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genepi / umi-pipeline-nf

Nextflow pipeline to analyze ONT UMI Sequencing data
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Pipeline stops after only the first step COPY_BED #73

Closed vmelichar closed 1 month ago

vmelichar commented 1 month ago

Hi,

I am trying to run the pipeline but came across a problem. On the test data, it works as expected (using the conda profile). But on my actual data, it stops after the first step and does nothing else. I would appreciate any help. Thanks.

This is the command: nextflow run genepi/umi-pipeline-nf -r v0.2.1 -c custom_copy.config -params-file params.yaml -profile custom,conda -with-conda environment.yml -name umi 1_2 -resume

This is the custom_copy.config file:

/*
 * -------------------------------------------------
 *  Nextflow config file for custom parameter settings
 * -------------------------------------------------
 *   nextflow run umi-pipeline-nf -profile custom
 */

// NEXTFLOW REPORTING
if(params.output != null){
        dag {
                enabled = true
                file = "${params.output}/nextflow_stats/dag.mmd"
                overwrite = true
        }
        report {
                enabled = true
                file = "${params.output}/nextflow_stats/report.html"
                overwrite = true
        }
        timeline {
                enabled = true
                file = "${params.output}/nextflow_stats/timeline.html"
                overwrite = true
        }
        trace {
                enabled = true
                fields = "task_id, process, tag, status, cpus, time, memory, start, complete, duration, %mem, %cpu, vmem"
                file = "${params.output}/nextflow_stats/trace.txt"
                overwrite = true
        }
}

This is the params.yaml file:

input: 'data'
output: 'results_UMI1'
reference: '/mnt/scratch/melichv/references/Mus_musculus/Mus_musculus.GRCm39.dna.toplevel.fa'
reference_fai: '/mnt/scratch/melichv/references/Mus_musculus/Mus_musculus.GRCm39.dna.toplevel.fa.fai'
bed: 'bed/amplicon_B6-Hs4-KV.bed'
threads: 20
call_variants: true
variant_caller: 'freebayes'
medaka_model: 'r1041_e82_400bps_sup_v5.0.0'
fwd_umi: 'NNNYRNNNYRNNNYRNNN'
rev_umi: 'NNNYRNNNYRNNNYRNNN'
min_length: 30
max_length: 45

And this is the nextflox log file:

