Command exit status: 127

[thanadol-git]

I got this error message, but I don't know how to handle it. I have checked my sdrf file and it looks fine. Let me know if you have any idea.

executor >  local (1)
[56/d29613] BIG…pis_dia.18plates.sdrf.tsv) | 0 of 1 ✘
[-        ] BIG…INPUT_CHANNEL:SDRF_PARSING -
[-        ] BIG…ILE_PREPARATION:DECOMPRESS -
[-        ] BIG…_PREPARATION:MZML_INDEXING -
[-        ] BIG…RATION:THERMORAWFILEPARSER -
[-        ] BIG…REPARATION:MZML_STATISTICS -
[-        ] BIG…MS:GENERATE_DECOY_DATABASE -
[-        ] BIG…TIDE_DATABASE_SEARCH:COMET -
[-        ] BIG…D:PSM_RESCORING:PERCOLATOR -
[-        ] BIG…:PSM_FDR_CONTROL:ID_FILTER -
[-        ] BIG…E_MAPPER:ISOBARIC_ANALYZER -
[-        ] BIG…T:FEATURE_MAPPER:ID_MAPPER -
[-        ] BIG…TMS:QUANTMS:TMT:FILE_MERGE -
[-        ] BIG…:PROTEIN_INFERENCE_GENERIC -
[-        ] BIG…ROTEIN_INFERENCE:ID_FILTER -
[-        ] BIG…QUANT:ID_CONFLICT_RESOLVER -
[-        ] BIG…N_QUANT:PROTEIN_QUANTIFIER -
[-        ] BIG…IN_QUANT:MSSTATS_CONVERTER -
[-        ] BIG…TIDE_DATABASE_SEARCH:COMET -
[-        ] BIG…D:PSM_RESCORING:PERCOLATOR -
Plus 10 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
-[bigbio/quantms] Pipeline completed with errors-
ERROR ~ Error executing process > 'BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (scapis_dia.18plates.sdrf.tsv)'

Caused by:
  Process `BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (scapis_dia.18plates.sdrf.tsv)` terminated with an error exit status (127)


Command executed:

  quantmsutilsc checksamplesheet --exp_design "scapis_dia.18plates.sdrf.tsv" --is_sdrf \
   \
   \
  --skip_factor_validation \
   \
  --use_ols_cache_only 2>&1 | tee input_check.log
  
  cat <<-END_VERSIONS > versions.yml
  "BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK":
      quantms-utils: $(pip show quantms-utils | grep "Version" | awk -F ': ' '{print $2}')
  END_VERSIONS

Command exit status:
  127

Command output:
  .command.sh: line 2: quantmsutilsc: command not found

Command error:
  .command.sh: line 2: quantmsutilsc: command not found

Work dir:
  /proj/naiss2025-3-66/users/x_thasu/pridepy/load/scapis/work/56/d29613d64bd1181da13875a907bc5f

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
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

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

[jpfeuffer]

Hi!
Which profile are you using? Do you have the command or the .nextflow.log or some of the nextflow reports?

I assume you are using the wrong conda/docker or no profile at all.

[thanadol-git]

Hi, @jpfeuffer

Here is the .nextflow.log.

