov-27 10:27:55.729 [Actor Thread 28] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /vast/palmer/scratch/mane/sm2556/raw_data/work/collect-file/0b87622d904e27ec764a88d0c2461550
Nov-27 10:27:55.730 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-27 10:27:55.731 [Task submitter] INFO  nextflow.Session - [6e/2fdfde] Submitted process > NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_PIGZ (p7_3_48_NT_plus_P)
Nov-27 10:27:55.736 [Actor Thread 28] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /vast/palmer/scratch/mane/sm2556/raw_data/work/collect-file/0b87622d904e27ec764a88d0c2461550
Nov-27 10:27:55.738 [Actor Thread 28] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-7737922413237019232
Nov-27 10:27:55.740 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Nov-27 10:27:55.741 [main] INFO  nextflow.Nextflow - -[nf-core/smrnaseq] Pipeline completed with errors-
Nov-27 10:27:55.743 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (1)
Nov-27 10:27:55.753 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=2; pendingCount=35; submittedCount=1; runningCount=-1; retriesCount=0; abortedCount=1; succeedDuration
=0ms; failedDuration=0ms; cachedDuration=2h 38m 6s;loadCpus=-2; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Nov-27 10:27:55.753 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Nov-27 10:27:55.755 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Nov-27 10:27:55.771 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":{"mean":88.77,"min":88.77,"q1":88.77,"q2":88.77,"q3":88.77,"max":88.77,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q1Label":"NFCORE_SMRNASEQ:SMRNA
SEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)"},"process":"INDEX_GENOME","mem":{"mean":6529531904,"min":6529531904,"q1":6529
531904,"q2":6529531904,"q3":6529531904,"max":6529531904,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME
(genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)"},"memUsage":{"mean":16.89,"min":16.89,"q1":16.89,"q2":16.89,"q3":16.89,"max":16.89,"minLabel":"NFCORE_SMRNA
SEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (geno
me.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)"},"timeUsage":{"mean":5.49,"min":5.49,"q1":5.49,"q2":5.49,"q3":5.49,"max":5.49,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SMRNASEQ:SMRNA
SEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)"},"
vmem":{"mean":7319445504,"min":7319445504,"q1":7319445504,"q2":7319445504,"q3":7319445504,"max":7319445504,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q1Label":"
NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)"},"reads":{"mean":42452223463,"min":42452223463,"q1":4245
2223463,"q2":42452223463,"q3":42452223463,"max":42452223463,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GEN
OME (genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)"},"cpu":{"mean":532.6,"min":532.6,"q1":532.6,"q2":532.6,"q3":532.6,"max":532.6,"minLabel":"NFCORE_SMRNAS
EQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)"},"time":{"mean":1581000,"min":1581000,"q1":1581000,"q2":1581000,"q3":1581000,"max":1581000,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SM
RNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (ge
nome.fa)"},"writes":{"mean":32955858606,"min":32955858606,"q1":32955858606,"q2":32955858606,"q3":32955858606,"max":32955858606,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (gen
ome.fa)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:INDEX_GENOME (genome.fa)"}},{"cpuUsage":{"mean":43.2,"min":43.
2,"q1":43.2,"q2":43.2,"q3":43.2,"max":43.2,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPL
ESHEET_CHECK (sample-sheet.csv)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)"},"process":"SAMPLESHEET_CHECK","mem":{"mean":9547776,"min":954777
6,"q1":9547776,"q2":9547776,"q3":9547776,"max":9547776,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT
_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)"},"memUsage":{"mean":0.15,"min":0.15,"q1":0.15,"q2":0.
15,"q3":0.15,"max":0.15,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sampl
e-sheet.csv)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)"},"timeUsage":null,"vmem":{"mean":33124352,"min":33124352,"q1":33124352,"q2":33124352
,"q3":33124352,"max":33124352,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
(sample-sheet.csv)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)"},"reads":{"mean":1501551,"min":1501551,"q1":1501551,"q2":1501551,"q3":1501551,
"max":1501551,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.cs
v)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)"},"cpu":{"mean":43.2,"min":43.2,"q1":43.2,"q2":43.2,"q3":43.2,"max":43.2,"minLabel":"NFCORE_SMR
NASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q2Label":"NFCORE_SMRNASEQ:SMRNA
SEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)"},"time":null,"writes":{"mean":1851,"min":1851,"q1":1851,"q2":1851,"q3":1851,"max":1851,"minLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_
CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","maxLabel":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q1Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)","q2Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPL
ESHEET_CHECK (sample-sheet.csv)","q3Label":"NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (sample-sheet.csv)"}},{"cpuUsage":null,"process":"MIRDEEP2_PIGZ","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null}
]
Nov-27 10:27:56.327 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Nov-27 10:27:56.530 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Nov-27 10:27:56.530 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin 'nf-validation@1.1.3'
Nov-27 10:27:56.530 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation
Nov-27 10:27:56.546 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Nov-27 10:27:56.546 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

  N E X T F L O W
  version 23.04.1 build 5866
  created 15-04-2023 06:51 UTC (02:51 EDT)
  cite doi:10.1038/nbt.3820
  http://nextflow.io

HPC, slurm, singularity, Linux, 2.2.4

apeltzer commented 10 months ago

See #303 for hopefully permanent fixes now