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nf-core / hicar

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
https://nf-co.re/hicar
MIT License
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R error - no package called ‘GenomeInfoDb’ #106

Open luciazifcakova opened 3 months ago

luciazifcakova commented 3 months ago

Description of the bug

do I need to use my local version of R?

Command used and terminal output

Hi guys, I have tested hicar 1.0.0 "nextflow run nf-core/hicar -r 1.0.0 -profile test --outdir ./" and got this error: -[nf-core/hicar] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig)'Caused by:
  Process `NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig)` terminated with an error exit status (1)Command executed:  #!/usr/bin/env Rscript
  pkgs <- c("GenomeInfoDb", "rtracklayer")
  versions <- c("NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2:")
  for(pkg in pkgs){
      # load library
      library(pkg, character.only=TRUE)
      # parepare for versions.yml
      versions <- c(versions,
          paste0("    ", pkg, ": ", as.character(packageVersion(pkg))))
  }
  writeLines(versions, "versions.yml") # write versions.yml  toUCSC = "toUCSC"=="toUCSC"
  inf = "wgEncodeCrgMapabilityAlign50mer.chr22.bigWig"
  ## check file format
  ## if it is bigwig file
  isBWF <- grepl("\\.(bw|bigwig)", inf, ignore.case=TRUE)
  if(isBWF){## decrease the memory cost
      bwfile <- BigWigFile(inf)
      seqinfo <- seqinfo(bwfile)
      seqstyle <- seqlevelsStyle(seqinfo)
  }else{
      data <- import(inf)
      seqstyle <- seqlevelsStyle(data)
  }
  readBWFile <- function(f, seqinfo){
      gr <- as(seqinfo, "GRanges")
      data <- GRanges()
      for(s in seq_along(gr)){
          dat <- import.bw(f, which = gr[s])
          dat <- coverage(dat, weight = dat$score)
          dat <- as(dat, "GRanges")
          dat <- dat[dat$score > 0] ## negative scores are not allowed
          data <- c(data, dat)
      }
      data <- coverage(data, weight = data$score)
      data <- as(data, "GRanges")
      data <- data[data$score > 0]
      return(data)
  }
  if(toUCSC){
      if(!"UCSC" %in% seqstyle){ ## convert to UCSC style
          if(isBWF){
              data <- readBWFile(inf, seqinfo)
          }
          seqlevelsStyle(data) <- "UCSC"
          ## double check
          if(sum(grepl("^chr", seqlevels(data)))==0){
              ids <- grepl("^((\\d{1,2})|(IX|IV|V?I{0,3})|([XYMT]{1,2}))$", seqlevels(data))
              seqlevels(data)[ids] <- paste0("chr", seqlevels(data)[ids])
          }
          export(data, file.path(dirname(inf), paste0("UCSC.", basename(inf))))
      }else{
          file.copy(inf, file.path(dirname(inf), paste0("UCSC.", basename(inf))))
      }
  }else{
      if(!"Ensembl" %in% seqstyle){## convert to Ensembl style
          if(isBWF){
              data <- readBWFile(inf, seqinfo)
          }
          seqlevelsStyle(data) <- "Ensembl"
          ## double check
          if(sum(grepl("^chr", seqlevels(data)))>0){
              ids <- grepl("^(chr)((\\d{1,2})|(IX|IV|V?I{0,3})|([XYMT]{1,2}))$", seqlevels(data))
              seqlevels(data)[ids] <- sub("chr", "", seqlevels(data)[ids])
          }
          export(data, file.path(dirname(inf), paste0("ENSEMBL.", basename(inf))))
      }else{
          file.copy(inf, file.path(dirname(inf), paste0("ENSEMBL.", basename(inf))))
      }
  }Command exit status:
  1Command output:
  (empty)Command error:
  Error in library(pkg, character.only = TRUE) :
    there is no package called ‘GenomeInfoDb’
  Execution haltedWork dir:
  /flash/MillerU/S_lessoniana_hic_maps/work/f1/e6998f6432e93593ef6fdbc198e662Tip: 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
4:07
when I checked .command.err i got: Error in library(pkg, character.only = TRUE) :
  there is no package called ‘GenomeInfoDb’
Execution halted
4:08