Feb-11 15:48:19.102 [main] DEBUG nextflow.cli.Launcher - $> nextflow run bigbio/quantms -r dev --input scapis_dia.18plates.sdrf.tsv --outdir results --database human_proteome.fasta --root_folder /home/x_thasu/naiss2025-3-66/pridepy/load/scapis --add_decoys true --local_input_type mzML --max_memory 64GB --max_cpu 8 --platform linux/amd64 --skip_post_msstats true
Feb-11 15:48:19.196 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 25.10.4
Feb-11 15:48:19.226 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/x_thasu/.nextflow/plugins; core-plugins: nf-amazon@3.4.4,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.5,nf-k8s@1.2.2,nf-tower@1.17.5,nf-wave@1.16.1
Feb-11 15:48:19.247 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-11 15:48:19.248 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-11 15:48:19.251 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Feb-11 15:48:19.265 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config
Feb-11 15:48:19.384 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Feb-11 15:48:19.396 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/x_thasu/.nextflow/scm
Feb-11 15:48:20.317 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/x_thasu/.nextflow/assets/bigbio/quantms/.git/config; branch: master; remote: origin; url: https://github.com/bigbio/quantms.git
Feb-11 15:48:20.374 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Feb-11 15:48:20.387 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/x_thasu/.nextflow/assets/bigbio/quantms/.git/config; branch: master; remote: origin; url: https://github.com/bigbio/quantms.git
Feb-11 15:48:23.454 [main] INFO  nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [545f484496]
Feb-11 15:48:23.468 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/x_thasu/.nextflow/assets/bigbio/quantms/nextflow.config
Feb-11 15:48:23.470 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/x_thasu/.nextflow/assets/bigbio/quantms/nextflow.config
Feb-11 15:48:23.482 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-11 15:48:24.382 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.5.1]
Feb-11 15:48:24.383 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-11 15:48:24.383 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.5.1]
Feb-11 15:48:24.579 [main] DEBUG n.plugin.HttpPluginRepository - Registry request: https://registry.nextflow.io/api/v1/plugins/dependencies?plugins=nf-schema%402.5.1&nextflowVersion=25.10.4
- code: 200
- body: {"plugins":[{"id":"nf-schema","downloadCount":190768,"downloadGhCount":530373,"releases":[{"version":"2.5.1","url":"https://registry.nextflow.io/api/v1/plugins/nf-schema/2.5.1/download/nf-schema-2.5.1.zip","date":"2025-09-02T14:48:39.714892Z","sha512sum":"82c9c17a9f77319386e670e7b52cf79b067320001f083ccdfec77dada9fd53499506200fd10b493cf8f6fc0420f42e2314481c353ca14b3a92f354bf07ad5c13","requires":">=25.04.0","dependsOn":[],"downloadCount":105777,"downloadGhCount":39150,"status":"PUBLISHED","spec":null,"description":null}],"projectUrl":"https://github.com/nextflow-io/nf-schema","provider":"nextflow-io","description":null}]}
Feb-11 15:48:24.617 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.5.1
Feb-11 15:48:24.627 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.5.1' resolved
Feb-11 15:48:24.627 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.5.1'
Feb-11 15:48:24.631 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.5.1
Feb-11 15:48:24.637 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/x_thasu/.nextflow/secrets/store.json
Feb-11 15:48:24.639 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@761f234c] - activable => nextflow.secret.LocalSecretsProvider@761f234c
Feb-11 15:48:24.640 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Feb-11 15:48:24.641 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/bigbio/quantms` [kickass_keller] DSL2 - revision: cc20b80cb9 [dev]
Feb-11 15:48:24.685 [main] DEBUG nextflow.Session - Session UUID: 39b846e1-a786-4d52-b4e7-a8c268604a7b
Feb-11 15:48:24.685 [main] DEBUG nextflow.Session - Run name: kickass_keller
Feb-11 15:48:24.686 [main] DEBUG nextflow.Session - Executor pool size: 8
Feb-11 15:48:24.694 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Feb-11 15:48:24.698 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-11 15:48:24.712 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 25.10.4 build 11173
  Created: 10-02-2026 15:17 UTC (16:17 CEST)
  System: Linux 5.14.0-611.24.1.el9_7.x86_64
  Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 17.0.6+10
  Encoding: UTF-8 (UTF-8)
  Process: 2085899@n132 [10.24.1.32]
  CPUs: 8 - Mem: 93.1 GB (71.7 GB) - Swap: 1.9 GB (1.9 GB)
Feb-11 15:48:24.726 [main] DEBUG nextflow.Session - Work-dir: /proj/naiss2025-3-66/users/x_thasu/pridepy/load/scapis/work [gpfs]
Feb-11 15:48:24.752 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-11 15:48:24.761 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Feb-11 15:48:24.763 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory
Feb-11 15:48:24.778 [main] DEBUG nextflow.Session - Observer factory (v2): ValidationObserverFactory
Feb-11 15:48:24.819 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-11 15:48:24.827 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Feb-11 15:48:24.904 [main] DEBUG nextflow.Session - Session start
Feb-11 15:48:24.911 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: results/pipeline_info/execution_trace_2026-02-11_15-48-23.txt
Feb-11 15:48:25.019 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-11 15:48:25.358 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Feb-11 15:48:25.387 [main] DEBUG n.validation.config.ValidationConfig - Set `validation.monochromeLogs` to false
