.nextflow.log

May-28 02:56:50.576 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/scrnaseq -r 4.0.0 --input /rds/projects/g/gendood-3dmucosa/Globus/htk_hgk_vu40t_samplesheet.csv --outdir /rds/projects/g/gendood-3dmucosa/Globus/htk_hgk_VU40T_QC_and_counts --genome GRCh38 -profile bluebear --aligner cellranger --cellranger_index /rds/projects/g/gendood-3dmucosa/BaseSpace/LPS_VU40T_QC_and_counts/cellranger/mkref/cellranger_reference/
May-28 02:56:50.647 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
May-28 02:56:50.672 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/rds/homes/d/daviesjp/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
May-28 02:56:50.686 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
May-28 02:56:50.687 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
May-28 02:56:50.691 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
May-28 02:56:50.705 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
May-28 02:56:50.729 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /rds/homes/d/daviesjp/.nextflow/scm
May-28 02:56:51.694 [main] WARN  nextflow.config.Manifest - Invalid config manifest attribute `contributors`
May-28 02:56:51.696 [main] DEBUG nextflow.scm.AssetManager - Git config: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/scrnaseq.git
May-28 02:56:51.755 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
May-28 02:56:51.765 [main] DEBUG nextflow.scm.AssetManager - Git config: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/scrnaseq.git
May-28 02:56:52.733 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/nextflow.config
May-28 02:56:52.734 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/nextflow.config
May-28 02:56:52.741 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /rds/homes/d/daviesjp/.nextflow/secrets/store.json
May-28 02:56:52.744 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@45bbc52f] - activable => nextflow.secret.LocalSecretsProvider@45bbc52f
May-28 02:56:52.755 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `bluebear`
May-28 02:56:54.140 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, giga, incliva, ilifu, ki_luria, uge, icr_alma, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, roslin, ccga_med, tes, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, test_cellrangermulti, pdc_kth, googlels, ceci_nic5, humantechnopole, stjude, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, seattlechildrens, icr_davros, ceres, arm, munin, rosalind, hasta, cfc, uzh, shu_bmrc, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, shifter, biohpc_gen, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, ceci_dragon2, imperial, maestro, software_license, cannon, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, alliance_canada, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, gpu, test_multiome, seg_globe, mssm, sanger, dkfz, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, seadragon, crukmi, csiro_petrichor, qmul_apocrita, wave, docker, engaging, gis, hypatia, psmn, eva, unity, cropdiversityhpc, nygc, fgcz, conda, crg, singularity, mpcdf_viper, pe2, self_hosted_runner, tufts, uw_hyak_pedslabs, binac2, debug, genouest, cbe, unsw_katana, gitpod, phoenix, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac, fsu_draco]
May-28 02:56:54.180 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
May-28 02:56:54.210 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/scrnaseq` [chaotic_ramanujan] DSL2 - revision: e0ddddbff9 [4.0.0]
May-28 02:56:54.211 [main] WARN  nextflow.plugin.PluginsFacade - Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-schema@2.3.0
May-28 02:56:54.281 [main] DEBUG nextflow.Session - Session UUID: 0ee3b1ea-7b00-4f10-a290-ce4dc655ef73
May-28 02:56:54.282 [main] DEBUG nextflow.Session - Run name: chaotic_ramanujan
May-28 02:56:54.282 [main] DEBUG nextflow.Session - Executor pool size: 16
May-28 02:56:54.291 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
May-28 02:56:54.297 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-28 02:56:54.318 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 24.04.2 build 5914
  Created: 29-05-2024 06:19 UTC (07:19 BST)
  System: Linux 4.18.0-553.el8_10.x86_64
  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 11.0.18+10
  Encoding: UTF-8 (UTF-8)
  Process: 2235761@bear-pg0207u17b.bear.cluster [10.20.20.59]
  CPUs: 16 - Mem: 64 GB (63.2 GB) - Swap: 0 (0)
May-28 02:56:54.336 [main] DEBUG nextflow.Session - Work-dir: /rds/homes/d/daviesjp/OralMucosa/work [gpfs]
May-28 02:56:54.397 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, AwsBatchExecutor, GoogleBatchExecutor]
May-28 02:56:54.415 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
May-28 02:56:54.438 [main] DEBUG nextflow.Session - Observer factory: WaveFactory
May-28 02:56:54.438 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
May-28 02:56:54.454 [main] WARN  nextflow.config.Manifest - Invalid config manifest attribute `contributors`
May-28 02:56:54.484 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
May-28 02:56:54.497 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
May-28 02:56:54.590 [main] DEBUG nextflow.Session - Session start
May-28 02:56:54.593 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /rds/projects/g/gendood-3dmucosa/Globus/htk_hgk_VU40T_QC_and_counts/pipeline_info/execution_trace_2025-05-28_02-56-52.txt
May-28 02:56:54.832 [main] DEBUG nextflow.Session - Using default localLib path: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/lib
May-28 02:56:54.836 [main] DEBUG nextflow.Session - Adding to the classpath library: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/lib
May-28 02:56:54.987 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
May-28 02:56:55.371 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: latest
May-28 02:56:55.699 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.3.0' resolved
May-28 02:56:55.699 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.3.0'
May-28 02:56:55.813 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.3.0
May-28 02:56:55.814 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema
May-28 02:56:55.948 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema
May-28 02:56:55.961 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
May-28 02:56:55.962 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema
May-28 02:56:56.770 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
May-28 02:56:56.982 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema
May-28 02:56:56.982 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema
May-28 02:56:56.984 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
May-28 02:56:56.985 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema
May-28 02:57:00.393 [main] INFO  nextflow.Nextflow - 
------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/scrnaseq 4.0.0
------------------------------------------------------
Input/output options
  input                     : /rds/projects/g/gendood-3dmucosa/Globus/htk_hgk_vu40t_samplesheet.csv
  outdir                    : /rds/projects/g/gendood-3dmucosa/Globus/htk_hgk_VU40T_QC_and_counts