Relevant files

Mar-13 16:14:15.059 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/hicar -r 1.0.0 -profile test --outdir ./ Mar-13 16:14:15.165 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1 Mar-13 16:14:15.186 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/l/lucia-zifcakova/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1 Mar-13 16:14:15.198 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Mar-13 16:14:15.199 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Mar-13 16:14:15.203 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Mar-13 16:14:15.213 [main] INFO org.pf4j.AbstractPluginManager - No plugins Mar-13 16:14:15.256 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/l/lucia-zifcakova/.nextflow/scm Mar-13 16:14:16.620 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/hicar.git Mar-13 16:14:16.673 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Mar-13 16:14:16.683 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/hicar.git Mar-13 16:14:17.626 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/nextflow.config Mar-13 16:14:17.627 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/nextflow.config Mar-13 16:14:17.637 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: test Mar-13 16:14:19.558 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, test_hichip, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, test_multi, icr_davros, ceres, munin, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, imperial, maestro, software_license, utd_europa, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, ethz_euler, test_full, imb, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, test_hipeak, phoenix, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] Mar-13 16:14:19.658 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Mar-13 16:14:19.659 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/nf-core/hicar [soggy_gates] DSL2 - revision: 429087d2b1 [1.0.0] Mar-13 16:14:19.660 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Mar-13 16:14:19.660 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Mar-13 16:14:19.662 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/l/lucia-zifcakova/.nextflow/secrets/store.json Mar-13 16:14:19.665 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@27e21083] - activable => nextflow.secret.LocalSecretsProvider@27e21083 Mar-13 16:14:19.727 [main] DEBUG nextflow.Session - Session UUID: 2f357e46-de1a-4c82-a9f7-c727d20d0353 Mar-13 16:14:19.727 [main] DEBUG nextflow.Session - Run name: soggy_gates Mar-13 16:14:19.728 [main] DEBUG nextflow.Session - Executor pool size: 2 Mar-13 16:14:19.737 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Mar-13 16:14:19.741 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Mar-13 16:14:19.771 [main] DEBUG nextflow.cli.CmdRun - Version: 23.10.1 build 5893 Created: 12-01-2024 23:26 UTC (13-01-2024 08:26 JDT) System: Linux 4.18.0-348.2.1.el8_5.x86_64 Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 14+36-1461 Encoding: UTF-8 (UTF-8) Process: 2498030@deigo-login3.oist.jp [10.145.10.23] CPUs: 2 - Mem: 8 GB (6.3 GB) - Swap: 8 GB (1.7 GB) Mar-13 16:14:19.793 [main] DEBUG nextflow.Session - Work-dir: /flash/MillerU/S_lessoniana_hic_maps/work [lustre] Mar-13 16:14:19.828 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, AwsBatchExecutor, GoogleBatchExecutor] Mar-13 16:14:19.841 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Mar-13 16:14:19.865 [main] DEBUG nextflow.Session - Observer factory: WaveFactory Mar-13 16:14:19.884 [main] DEBUG i.s.wave.plugin.config.WaveConfig - Wave strategy not specified - using default: [container, dockerfile, conda, spack] Mar-13 16:14:19.894 [main] DEBUG io.seqera.wave.plugin.WaveClient - Wave config: WaveConfig(enabled:null, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.1; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null) Mar-13 16:14:19.916 [main] DEBUG nextflow.Session - Observer factory: TowerFactory Mar-13 16:14:19.968 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Mar-13 16:14:19.978 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000 Mar-13 16:14:20.076 [main] DEBUG nextflow.Session - Session start Mar-13 16:14:20.080 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /flash/MillerU/S_lessoniana_hic_maps/pipeline_info/execution_trace_2024-03-13_16-14-18.txt Mar-13 16:14:20.091 [main] DEBUG nextflow.Session - Using default localLib path: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/lib Mar-13 16:14:20.095 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/lib Mar-13 16:14:20.096 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/lib/nfcore_external_java_deps.jar Mar-13 16:14:21.064 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Mar-13 16:14:21.234 [main] INFO nextflow.Nextflow - 

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | | / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,' nf-core/hicar v1.0.0