Feb-11 15:48:25.389 [main] DEBUG n.validation.config.ValidationConfig - Added the following parameters to the ignored parameters: [genomes]
Feb-11 15:48:25.663 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Feb-11 15:48:31.925 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Feb-11 15:48:32.137 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_tiny` matches labels `process_tiny` for process with name BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK
Feb-11 15:48:32.140 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK` matches process BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK
Feb-11 15:48:32.143 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.144 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.153 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-11 15:48:32.158 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=93.1 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
Feb-11 15:48:32.160 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Feb-11 15:48:32.180 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK': maxForks=0; fair=false; array=0
Feb-11 15:48:32.230 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_tiny` matches labels `process_tiny` for process with name BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRF_PARSING
Feb-11 15:48:32.231 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:SDRF_PARSING` matches process BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRF_PARSING
Feb-11 15:48:32.233 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.233 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.234 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRF_PARSING': maxForks=0; fair=false; array=0
Feb-11 15:48:32.272 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low,error_retry` for process with name BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS
Feb-11 15:48:32.272 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:error_retry` matches labels `process_low,error_retry` for process with name BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS
Feb-11 15:48:32.274 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.274 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.275 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS': maxForks=0; fair=false; array=0
Feb-11 15:48:32.288 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low,openms` for process with name BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_INDEXING
Feb-11 15:48:32.293 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.293 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.293 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_INDEXING': maxForks=0; fair=false; array=0
Feb-11 15:48:32.299 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_low,process_single,error_retry` for process with name BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER
Feb-11 15:48:32.300 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low,process_single,error_retry` for process with name BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER
Feb-11 15:48:32.300 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:error_retry` matches labels `process_low,process_single,error_retry` for process with name BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER
Feb-11 15:48:32.302 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.302 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.302 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.311 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_very_low,process_single` for process with name BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_STATISTICS
Feb-11 15:48:32.311 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_very_low` matches labels `process_very_low,process_single` for process with name BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_STATISTICS
Feb-11 15:48:32.313 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.313 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.314 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_STATISTICS': maxForks=0; fair=false; array=0
Feb-11 15:48:32.346 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_very_low` matches labels `process_very_low,openms` for process with name BIGBIO_QUANTMS:QUANTMS:GENERATE_DECOY_DATABASE
Feb-11 15:48:32.348 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.349 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.349 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:GENERATE_DECOY_DATABASE': maxForks=0; fair=false; array=0
Feb-11 15:48:32.362 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:ID:PEPTIDE_DATABASE_SEARCH:COMET
Feb-11 15:48:32.364 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.364 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.365 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:ID:PEPTIDE_DATABASE_SEARCH:COMET': maxForks=0; fair=false; array=0
Feb-11 15:48:32.386 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_RESCORING:PERCOLATOR
Feb-11 15:48:32.387 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:PERCOLATOR` matches process BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_RESCORING:PERCOLATOR
Feb-11 15:48:32.389 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.390 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.390 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_RESCORING:PERCOLATOR': maxForks=0; fair=false; array=0
Feb-11 15:48:32.402 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_very_low,process_single,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_FDR_CONTROL:ID_FILTER
Feb-11 15:48:32.402 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_very_low` matches labels `process_very_low,process_single,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_FDR_CONTROL:ID_FILTER