Mandatory arguments
  aligner                   : cellranger

Reference genome options
  genome                    : GRCh38
  save_align_intermeds      : true

Cellranger Options
  cellranger_index          : /rds/projects/g/gendood-3dmucosa/BaseSpace/LPS_VU40T_QC_and_counts/cellranger/mkref/cellranger_reference/

Institutional config options
  config_profile_description: BlueBEAR cluster profile
  config_profile_contact    : Alex Lyttle (@alexlyttle)
  config_profile_url        : https://docs.bear.bham.ac.uk/

Generic options
  trace_report_suffix       : 2025-05-28_02-56-52

Core Nextflow options
  revision                  : 4.0.0
  runName                   : chaotic_ramanujan
  containerEngine           : singularity
  launchDir                 : /rds/homes/d/daviesjp/OralMucosa
  workDir                   : /rds/homes/d/daviesjp/OralMucosa/work
  projectDir                : /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq
  userName                  : daviesjp
  profile                   : bluebear
  configFiles               : /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.5281/zenodo.3568187

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

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

May-28 02:57:00.399 [main] DEBUG n.validation.ValidationExtension - Starting parameters validation
May-28 02:57:00.475 [main] WARN  n.validation.ValidationExtension - The following invalid input values have been detected:

* --monochromeLogs: null
* --monochrome-logs: null
* --max_memory: 512 GB
* --max_cpus: 112
* --max_time: 10d