Core Nextflow options revision : 1.0.0 runName : soggy_gates launchDir : /flash/MillerU/S_lessoniana_hic_maps workDir : /flash/MillerU/S_lessoniana_hic_maps/work projectDir : /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar userName : lucia-zifcakova profile : test configFiles : /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/nextflow.config

Input/output options input : /home/l/lucia-zifcakova/.nextflow/assets/nf-core/hicar/assets/samplesheet.csv outdir : ./

Reference genome options fasta : https://raw.githubusercontent.com/nf-core/test-datasets/hicar/data/genomics/homo_sapiens/fasta/chr22.fa.gz gtf : https://raw.githubusercontent.com/nf-core/test-datasets/hicar/data/genomics/homo_sapiens/annotation/chr22.gtf.gz mappability : https://raw.githubusercontent.com/nf-core/test-datasets/hicar/data/genomics/homo_sapiens/mappability/wgEncodeCrgMapabilityAlign50mer.chr22.bigWig macs_gsize : 3e7

Experiment design options restriction_sites_cut_off : 0.1

MACS2 peak calling options qval_thresh : 0.05

MAPS peak calling options maps_digest_file : null maps_cutoff_counts : 6 peak_pair_block : 1E+8

Options related to tracks, juicer_tools, and circos juicer_tools_jar : https://github.com/aidenlab/Juicebox/releases/download/v2.13.06/juicer_tools_2.13.06.jar

Other options not expose enrichment_fdr : 0.05

Institutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function

Max job request options max_cpus : 2 max_memory : 6.GB max_time : 6.h

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/hicar for your analysis please cite:

....

NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig); status: COMPLETED; exit: 1; error: -; workDir: /flash/MillerU/S_lessoniana_hic_maps/work/de/3fe7af70d2471fd9a2748c8951aa40] Mar-13 16:14:47.062 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig); work-dir=/flash/MillerU/S_lessoniana_hic_maps/work/de/3fe7af70d2471fd9a2748c8951aa40 error [nextflow.exception.ProcessFailedException]: Process NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig) terminated with an error exit status (1) Mar-13 16:14:47.063 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Mar-13 16:14:47.063 [Task submitter] INFO nextflow.Session - [ad/da663d] Submitted process > NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig) Mar-13 16:14:47.071 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig)'

Caused by: Process NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig) terminated with an error exit status (1)

Command executed:

!/usr/bin/env Rscript

pkgs <- c("GenomeInfoDb", "rtracklayer") versions <- c("NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2:") for(pkg in pkgs){

load library

  library(pkg, character.only=TRUE)
  # parepare for versions.yml
  versions <- c(versions,
      paste0("    ", pkg, ": ", as.character(packageVersion(pkg))))

} writeLines(versions, "versions.yml") # write versions.yml

toUCSC = "toUCSC"=="toUCSC" inf = "wgEncodeCrgMapabilityAlign50mer.chr22.bigWig"

check file format

if it is bigwig file

isBWF <- grepl("\.(bw|bigwig)", inf, ignore.case=TRUE) if(isBWF){## decrease the memory cost bwfile <- BigWigFile(inf) seqinfo <- seqinfo(bwfile) seqstyle <- seqlevelsStyle(seqinfo) }else{ data <- import(inf) seqstyle <- seqlevelsStyle(data) } readBWFile <- function(f, seqinfo){ gr <- as(seqinfo, "GRanges") data <- GRanges() for(s in seq_along(gr)){ dat <- import.bw(f, which = gr[s]) dat <- coverage(dat, weight = dat$score) dat <- as(dat, "GRanges") dat <- dat[dat$score > 0] ## negative scores are not allowed data <- c(data, dat) } data <- coverage(data, weight = data$score) data <- as(data, "GRanges") data <- data[data$score > 0] return(data) } if(toUCSC){ if(!"UCSC" %in% seqstyle){ ## convert to UCSC style if(isBWF){ data <- readBWFile(inf, seqinfo) } seqlevelsStyle(data) <- "UCSC"

double check

      if(sum(grepl("^chr", seqlevels(data)))==0){
          ids <- grepl("^((\\d{1,2})|(IX|IV|V?I{0,3})|([XYMT]{1,2}))$", seqlevels(data))
          seqlevels(data)[ids] <- paste0("chr", seqlevels(data)[ids])
      }
      export(data, file.path(dirname(inf), paste0("UCSC.", basename(inf))))
  }else{
      file.copy(inf, file.path(dirname(inf), paste0("UCSC.", basename(inf))))
  }