Feb-11 15:48:32.403 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:ID:PSM_FDR_CONTROL:ID_FILTER` matches process BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_FDR_CONTROL:ID_FILTER
Feb-11 15:48:32.404 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.404 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.405 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_FDR_CONTROL:ID_FILTER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.416 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ISOBARIC_ANALYZER
Feb-11 15:48:32.418 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.419 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.419 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ISOBARIC_ANALYZER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.427 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ID_MAPPER
Feb-11 15:48:32.429 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:TMT:.*:ID_MAPPER` matches process BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ID_MAPPER
Feb-11 15:48:32.430 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.430 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.430 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ID_MAPPER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.438 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_medium,process_single,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:FILE_MERGE
Feb-11 15:48:32.439 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,process_single,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:FILE_MERGE
Feb-11 15:48:32.440 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.440 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.441 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:FILE_MERGE': maxForks=0; fair=false; array=0
Feb-11 15:48:32.448 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:PROTEIN_INFERENCE_GENERIC
Feb-11 15:48:32.450 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.450 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.451 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:PROTEIN_INFERENCE_GENERIC': maxForks=0; fair=false; array=0
Feb-11 15:48:32.459 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_very_low,process_single,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:ID_FILTER
Feb-11 15:48:32.460 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_very_low` matches labels `process_very_low,process_single,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:ID_FILTER
Feb-11 15:48:32.460 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:TMT:PROTEIN_INFERENCE:ID_FILTER` matches process BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:ID_FILTER
Feb-11 15:48:32.462 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.462 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.462 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:ID_FILTER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.473 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:ID_CONFLICT_RESOLVER
Feb-11 15:48:32.475 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.475 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.476 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:ID_CONFLICT_RESOLVER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.482 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER
Feb-11 15:48:32.482 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|FINAL_QUANTIFICATION|CONVERT_RESULTS` matches process BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER
Feb-11 15:48:32.483 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER` matches process BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER
Feb-11 15:48:32.485 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.485 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.485 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.492 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low,openms` for process with name BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER
Feb-11 15:48:32.493 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|FINAL_QUANTIFICATION|CONVERT_RESULTS` matches process BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER
Feb-11 15:48:32.493 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER` matches process BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER
Feb-11 15:48:32.494 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.494 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.495 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.525 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,openms` for process with name BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PEPTIDE_DATABASE_SEARCH:COMET
Feb-11 15:48:32.527 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.527 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.528 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PEPTIDE_DATABASE_SEARCH:COMET': maxForks=0; fair=false; array=0
Feb-11 15:48:32.551 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,openms` for process with name BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_RESCORING:PERCOLATOR
Feb-11 15:48:32.552 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:PERCOLATOR` matches process BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_RESCORING:PERCOLATOR
Feb-11 15:48:32.553 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.553 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.554 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_RESCORING:PERCOLATOR': maxForks=0; fair=false; array=0
Feb-11 15:48:32.569 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_very_low,process_single,openms` for process with name BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_FDR_CONTROL:ID_FILTER