May-28 02:57:00.740 [main] DEBUG nextflow.validation.SchemaEvaluator - Started validating /rds/projects/g/gendood-3dmucosa/Globus/htk_hgk_vu40t_samplesheet.csv
May-28 02:57:00.825 [main] DEBUG nextflow.validation.SchemaEvaluator - Validation of file '/rds/projects/g/gendood-3dmucosa/Globus/htk_hgk_vu40t_samplesheet.csv' passed!
May-28 02:57:00.826 [main] DEBUG n.v.FormatDirectoryPathEvaluator - Cloud blob storage paths are not supported by 'FormatDirectoryPathEvaluator': 's3://ngi-igenomes/igenomes/'
May-28 02:57:00.834 [main] DEBUG n.validation.ValidationExtension - Finishing parameters validation
May-28 02:57:01.087 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC
May-28 02:57:01.089 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC
May-28 02:57:01.097 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
May-28 02:57:01.097 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
May-28 02:57:01.106 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm
May-28 02:57:01.112 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 60; pollInterval: 5s; dumpInterval: 5m 
May-28 02:57:01.114 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm)
May-28 02:57:01.115 [main] DEBUG n.processor.TaskPollingMonitor - Creating submit rate limit of 1 submissions per 1 seconds
May-28 02:57:01.119 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
May-28 02:57:01.192 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT
May-28 02:57:01.193 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CELLRANGER_COUNT` matches process NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT
May-28 02:57:01.194 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
May-28 02:57:01.195 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
May-28 02:57:01.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD
May-28 02:57:01.218 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MTX_TO_H5AD|CONCAT_H5AD|ANNDATAR_CONVERT` matches process NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD
May-28 02:57:01.219 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
May-28 02:57:01.220 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
May-28 02:57:01.242 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,process_gpu` for process with name NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:CELLBENDER_REMOVEBACKGROUND
May-28 02:57:01.242 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_gpu` matches labels `process_medium,process_gpu` for process with name NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:CELLBENDER_REMOVEBACKGROUND
May-28 02:57:01.242 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CELLBENDER_REMOVEBACKGROUND` matches process NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:CELLBENDER_REMOVEBACKGROUND
May-28 02:57:01.245 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
May-28 02:57:01.246 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
May-28 02:57:01.263 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:ANNDATA_BARCODES
May-28 02:57:01.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ANNDATA_BARCODES` matches process NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:ANNDATA_BARCODES
May-28 02:57:01.266 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
May-28 02:57:01.266 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
May-28 02:57:01.278 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION:CONCAT_H5AD
May-28 02:57:01.279 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MTX_TO_H5AD|CONCAT_H5AD|ANNDATAR_CONVERT` matches process NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION:CONCAT_H5AD
May-28 02:57:01.283 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
May-28 02:57:01.283 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
May-28 02:57:01.297 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION:ANNDATAR_CONVERT
May-28 02:57:01.299 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MTX_TO_H5AD|CONCAT_H5AD|ANNDATAR_CONVERT` matches process NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION:ANNDATAR_CONVERT
May-28 02:57:01.300 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
May-28 02:57:01.300 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
May-28 02:57:01.391 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC
May-28 02:57:01.393 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC
May-28 02:57:01.395 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
May-28 02:57:01.395 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
May-28 02:57:01.409 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
May-28 02:57:01.411 [main] DEBUG nextflow.Session - Igniting dataflow network (23)
May-28 02:57:01.413 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC
May-28 02:57:01.415 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT
May-28 02:57:01.415 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD
May-28 02:57:01.416 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:CELLBENDER_REMOVEBACKGROUND
May-28 02:57:01.416 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:ANNDATA_BARCODES
May-28 02:57:01.416 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION:CONCAT_H5AD
May-28 02:57:01.416 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION:ANNDATAR_CONVERT