Oct-26 15:22:54.603 [main] DEBUG nextflow.cli.Launcher - $> nextflow run genepi/umi-pipeline-nf -r v0.2.1 -c custom_copy.config -params-file params.yaml -profile custom,conda -with-conda environment.yml -name umi1_2 -resume
Oct-26 15:22:54.734 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Oct-26 15:22:54.770 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/melichv/.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
Oct-26 15:22:54.788 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-26 15:22:54.789 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-26 15:22:54.794 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Oct-26 15:22:54.813 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Oct-26 15:22:54.833 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/melichv/.nextflow/scm
Oct-26 15:22:55.735 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/.git/config; branch: master; remote: origin; url: https://github.com/genepi/umi-pipeline-nf.git
Oct-26 15:22:55.784 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Oct-26 15:22:55.799 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/.git/config; branch: master; remote: origin; url: https://github.com/genepi/umi-pipeline-nf.git
Oct-26 15:22:56.757 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/nextflow.config
Oct-26 15:22:56.762 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /mnt/scratch/melichv/24_10_jansa/custom_copy.config
Oct-26 15:22:56.765 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/nextflow.config
Oct-26 15:22:56.765 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/scratch/melichv/24_10_jansa/custom_copy.config
Oct-26 15:22:56.778 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/melichv/.nextflow/secrets/store.json
Oct-26 15:22:56.783 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@14422d9d] - activable => nextflow.secret.LocalSecretsProvider@14422d9d
Oct-26 15:22:56.847 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `custom,conda`
Oct-26 15:22:57.210 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `custom,conda`
Oct-26 15:22:57.266 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [test, custom, conda, singularity, docker]
Oct-26 15:22:57.278 [main] WARN  nextflow.config.ConfigBuilder - It appears you have never run this project before -- Option `-resume` is ignored
Oct-26 15:22:57.312 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Oct-26 15:22:57.314 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/genepi/umi-pipeline-nf` [umi1_2] DSL2 - revision: 0b0f4b4ef4 [v0.2.1]
Oct-26 15:22:57.316 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-26 15:22:57.316 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-26 15:22:57.383 [main] DEBUG nextflow.Session - Session UUID: 58c14906-6fae-4386-b79a-bea2b1615f22
Oct-26 15:22:57.383 [main] DEBUG nextflow.Session - Run name: umi1_2
Oct-26 15:22:57.384 [main] DEBUG nextflow.Session - Executor pool size: 96
Oct-26 15:22:57.394 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Oct-26 15:22:57.427 [main] DEBUG nextflow.cli.CmdRun -
  Version: 24.04.2 build 5914
  Created: 29-05-2024 06:19 UTC (08:19 CEST)
  System: Linux 6.8.0-41-generic
  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 21.0.4+7-Ubuntu-1ubuntu224.04
  Encoding: UTF-8 (UTF-8)
  Process: 3370499@beluga.img.local [192.168.22.37]
  CPUs: 96 - Mem: 1007.8 GB (982.5 GB) - Swap: 4 GB (3.7 GB) - Virtual threads ON
Oct-26 15:22:57.460 [main] DEBUG nextflow.Session - Work-dir: /mnt/scratch/melichv/24_10_jansa/work [nfs]
Oct-26 15:22:57.513 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-26 15:22:57.540 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-26 15:22:57.677 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-26 15:22:57.690 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool
Oct-26 15:22:57.791 [main] DEBUG nextflow.Session - Session start
Oct-26 15:22:57.795 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/scratch/melichv/24_10_jansa/results_UMI1/nextflow_stats/trace.txt
Oct-26 15:22:57.807 [main] DEBUG nextflow.Session - Using default localLib path: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/lib
Oct-26 15:22:57.811 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/lib
Oct-26 15:22:57.991 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-26 15:22:58.010 [main] INFO  nextflow.Nextflow -
Oct-26 15:22:58.011 [main] INFO  nextflow.Nextflow -          ===============================================
Oct-26 15:22:58.011 [main] INFO  nextflow.Nextflow -           U M I - P I P E L I N E - N F
Oct-26 15:22:58.012 [main] INFO  nextflow.Nextflow -          ===============================================
Oct-26 15:22:58.013 [main] INFO  nextflow.Nextflow -          ~ version 0.2.1
Oct-26 15:22:58.014 [main] INFO  nextflow.Nextflow -
Oct-26 15:22:58.014 [main] INFO  nextflow.Nextflow -          input dir    : data
Oct-26 15:22:58.015 [main] INFO  nextflow.Nextflow -          reference    : /mnt/scratch/melichv/references/Mus_musculus/Mus_musculus.GRCm39.dna.toplevel.fa
Oct-26 15:22:58.016 [main] INFO  nextflow.Nextflow -          bed          : bed/amplicon_B6-Hs4-KV.bed
Oct-26 15:22:58.016 [main] INFO  nextflow.Nextflow -          output dir   : results_UMI1
Oct-26 15:22:58.017 [main] INFO  nextflow.Nextflow -