Feb-11 15:48:32.569 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_very_low` matches labels `process_very_low,process_single,openms` for process with name BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_FDR_CONTROL:ID_FILTER
Feb-11 15:48:32.570 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:ID:PSM_FDR_CONTROL:ID_FILTER` matches process BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_FDR_CONTROL:ID_FILTER
Feb-11 15:48:32.571 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.571 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.571 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_FDR_CONTROL:ID_FILTER': maxForks=0; fair=false; array=0
Feb-11 15:48:32.595 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_high` matches labels `process_high,openms` for process with name BIGBIO_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ
Feb-11 15:48:32.596 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|FINAL_QUANTIFICATION|CONVERT_RESULTS` matches process BIGBIO_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ
Feb-11 15:48:32.596 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:LFQ:PROTEOMICSLFQ` matches process BIGBIO_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ
Feb-11 15:48:32.597 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.597 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.598 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ': maxForks=0; fair=false; array=0
Feb-11 15:48:32.634 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_tiny` matches labels `process_tiny` for process with name BIGBIO_QUANTMS:QUANTMS:DIA:GENERATE_CFG
Feb-11 15:48:32.636 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.636 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.637 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:DIA:GENERATE_CFG': maxForks=0; fair=false; array=0
Feb-11 15:48:32.643 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium,diann` for process with name BIGBIO_QUANTMS:QUANTMS:DIA:INSILICO_LIBRARY_GENERATION
Feb-11 15:48:32.644 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:DIA:INSILICO_LIBRARY_GENERATION` matches process BIGBIO_QUANTMS:QUANTMS:DIA:INSILICO_LIBRARY_GENERATION
Feb-11 15:48:32.645 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.645 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.646 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:DIA:INSILICO_LIBRARY_GENERATION': maxForks=0; fair=false; array=0
Feb-11 15:48:32.657 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_high` matches labels `process_high,diann` for process with name BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS
Feb-11 15:48:32.658 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:DIA:PRELIMINARY_ANALYSIS` matches process BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS
Feb-11 15:48:32.658 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.658 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.659 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS': maxForks=0; fair=false; array=0
Feb-11 15:48:32.667 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low,diann` for process with name BIGBIO_QUANTMS:QUANTMS:DIA:ASSEMBLE_EMPIRICAL_LIBRARY
Feb-11 15:48:32.668 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.668 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.669 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:DIA:ASSEMBLE_EMPIRICAL_LIBRARY': maxForks=0; fair=false; array=0
Feb-11 15:48:32.683 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_high` matches labels `process_high,diann` for process with name BIGBIO_QUANTMS:QUANTMS:DIA:INDIVIDUAL_ANALYSIS
Feb-11 15:48:32.685 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.685 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.686 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:DIA:INDIVIDUAL_ANALYSIS': maxForks=0; fair=false; array=0
Feb-11 15:48:32.698 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_high` matches labels `process_high,diann` for process with name BIGBIO_QUANTMS:QUANTMS:DIA:FINAL_QUANTIFICATION
Feb-11 15:48:32.698 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|FINAL_QUANTIFICATION|CONVERT_RESULTS` matches process BIGBIO_QUANTMS:QUANTMS:DIA:FINAL_QUANTIFICATION
Feb-11 15:48:32.700 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.700 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.700 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:DIA:FINAL_QUANTIFICATION': maxForks=0; fair=false; array=0
Feb-11 15:48:32.721 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name BIGBIO_QUANTMS:QUANTMS:DIA:CONVERT_RESULTS
Feb-11 15:48:32.722 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|FINAL_QUANTIFICATION|CONVERT_RESULTS` matches process BIGBIO_QUANTMS:QUANTMS:DIA:CONVERT_RESULTS
Feb-11 15:48:32.723 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.723 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.724 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:DIA:CONVERT_RESULTS': maxForks=0; fair=false; array=0
Feb-11 15:48:32.864 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_high` matches labels `process_high` for process with name BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE
Feb-11 15:48:32.867 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE` matches process BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE
Feb-11 15:48:32.868 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-11 15:48:32.868 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-11 15:48:32.868 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE': maxForks=0; fair=false; array=0