}else{ if(!"Ensembl" %in% seqstyle){## convert to Ensembl style if(isBWF){ data <- readBWFile(inf, seqinfo) } seqlevelsStyle(data) <- "Ensembl"

double check

      if(sum(grepl("^chr", seqlevels(data)))>0){
          ids <- grepl("^(chr)((\\d{1,2})|(IX|IV|V?I{0,3})|([XYMT]{1,2}))$", seqlevels(data))
          seqlevels(data)[ids] <- sub("chr", "", seqlevels(data)[ids])
      }
      export(data, file.path(dirname(inf), paste0("ENSEMBL.", basename(inf))))
  }else{
      file.copy(inf, file.path(dirname(inf), paste0("ENSEMBL.", basename(inf))))
  }

}

Command exit status: 1

Command output: (empty)

Command error: Error in library(pkg, character.only = TRUE) : there is no package called ‘GenomeInfoDb’ Execution halted

Work dir: /flash/MillerU/S_lessoniana_hic_maps/work/de/3fe7af70d2471fd9a2748c8951aa40

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line Mar-13 16:14:47.082 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Mar-13 16:14:47.085 [main] DEBUG nextflow.Session - Session await > all processes finished Mar-13 16:14:47.089 [Actor Thread 14] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Mar-13 16:14:47.091 [Actor Thread 1] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.002 s; total time: 0.002 s Mar-13 16:14:47.094 [Actor Thread 1] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /flash/MillerU/S_lessoniana_hic_maps/work/collect-file/130a6013f52bc794b288d6ca01a1439a Mar-13 16:14:47.096 [Actor Thread 1] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/nxf-1485926341548380127 Mar-13 16:14:47.417 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig); status: COMPLETED; exit: 1; error: -; workDir: /flash/MillerU/S_lessoniana_hic_maps/work/ad/da663dcc4dcc76f061c32c2fb9ddba] Mar-13 16:14:47.418 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig); work-dir=/flash/MillerU/S_lessoniana_hic_maps/work/ad/da663dcc4dcc76f061c32c2fb9ddba error [nextflow.exception.ProcessFailedException]: Process NFCORE_HICAR:HICAR:MAPS_MULTIENZYME:ENSEMBL_UCSC_CONVERT2 (wgEncodeCrgMapabilityAlign50mer.chr22.bigWig) terminated with an error exit status (1) Mar-13 16:14:47.421 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Mar-13 16:14:47.422 [main] DEBUG nextflow.Session - Session await > all barriers passed Mar-13 16:14:47.425 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Mar-13 16:14:47.427 [main] INFO nextflow.Nextflow - -[nf-core/hicar] Pipeline completed with errors- Mar-13 16:14:47.431 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=3; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=8; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=1.8s; failedDuration=14.6s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=2; peakMemory=6 GB; ] Mar-13 16:14:47.432 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Mar-13 16:14:47.434 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Mar-13 16:14:48.125 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Mar-13 16:15:04.506 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Mar-13 16:15:04.530 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Mar-13 16:15:04.531 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

Version: 23.10.1 build 5893 Created: 12-01-2024 23:26 UTC (13-01-2024 08:26 JDT) System: Linux 4.18.0-348.2.1.el8_5.x86_64 Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 14+36-1461 Encoding: UTF-8 (UTF-8) Process: 2498030@deigo-login3.oist.jp [10.145.10.23] CPUs: 2 - Mem: 8 GB (6.3 GB) - Swap: 8 GB (1.7 GB)

jianhong commented 2 months ago

Your command is: nextflow run nf-core/hicar -r 1.0.0 -profile test --outdir ./. That will assume that you have all tools available in your PATH. Could you please try it with predifined profile such as conda, docker, or singularity?

luciazifcakova commented 2 months ago

Thank you jianhong, adding singularity profile did work for test profile.