Oct-26 15:22:58.017 [main] INFO  nextflow.Nextflow -          ===============================================
Oct-26 15:22:58.017 [main] INFO  nextflow.Nextflow -          RUN NAME: umi1_2
Oct-26 15:22:58.018 [main] INFO  nextflow.Nextflow -
Oct-26 15:22:59.880 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:22:59.881 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:22:59.890 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-26 15:22:59.902 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=96; memory=1007.8 GB; capacity=96; pollInterval=100ms; dumpInterval=5m
Oct-26 15:22:59.905 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Oct-26 15:23:00.016 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.016 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.045 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.045 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.066 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.067 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.085 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.085 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.103 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.104 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.125 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.125 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.160 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:POLISH_CLUSTER` matches process UMI_PIPELINE:POLISH_CLUSTER
Oct-26 15:23:00.163 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.163 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.188 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.188 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.204 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.204 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.215 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.215 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.225 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.226 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.236 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.236 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.248 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.248 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.258 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.258 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.273 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.273 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.283 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-26 15:23:00.283 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-26 15:23:00.290 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: UMI_PIPELINE:FREEBAYES_CONSENSUS, UMI_PIPELINE:FREEBAYES_FINAL_CONSENSUS, COPY_BED, MAP_CONSENSUS, UMI_PIPELINE:POLISH_CLUSTER, UMI_PIPELINE:MERGE_CONSENSUS_FASTQ, UMI_PIPELINE:REFORMAT_CONSENSUS_CLUSTER, MAP_READS, MERGE_CONSENSUS_FASTQ, REFORMAT_CONSENSUS_CLUSTER, LOFREQ, UMI_PIPELINE:CLUSTER_CONSENSUS, SPLIT_READS, FILTER_CONSENSUS_FASTQ, SUBSAMPLING, FREEBAYES_CONSENSUS, UMI_PIPELINE:REFORMAT_FILTER_CLUSTER, FREEBAYES, MERGE_FASTQ, DETECT_UMI_CONSENSUS_FASTQ, FREEBAYES_FINAL_CONSENSUS, CLUSTER, LOFREQ_FINAL_CONSENSUS, REFORMAT_FILTER_CLUSTER, MAP_FINAL_CONSENSUS, MUTSERVE_CONSENSUS, MUTSERVE_FINAL_CONSENSUS, UMI_PIPELINE:SPLIT_READS, UMI_PIPELINE:CLUSTER, UMI_PIPELINE:MAP_READS, UMI_PIPELINE:FILTER_CONSENSUS_FASTQ, UMI_PIPELINE:MAP_CONSENSUS, LOFREQ_CONSENSUS, UMI_PIPELINE:DETECT_UMI_FASTQ, UMI_PIPELINE:COPY_BED, UMI_PIPELINE:MERGE_FASTQ, CLUSTER_CONSENSUS, UMI_PIPELINE:MAP_FINAL_CONSENSUS, MUTSERVE, DETECT_UMI_FASTQ, POLISH_CLUSTER, UMI_PIPELINE:DETECT_UMI_CONSENSUS_FASTQ
Oct-26 15:23:00.292 [main] DEBUG nextflow.Session - Igniting dataflow network (18)
Oct-26 15:23:00.299 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: data/; pattern: *; options: [type:dir]
Oct-26 15:23:00.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:COPY_BED
Oct-26 15:23:00.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:MERGE_FASTQ
Oct-26 15:23:00.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:MAP_READS
Oct-26 15:23:00.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:SPLIT_READS
Oct-26 15:23:00.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:DETECT_UMI_FASTQ
Oct-26 15:23:00.302 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:CLUSTER
Oct-26 15:23:00.302 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:REFORMAT_FILTER_CLUSTER
Oct-26 15:23:00.303 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:POLISH_CLUSTER
Oct-26 15:23:00.303 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:MERGE_CONSENSUS_FASTQ
Oct-26 15:23:00.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:FILTER_CONSENSUS_FASTQ
Oct-26 15:23:00.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:MAP_CONSENSUS
Oct-26 15:23:00.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:DETECT_UMI_CONSENSUS_FASTQ
Oct-26 15:23:00.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:CLUSTER_CONSENSUS
Oct-26 15:23:00.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:REFORMAT_CONSENSUS_CLUSTER
Oct-26 15:23:00.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:MAP_FINAL_CONSENSUS
Oct-26 15:23:00.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:FREEBAYES_CONSENSUS