Feb-11 15:48:32.889 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
Feb-11 15:48:32.892 [main] DEBUG nextflow.Session - Igniting dataflow network (88)
Feb-11 15:48:32.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK
Feb-11 15:48:32.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRF_PARSING
Feb-11 15:48:32.894 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS
Feb-11 15:48:32.894 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_INDEXING
Feb-11 15:48:32.894 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER
Feb-11 15:48:32.894 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_STATISTICS
Feb-11 15:48:32.894 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:GENERATE_DECOY_DATABASE
Feb-11 15:48:32.894 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:ID:PEPTIDE_DATABASE_SEARCH:COMET
Feb-11 15:48:32.896 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_RESCORING:PERCOLATOR
Feb-11 15:48:32.896 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_FDR_CONTROL:ID_FILTER
Feb-11 15:48:32.896 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ISOBARIC_ANALYZER
Feb-11 15:48:32.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ID_MAPPER
Feb-11 15:48:32.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:FILE_MERGE
Feb-11 15:48:32.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:PROTEIN_INFERENCE_GENERIC
Feb-11 15:48:32.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:ID_FILTER
Feb-11 15:48:32.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:ID_CONFLICT_RESOLVER
Feb-11 15:48:32.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER
Feb-11 15:48:32.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER
Feb-11 15:48:32.898 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PEPTIDE_DATABASE_SEARCH:COMET
Feb-11 15:48:32.898 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_RESCORING:PERCOLATOR
Feb-11 15:48:32.898 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_FDR_CONTROL:ID_FILTER
Feb-11 15:48:32.898 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ
Feb-11 15:48:32.903 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:DIA:GENERATE_CFG
Feb-11 15:48:32.903 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:DIA:INSILICO_LIBRARY_GENERATION
Feb-11 15:48:32.903 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS
Feb-11 15:48:32.903 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:DIA:ASSEMBLE_EMPIRICAL_LIBRARY
Feb-11 15:48:32.903 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:DIA:INDIVIDUAL_ANALYSIS
Feb-11 15:48:32.903 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:DIA:FINAL_QUANTIFICATION
Feb-11 15:48:32.903 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:DIA:CONVERT_RESULTS
Feb-11 15:48:32.904 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE
Feb-11 15:48:32.906 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_d2c1c1c44c7ebd74: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/bigbio/thermorawfileparser/main.nf
  Script_7a5a914d4decbfef: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/tdf2mzml/main.nf
  Script_0ee92f06db6706e9: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/diann/individual_analysis/main.nf
  Script_c9ab84d08b039e3f: /home/x_thasu/.nextflow/assets/bigbio/quantms/main.nf
  Script_e82ae65a3d3865d7: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/decompress_dotd/main.nf
  Script_09f4757444c0862c: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/psm_fdr_control/main.nf
  Script_6fb7e823aa319a8d: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/diann/final_quantification/main.nf
  Script_f3fc3d05a7d5ff31: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/msstats/msstats_lfq/main.nf
  Script_6ae2189e6716569b: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/mzml_indexing/main.nf
  Script_d67accf348acdb01: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/diann/convert_results/main.nf
  Script_ef442d4ac2211bae: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/psm_conversion/main.nf
  Script_19f944edbdb7487e: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/utils_nfcore_quantms_pipeline/main.nf
  Script_4e10e1593539d348: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/protein_inference/main.nf
  Script_055abac88b107887: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/create_input_channel/main.nf
  Script_d0134e2c20ba4b0c: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/openms_peak_picker/main.nf
  Script_1e2e87202155a7a7: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/file_merge/main.nf
  Script_22d1caa0d150b279: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/id_filter/main.nf
  Script_5e743957e29a0de0: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/id_ripper/main.nf
  Script_c4b21e90970e32e6: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/phospho_scoring/main.nf
  Script_7750df89294b8a8e: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/protein_quant/main.nf
  Script_800ed8b2e7278021: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/file_preparation/main.nf
  Script_0cfe80d06b342275: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/protein_inference_generic/main.nf
  Script_a43bebda90062b9b: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/diann/assemble_empirical_library/main.nf
  Script_09e924c24e7f29bf: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/id/main.nf
  Script_11812bfcba44edf4: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/protein_inference_epifany/main.nf
  Script_dfb6b823e660eeb6: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/sage/main.nf
  Script_bc53707d5586d966: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/msgf_db_indexing/main.nf
  Script_d6d82d1b2ee91a1c: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/diann/preliminary_analysis/main.nf