May-28 02:57:01.429 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC
May-28 02:57:01.432 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_116619ccb325236c: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellranger/count/main.nf
  Script_2cdf1dd129ca8d6b: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/kallisto_bustools.nf
  Script_2422cb5c866a3f02: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellranger/mkgtf/main.nf
  Script_215a636da7ab24a2: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./subworkflows/local/utils_nfcore_scrnaseq_pipeline/../../nf-core/utils_nfschema_plugin/main.nf
  Script_17ce930509503341: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/starsolo.nf
  Script_a5e3a56fa0f5753f: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/align_cellrangerarc.nf
  Script_5c4e8d4051efa81e: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/utils_nfcore_scrnaseq_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf
  Script_2ce2cea66f33b0c9: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/local/parse_cellrangermulti_samplesheet.nf
  Script_01678c41b497280c: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/local/alevinqc.nf
  Script_b6f2f5397ff1b307: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../modules/local/gtf_gene_filter.nf
  Script_0690c94ccbc80cf8: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/nf-core/h5ad_removebackground_barcodes_cellbender_anndata/../../../modules/nf-core/anndata/barcodes/main.nf
  Script_85014429899d4eed: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellrangerarc/count/main.nf
  Script_f484bb04f71d5cb3: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellranger/multi/main.nf
  Script_2b5dc2db40c0c7f1: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/simpleaf.nf
  Script_0fdb2e5f8575be0c: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../modules/nf-core/multiqc/main.nf
  Script_9920ace3f63f7548: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/local/concat_h5ad.nf
  Script_a242b7d3e1522c1a: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/align_cellranger.nf
  Script_67f289d1fa44410a: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/kallistobustools/count/main.nf
  Script_c224a5d34be70db1: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/nf-core/h5ad_removebackground_barcodes_cellbender_anndata/main.nf
  Script_0cb99b50b73564f3: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/simpleaf/index/main.nf
  Script_e6da1e6a0fbb4bd4: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/simpleaf/quant/main.nf
  Script_b8ef320e712f03dd: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellrangerarc/mkgtf/main.nf
  Script_4f612cfd8c52e8cd: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./subworkflows/local/utils_nfcore_scrnaseq_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf
  Script_c12f64b9d72aaf58: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/local/star_align.nf
  Script_3c99494cecee2398: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/h5ad_conversion.nf
  Script_8b4cd5023b0747bc: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/star/genomegenerate/main.nf
  Script_7db0c40b9e083db8: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/local/mtx_to_h5ad.nf
  Script_e04fff270dc1ec83: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/main.nf
  Script_7fc9d40ebc5611d3: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellranger/mkref/main.nf
  Script_bbcd84f7538bc350: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/utils_nfcore_scrnaseq_pipeline/main.nf
  Script_f535f8fb412be0f3: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/scrnaseq.nf
  Script_7d26d205472ec618: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/fastqc.nf
  Script_dc41886bdbd95b0b: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/fastqc/main.nf
  Script_a415462e1630ff87: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/nf-core/h5ad_removebackground_barcodes_cellbender_anndata/../../../modules/nf-core/cellbender/removebackground/main.nf
  Script_b6e854e2f4a9b0b7: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/kallistobustools/ref/main.nf
  Script_ee6d5a1dfbefe9e1: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellranger/mkvdjref/main.nf
  Script_a6b84a8d8db37c9d: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/gunzip/main.nf
  Script_13d4ec1d4f43657c: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/local/anndatar_convert.nf
  Script_fd9ffb2ce3d24fd1: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellrangerarc/mkref/main.nf
  Script_cf189f8d1668d163: /rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/align_cellrangermulti.nf
May-28 02:57:01.432 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
May-28 02:57:01.432 [main] DEBUG nextflow.Session - Session await
May-28 02:57:01.556 [Actor Thread 10] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.027 s; total time: 0.028 s
May-28 02:57:01.556 [Actor Thread 11] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.003 s; external sort time: 0.027 s; total time: 0.03 s
May-28 02:57:01.565 [Actor Thread 10] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /rds/homes/d/daviesjp/OralMucosa/work/collect-file/6b5f1f98092e82a1399f51190f2d58d4