Oct-26 15:23:00.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > UMI_PIPELINE:FREEBAYES_FINAL_CONSENSUS
Oct-26 15:23:00.308 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_e926593a02575b5b: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/cluster.nf
  Script_4b6de693176bdacf: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/map_reads.nf
  Script_882074a4bd670c6d: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/merge_input.nf
  Script_46aeb350d0f6f183: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/detect_umi_fastq.nf
  Script_80d5a6002f30f6d7: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/reformat_consensus_cluster.nf
  Script_33565648cf182249: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/filter_consensus_fastq.nf
  Script_2f9dc537588c645c: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/umi-pipeline.nf
  Script_275c1a30946876f6: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/main.nf
  Script_6521a175511f9b50: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/split_reads.nf
  Script_66ac78090347bc3e: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/variant_calling/lofreq.nf
  Script_327edc60407f355c: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/polish_cluster.nf
  Script_1ab33603b5cc251f: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/reformat_filter_cluster.nf
  Script_b568d7c2d8c6f1f4: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/copy_bed.nf
  Script_00bcf66fab070002: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/variant_calling/freebayes.nf
  Script_9602f0c7e01e9fc4: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/subsampling.nf
  Script_a30d1eca88fa21e9: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/merge_consensus_fastq.nf
  Script_fffe1a94c25cd60f: /home/melichv/.nextflow/assets/genepi/umi-pipeline-nf/./lib/workflows/../processes/variant_calling/mutserve.nf
Oct-26 15:23:00.308 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Oct-26 15:23:00.308 [main] DEBUG nextflow.Session - Session await
Oct-26 15:23:00.432 [Actor Thread 68] DEBUG nextflow.conda.CondaCache - conda found local env for environment=environment.yml; path=/mnt/scratch/melichv/24_10_jansa/work/conda/umi-pipeline-nf-b514227d48dd411b4cd5963569f4e676
Oct-26 15:23:00.562 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-26 15:23:00.565 [Task submitter] INFO  nextflow.Session - [16/fc27c4] Submitted process > UMI_PIPELINE:COPY_BED
Oct-26 15:23:01.865 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: UMI_PIPELINE:COPY_BED; status: COMPLETED; exit: 0; error: -; workDir: /mnt/scratch/melichv/24_10_jansa/work/16/fc27c4cedfb65eff516ecd2f5fd1d7]
Oct-26 15:23:01.911 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-26 15:23:01.962 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Oct-26 15:23:01.962 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-26 15:23:01.965 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Oct-26 15:23:01.965 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Oct-26 15:23:01.967 [main] INFO  nextflow.Nextflow -
Oct-26 15:23:01.967 [main] INFO  nextflow.Nextflow -          Pipeline execution summary
Oct-26 15:23:01.969 [main] INFO  nextflow.Nextflow -          ---------------------------
Oct-26 15:23:01.969 [main] INFO  nextflow.Nextflow -          Name         : umi1_2
Oct-26 15:23:01.970 [main] INFO  nextflow.Nextflow -          Profile      : custom,conda
Oct-26 15:23:01.971 [main] INFO  nextflow.Nextflow -          Launch dir   : /mnt/scratch/melichv/24_10_jansa
Oct-26 15:23:01.971 [main] INFO  nextflow.Nextflow -          Work dir     : /mnt/scratch/melichv/24_10_jansa/work (cleared)
Oct-26 15:23:01.972 [main] INFO  nextflow.Nextflow -          Status       : success
Oct-26 15:23:01.972 [main] INFO  nextflow.Nextflow -          Error report : -
Oct-26 15:23:01.972 [main] INFO  nextflow.Nextflow -
Oct-26 15:23:02.046 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=25ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Oct-26 15:23:02.046 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Oct-26 15:23:02.048 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Oct-26 15:23:03.011 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Oct-26 15:23:03.346 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-26 15:23:03.375 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Oct-26 15:23:03.375 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
vmelichar commented 1 month ago

I found out a solution to my problem. The input directory has to have a specific structure (dirs named barcodeXX where XX is a 2 digit number). I did not know that because I had just one sample in one fastq file. Might be helpful to state this in the usage doc.

AmstlerStephan commented 1 month ago

Hi, I am glad you could already find a solution to your problem. Thank you for raising the issue. I will update the doc in the next release and/or add a singleplex sample where no barcode subdirectory is necessary.

When checking your config file, I saw that you specified the newest v5 models for Medaka. I am currently preparing a new release of the pipeline supporting the newest version of Medaka and v5 models. Currently, the latest supported model is v4.3. The new release should be available by the end of next week.

Kind regards, Stephan