  Script_9043fb6d4a9ed91b: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/isobaric_analyzer/main.nf
  Script_e1e79494c2792ffa: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/psm_clean/main.nf
  Script_f10ebc01b8e9d0ae: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/psm_rescoring/main.nf
  Script_c6438e98a7f82c81: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/msgf/main.nf
  Script_1ce3428f8dcc04d7: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/comet/main.nf
  Script_db9a98c6a17fe161: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/id_score_switcher/main.nf
  Script_69773ac361b48446: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/id_merger/main.nf
  Script_a11e37cab6af8e85: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/msrescore_fine_tuning/main.nf
  Script_76fd801ace5b5f25: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/id_mapper/main.nf
  Script_e9586de13fd07cc0: /home/x_thasu/.nextflow/assets/bigbio/quantms/workflows/quantms.nf
  Script_a93935ad04cbe427: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/input_check/main.nf
  Script_922affc93f193264: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/diann/generate_cfg/main.nf
  Script_b01d75257f08503c: /home/x_thasu/.nextflow/assets/bigbio/quantms/workflows/lfq.nf
  Script_f249995d273b0fc7: /home/x_thasu/.nextflow/assets/bigbio/quantms/workflows/dia.nf
  Script_020a73134dd7b1c0: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/diann/insilico_library_generation/main.nf
  Script_734be247454fa258: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/id_conflict_resolver/main.nf
  Script_4acaef13b0cf2a7d: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/generate_decoy_database/main.nf
  Script_1f86eaaf1a133c9f: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/samplesheet_check/main.nf
  Script_eaf2c4f9307054c2: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/extract_sample/main.nf
  Script_10cac95d8375377c: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/bigbio/onsite/main.nf
  Script_2ed4ae9a7fe6efa2: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/mzml_statistics/main.nf
  Script_85bdf8cabc1e2aae: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/spectrum_features/main.nf
  Script_4f612cfd8c52e8cd: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
  Script_597d4d047e9298e5: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/percolator/main.nf
  Script_5977f542cd315b9b: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
  Script_3592f3e1c5b1751a: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/protein_quantifier/main.nf
  Script_a43fc06127d51ba2: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/proteomicslfq/main.nf
  Script_bca0e8c82cd3260b: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/utils/msrescore_features/main.nf
  Script_44a9e7f7354783b7: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/msstats/msstats_tmt/main.nf
  Script_b69160527ce0b9d9: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/feature_mapper/main.nf
  Script_785c496c44ede21c: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/peptide_database_search/main.nf
  Script_9793fe099ff6e70c: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/pmultiqc/main.nf
  Script_c3a1e929c1c619d7: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/sdrf_parsing/main.nf
  Script_cf555edb08d2082d: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/msstats_converter/main.nf
  Script_45bb6d2f2bcbe1e2: /home/x_thasu/.nextflow/assets/bigbio/quantms/workflows/tmt.nf
  Script_a70b69a5d894e1f0: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/preprocess_expdesign/main.nf
  Script_8ce8997428acd6f2: /home/x_thasu/.nextflow/assets/bigbio/quantms/subworkflows/local/dda_id/main.nf
  Script_faf9bf6bdd515c5a: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/consensusid/main.nf
  Script_d2d2137680680ff6: /home/x_thasu/.nextflow/assets/bigbio/quantms/modules/local/openms/false_discovery_rate/main.nf
Feb-11 15:48:32.906 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Feb-11 15:48:32.906 [main] DEBUG nextflow.Session - Session await
Feb-11 15:48:32.910 [Actor Thread 11] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-13095052908390593400
Feb-11 15:48:33.011 [Actor Thread 14] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.039 s; total time: 0.04 s
Feb-11 15:48:33.022 [Actor Thread 14] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /proj/naiss2025-3-66/users/x_thasu/pridepy/load/scapis/work/collect-file/9948562b70185d11ba9c6b15699c1064
Feb-11 15:48:33.028 [Actor Thread 14] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-13633400396265906527
Feb-11 15:48:33.074 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-11 15:48:33.078 [Task submitter] INFO  nextflow.Session - [c0/431149] Submitted process > BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (scapis_dia.18plates.sdrf.tsv)
Feb-11 15:48:33.172 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (scapis_dia.18plates.sdrf.tsv); status: COMPLETED; exit: 127; error: -; workDir: /proj/naiss2025-3-66/users/x_thasu/pridepy/load/scapis/work/c0/4311493e39280df028486391a18990]
Feb-11 15:48:33.173 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-11 15:48:33.184 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (scapis_dia.18plates.sdrf.tsv); work-dir=/proj/naiss2025-3-66/users/x_thasu/pridepy/load/scapis/work/c0/4311493e39280df028486391a18990
  error [nextflow.exception.ProcessFailedException]: Process `BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (scapis_dia.18plates.sdrf.tsv)` terminated with an error exit status (127)
Feb-11 15:48:33.203 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (scapis_dia.18plates.sdrf.tsv)'