May-28 02:57:01.576 [Actor Thread 11] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /rds/homes/d/daviesjp/OralMucosa/work/collect-file/4307ba84c444b9e994cb42ab03b46463
May-28 02:57:01.582 [Actor Thread 10] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-17510128378688608190
May-28 02:57:01.582 [Actor Thread 11] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-8439279239671131334
May-28 02:57:01.589 [Actor Thread 15] DEBUG i.s.wave.plugin.config.WaveConfig - Wave strategy not specified - using default: [container, dockerfile, conda, spack]
May-28 02:57:01.597 [Actor Thread 15] DEBUG io.seqera.wave.plugin.WaveClient - Wave config: WaveConfig(enabled:null, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.8-lunar; 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, preserveFileTimestamp:null)
May-28 02:57:01.650 [Actor Thread 10] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0; path=/rds/projects/g/gendood-3dmucosa/.apptainer/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img
May-28 02:57:01.650 [Actor Thread 11] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://quay.io/nf-core/cellranger:8.0.0; path=/rds/projects/g/gendood-3dmucosa/.apptainer/quay.io-nf-core-cellranger-8.0.0.img
May-28 02:57:01.840 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_HGK_S4) > jobId: 23186106; workDir: /rds/homes/d/daviesjp/OralMucosa/work/2f/5a2dd198cc0371ed6c171da3a10be9
May-28 02:57:01.840 [Task submitter] INFO  nextflow.Session - [2f/5a2dd1] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_HGK_S4)
May-28 02:57:02.150 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R2-VU40T_S2) > jobId: 23186108; workDir: /rds/homes/d/daviesjp/OralMucosa/work/3f/c81d4055ea0c252eb12f8833fdf054
May-28 02:57:02.150 [Task submitter] INFO  nextflow.Session - [3f/c81d40] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R2-VU40T_S2)
May-28 02:57:03.160 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_HTK_S5) > jobId: 23186109; workDir: /rds/homes/d/daviesjp/OralMucosa/work/74/4d8dff2c7bc8c444e33909ac9dd06f
May-28 02:57:03.160 [Task submitter] INFO  nextflow.Session - [74/4d8dff] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_HTK_S5)
May-28 02:57:04.162 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_R2-HGK_S3) > jobId: 23186110; workDir: /rds/homes/d/daviesjp/OralMucosa/work/39/539ba6011fb587b8a2e6262495129a
May-28 02:57:04.163 [Task submitter] INFO  nextflow.Session - [39/539ba6] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_R2-HGK_S3)
May-28 02:57:05.172 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_R1-A_S1) > jobId: 23186111; workDir: /rds/homes/d/daviesjp/OralMucosa/work/5e/24469356a295eb8ab228604c40d52f
May-28 02:57:05.173 [Task submitter] INFO  nextflow.Session - [5e/244693] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_R1-A_S1)
May-28 02:57:06.149 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_R2-VU40T_S2) > jobId: 23186112; workDir: /rds/homes/d/daviesjp/OralMucosa/work/91/1ac8db6161753e964100ca8001925b
May-28 02:57:06.150 [Task submitter] INFO  nextflow.Session - [91/1ac8db] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_R2-VU40T_S2)
May-28 02:57:07.159 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R1-A_S1) > jobId: 23186113; workDir: /rds/homes/d/daviesjp/OralMucosa/work/d0/9d5787ce0eb5ff388a3a111f33638c
May-28 02:57:07.159 [Task submitter] INFO  nextflow.Session - [d0/9d5787] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R1-A_S1)
May-28 02:57:08.160 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_HTK_S5) > jobId: 23186114; workDir: /rds/homes/d/daviesjp/OralMucosa/work/80/230609964a3cad09d1aa2c7599a00c
May-28 02:57:08.161 [Task submitter] INFO  nextflow.Session - [80/230609] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (GB240624-MW_HTK_S5)
May-28 02:57:09.148 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R2-HGK_S3) > jobId: 23186116; workDir: /rds/homes/d/daviesjp/OralMucosa/work/87/2a40884540f859ebc802307480b13f
May-28 02:57:09.148 [Task submitter] INFO  nextflow.Session - [87/2a4088] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R2-HGK_S3)
May-28 02:57:10.165 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_HGK_S4) > jobId: 23186117; workDir: /rds/homes/d/daviesjp/OralMucosa/work/9e/4817e141441d060e8fe79a823184b5
May-28 02:57:10.165 [Task submitter] INFO  nextflow.Session - [9e/4817e1] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_HGK_S4)
May-28 02:57:16.142 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 23186113; id: 5; name: NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R1-A_S1); status: COMPLETED; exit: 1; error: -; workDir: /rds/homes/d/daviesjp/OralMucosa/work/d0/9d5787ce0eb5ff388a3a111f33638c started: 1748397436137; exited: 2025-05-28T01:57:14.725892Z; ]
May-28 02:57:16.143 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-28 02:57:16.149 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R1-A_S1); work-dir=/rds/homes/d/daviesjp/OralMucosa/work/d0/9d5787ce0eb5ff388a3a111f33638c
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R1-A_S1)` terminated with an error exit status (1)
May-28 02:57:16.191 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R1-A_S1)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R1-A_S1)` terminated with an error exit status (1)