Caused by:
  Process `BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (scapis_dia.18plates.sdrf.tsv)` terminated with an error exit status (127)


Command executed:

  quantmsutilsc checksamplesheet --exp_design "scapis_dia.18plates.sdrf.tsv" --is_sdrf \
   \
   \
  --skip_factor_validation \
   \
  --use_ols_cache_only \
   \
  2>&1 | tee input_check.log
  
  cat <<-END_VERSIONS > versions.yml
  "BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK":
      quantms-utils: $(pip show quantms-utils | grep "Version" | awk -F ': ' '{print $2}')
  END_VERSIONS

Command exit status:
  127

Command output:
  .command.sh: line 2: quantmsutilsc: command not found

Command error:
  .command.sh: line 2: quantmsutilsc: command not found

Work dir:
  /proj/naiss2025-3-66/users/x_thasu/pridepy/load/scapis/work/c0/4311493e39280df028486391a18990

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Feb-11 15:48:33.224 [Actor Thread 18] 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
Feb-11 15:48:33.226 [TaskFinalizer-1] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Feb-11 15:48:33.231 [TaskFinalizer-1] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
Feb-11 15:48:33.232 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Feb-11 15:48:33.232 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-11 15:48:33.232 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-11 15:48:33.241 [Actor Thread 18] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /proj/naiss2025-3-66/users/x_thasu/pridepy/load/scapis/work/collect-file/d572df3692decd310024a4937631a16d
Feb-11 15:48:33.243 [Actor Thread 18] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-66856794851689204
Feb-11 15:48:33.246 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Feb-11 15:48:33.250 [main] INFO  nextflow.Nextflow - -[bigbio/quantms] Pipeline completed with errors-
Feb-11 15:48:33.258 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=24ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=1 GB; ]
Feb-11 15:48:33.523 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Feb-11 15:48:34.010 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Feb-11 15:48:34.070 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Feb-11 15:48:34.075 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-11 15:48:34.095 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.5.1'
Feb-11 15:48:34.095 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema
Feb-11 15:48:34.096 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Feb-11 15:48:34.097 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

[thanadol-git]

Here is how I submit the job.

#!/bin/bash


# Set work directory variable
WORK_DIR=""
# Set SDRF file variable
SDRF_FILE="scapis_dia.18plates.sdrf.tsv"

# Load necessary modules
ml Java/17.0.6-hpc1-bdist           # Ensure the correct Java environment is loaded

# Set the working directory from work directory variable and ensure the path is correct
cd "$WORK_DIR" || exit

# Ensure nextflow: prefer local copy in WORK_DIR, then system, otherwise install locally
if [ -x "${WORK_DIR}/nextflow" ]; then
    echo "Using local nextflow at ${WORK_DIR}/nextflow"
    NEXTFLOW_EXEC="${WORK_DIR}/nextflow"
elif command -v nextflow >/dev/null 2>&1; then
    NEXTFLOW_EXEC=$(command -v nextflow)
    echo "Using nextflow from PATH: $NEXTFLOW_EXEC"
else
    echo "Nextflow not found. Installing to ${WORK_DIR}..."
    # download using curl/wget and install into WORK_DIR
    if command -v curl >/dev/null 2>&1; then
        curl -fsSL https://get.nextflow.io -o nextflow || { echo "Failed to download nextflow"; exit 1; }
    elif command -v wget >/dev/null 2>&1; then
        wget -q -O nextflow https://get.nextflow.io || { echo "Failed to download nextflow"; exit 1; }
    else
        echo "Neither curl nor wget available to download nextflow. Install manually.";
        exit 1
    fi
    chmod +x nextflow
    mv nextflow "${WORK_DIR}/nextflow"
    NEXTFLOW_EXEC="${WORK_DIR}/nextflow"
fi


# Execute the Nextflow script using the chosen executable
"${NEXTFLOW_EXEC}" run bigbio/quantms -r dev \
  --input 'scapis_dia.18plates.sdrf.tsv' \
  --outdir 'results' \
  --database 'human_proteome.fasta' \
  --root_folder "${WORK_DIR}" \
  --add_decoys true \
  --local_input_type mzML \
  --max_memory 64GB \
  --max_cpu 8 \
  --platform linux/amd64 \
  --skip_post_msstats true

[thanadol-git]

@jpfeuffer
You are right. I forgot one line on profile. It should be now working. Thanks for always helping.