Command executed [/rds/homes/d/daviesjp/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/local/../../modules/nf-core/cellranger/count/templates/cellranger_count.py]:

  #!/usr/bin/env python3
  """
  Automatically rename staged files for input into cellranger count.
  
  Copyright (c) Gregor Sturm 2023 - MIT License
  """
  
  from subprocess import run
  from pathlib import Path
  from textwrap import dedent
  import shlex
  import re
  
  
  def chunk_iter(seq, size):
      """iterate over `seq` in chunks of `size`"""
      return (seq[pos : pos + size] for pos in range(0, len(seq), size))
  
  
  sample_id = "GB240624-MW_R1-A_S1"
  
  # get fastqs, ordered by path. Files are staged into
  #   - "fastq_001/{original_name.fastq.gz}"
  #   - "fastq_002/{oritinal_name.fastq.gz}"
  #   - ...
  # Since we require fastq files in the input channel to be ordered such that a R1/R2 pair
  # of files follows each other, ordering will get us a sequence of [R1, R2, R1, R2, ...]
  fastqs = sorted(Path(".").glob("fastq_*/*"))
  assert len(fastqs) % 2 == 0
  
  # target directory in which the renamed fastqs will be placed
  fastq_all = Path("./fastq_all")
  fastq_all.mkdir(exist_ok=True)
  
  # Match R1 in the filename, but only if it is followed by a non-digit or non-character
  # match "file_R1.fastq.gz", "file.R1_000.fastq.gz", etc. but
  # do not match "SRR12345", "file_INFIXR12", etc
  filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])"
  
  for i, (r1, r2) in enumerate(chunk_iter(fastqs, 2), start=1):
      # double escapes are required because nextflow processes this python 'template'
      if re.sub(filename_pattern, r"\1R2\2", r1.name) != r2.name:
          raise AssertionError(
              dedent(
                  f"""                We expect R1 and R2 of the same sample to have the same filename except for R1/R2.
                  This has been checked by replacing "R1" with "R2" in the first filename and comparing it to the second filename.
                  If you believe this check shouldn't have failed on your filenames, please report an issue on GitHub!
  
                  Files involved:
                      - {r1}
                      - {r2}
                  """
              )
          )
      r1.rename(fastq_all / f"{sample_id}_S1_L{i:03d}_R1_001.fastq.gz")
      r2.rename(fastq_all / f"{sample_id}_S1_L{i:03d}_R2_001.fastq.gz")
  
  # fmt: off
  run(
      [
          "cellranger", "count",
          "--id", "GB240624-MW_R1-A_S1",
          "--fastqs", str(fastq_all),
          "--transcriptome", "cellranger_reference",
          "--localcores", "12",
          "--localmem", "72",
          *shlex.split("""--chemistry auto --create-bam true """),
      ],
      check=True,
  )
  # fmt: on
  
  # Output version information
  version = run(
      ["cellranger", "-V"],
      text=True,
      check=True,
      capture_output=True,
  ).stdout.replace("cellranger cellranger-", "")
  
  # alas, no `pyyaml` pre-installed in the cellranger container
  with open("versions.yml", "w") as f:
      f.write('"NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT":\n')
      f.write(f'  cellranger: "{version}"\n')

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Traceback (most recent call last):
    File ".command.sh", line 43, in <module>
      raise AssertionError(
  AssertionError: We expect R1 and R2 of the same sample to have the same filename except for R1/R2.
  This has been checked by replacing "R1" with "R2" in the first filename and comparing it to the second filename.
  If you believe this check shouldn't have failed on your filenames, please report an issue on GitHub!
  
  Files involved:
      - fastq_001/GB240624-MW_R1-A_S1_L001_R1_001.fastq.gz
      - fastq_002/GB240624-MW_R1-A_S1_L001_R2_001.fastq.gz

Work dir:
  /rds/homes/d/daviesjp/OralMucosa/work/d0/9d5787ce0eb5ff388a3a111f33638c

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
May-28 02:57:16.210 [TaskFinalizer-1] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
May-28 02:57:16.214 [TaskFinalizer-1] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
May-28 02:57:16.215 [main] DEBUG nextflow.Session - Session await > all processes finished
May-28 02:57:16.249 [Actor Thread 5] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.003 s; total time: 0.004 s
May-28 02:57:16.252 [Actor Thread 5] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /rds/homes/d/daviesjp/OralMucosa/work/collect-file/1fd087ef95e2fdfee1ef647fe2c75109
May-28 02:57:16.256 [Actor Thread 5] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-2238283851231865713
May-28 02:59:11.874 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 23186116; id: 7; name: NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R2-HGK_S3); status: COMPLETED; exit: 1; error: -; workDir: /rds/homes/d/daviesjp/OralMucosa/work/87/2a40884540f859ebc802307480b13f started: 1748397436154; exited: 2025-05-28T01:59:11.073816Z; ]
May-28 02:59:11.877 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R2-HGK_S3); work-dir=/rds/homes/d/daviesjp/OralMucosa/work/87/2a40884540f859ebc802307480b13f
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (GB240624-MW_R2-HGK_S3)` terminated with an error exit status (1)
May-28 02:59:51.221 [Task monitor] DEBUG nextflow.file.FileHelper - NFS path (false): /rds/homes/d/daviesjp/OralMucosa/work