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Process pipeline:build_index terminated with an error exit status (1) #6

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claireherrington opened this issue Feb 2, 2024 · 1 comment
Open

Process pipeline:build_index terminated with an error exit status (1) #6

claireherrington opened this issue Feb 2, 2024 · 1 comment

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@claireherrington
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Operating System

Windows 10

Other Linux

No response

Workflow Version

v0.1.12

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

v5.1.8

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

When I attempt to run wf-cas9 using my fastq data as input, it fails after a few minutes due to Command Exit Status 1. The process 'pipeline:build_index' is failing. In the past, I have received command exit status 137, so I installed 64GB of memory into my computer as I thought this might be the issue. Now, I am receiving command exit status 1 and I am unsure of how to proceed. I am looking for solutions to errors executing process pipeline:build_index.

Relevant log output

Feb-02 00:00:03.211 [main] DEBUG nextflow.cli.Launcher - $> /mnt/c/Users/Claire Herrington/AppData/Local/EPI2ME/app-5.1.8/resources/nextflow-all -log '/mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/nextflow.log' run '/mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9/main.nf' -params-file '/mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/params.json' -w '/mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work' -ansi-log false -offline -profile standard -with-weblog 'http://172.24.32.1:50343' -name pedantic_jang
Feb-02 00:00:03.261 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.04.2
Feb-02 00:00:03.300 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/mnt/c/Users/Claire Herrington/epi2melabs/workflows/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.3
Feb-02 00:00:03.327 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-02 00:00:03.332 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-02 00:00:03.343 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Feb-02 00:00:03.387 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Feb-02 00:00:03.434 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9/nextflow.config
Feb-02 00:00:03.437 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9/nextflow.config
Feb-02 00:00:03.479 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-02 00:00:04.472 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Feb-02 00:00:04.483 [main] INFO  nextflow.cli.CmdRun - Launching `/mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9/main.nf` [pedantic_jang] DSL2 - revision: b7aae7380b
Feb-02 00:00:04.484 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-02 00:00:04.484 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Feb-02 00:00:04.514 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /mnt/c/Users/Claire Herrington/epi2melabs/workflows/.nextflow/secrets/store.json
Feb-02 00:00:04.518 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5696c927] - activable => nextflow.secret.LocalSecretsProvider@5696c927
Feb-02 00:00:04.601 [main] DEBUG nextflow.Session - Session UUID: 9da6a82d-4447-4d29-81ec-dec1d4c6b204
Feb-02 00:00:04.602 [main] DEBUG nextflow.Session - Run name: pedantic_jang
Feb-02 00:00:04.602 [main] DEBUG nextflow.Session - Executor pool size: 24
Feb-02 00:00:04.616 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=72; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Feb-02 00:00:04.642 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.04.2 build 5871
  Created: 08-06-2023 09:33 UTC (09:33 GMT)
  System: Linux 5.15.133.1-microsoft-standard-WSL2
  Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 11.0.21+9-post-Ubuntu-0ubuntu122.04
  Encoding: UTF-8 (UTF-8)
  Process: 1743@Herrington-PC [127.0.1.1]
  CPUs: 24 - Mem: 31.2 GB (30 GB) - Swap: 8 GB (8 GB)
Feb-02 00:00:04.679 [main] DEBUG nextflow.file.FileHelper - Can't check if specified path is NFS (1): /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work

Feb-02 00:00:04.679 [main] DEBUG nextflow.Session - Work-dir: /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work [null]
Feb-02 00:00:04.730 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, AwsBatchExecutor, GoogleBatchExecutor]
Feb-02 00:00:04.745 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-02 00:00:04.790 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000
Feb-02 00:00:04.796 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Feb-02 00:00:04.858 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-02 00:00:05.138 [main] DEBUG nextflow.Session - Session start
Feb-02 00:00:05.145 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/output/execution/trace.txt
Feb-02 00:00:05.170 [main] DEBUG nextflow.Session - Using default localLib path: /mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9/lib
Feb-02 00:00:05.205 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9/lib
Feb-02 00:00:05.210 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9/lib/nfcore_external_java_deps.jar
Feb-02 00:00:05.285 [Actor Thread 2] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:06.665 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-02 00:00:07.270 [main] INFO  nextflow.Nextflow - 
�[0;92m||||||||||   �[0m�[2m_____ ____ ___ ____  __  __ _____      _       _
�[0;92m||||||||||  �[0m�[2m| ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
�[0;33m|||||       �[0m�[2m|  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
�[0;33m|||||       �[0m�[2m| |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
�[0;94m||||||||||  �[0m�[2m|_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
�[0;94m||||||||||  �[0m�[1mwf-cas9 v0.1.12�[0m
�[2m--------------------------------------------------------------------------------�[0m
�[1mCore Nextflow options�[0m
  �[0;34mrunName            : �[0;32mpedantic_jang�[0m
  �[0;34mcontainerEngine    : �[0;32mdocker�[0m
  �[0;34mlaunchDir          : �[0;32m/mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV�[0m
  �[0;34mworkDir            : �[0;32m/mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work�[0m
  �[0;34mprojectDir         : �[0;32m/mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9�[0m
  �[0;34muserName           : �[0;32mepi2mewsl�[0m
  �[0;34mprofile            : �[0;32mstandard�[0m
  �[0;34mconfigFiles        : �[0;32m/mnt/c/Users/Claire Herrington/epi2melabs/workflows/epi2me-labs/wf-cas9/nextflow.config�[0m

�[1mInput Options�[0m
  �[0;34mfastq              : �[0;32m/mnt/c/Users/Claire Herrington/Desktop/Makoto Taniguchi/Fastq data�[0m
  �[0;34mreference_genome   : �[0;32m/mnt/c/Users/Claire Herrington/Desktop/Makoto Taniguchi/Refgenome/reference_genome.gz�[0m
  �[0;34mtargets            : �[0;32m/mnt/c/Users/Claire Herrington/Desktop/Makoto Taniguchi/Target Seq/Npas4 Nanopore target sequence.txt�[0m

�[1mOutput Options�[0m
  �[0;34mout_dir            : �[0;32m/mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/output�[0m

�[1mAdvanced Options�[0m
  �[0;34mminimap2_max_memory: �[0;32m48 GB�[0m

!! Only displaying parameters that differ from the pipeline defaults !!
�[2m--------------------------------------------------------------------------------�[0m
If you use epi2me-labs/wf-cas9 for your analysis please cite:

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


�[2m--------------------------------------------------------------------------------�[0m
This is epi2me-labs/wf-cas9 v0.1.12.
�[2m--------------------------------------------------------------------------------�[0m
Feb-02 00:00:08.093 [main] INFO  nextflow.Nextflow - Checking fastq input.
Feb-02 00:00:08.273 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `fastq_ingress,wf_common` for process with name fastcat
Feb-02 00:00:08.278 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.278 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.284 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-02 00:00:08.292 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=16 GB; capacity=24; pollInterval=100ms; dumpInterval=5m
Feb-02 00:00:08.386 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:build_index
Feb-02 00:00:08.387 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.387 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.392 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:getVersions
Feb-02 00:00:08.393 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.394 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.395 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:getParams
Feb-02 00:00:08.396 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.396 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.401 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:align_reads
Feb-02 00:00:08.401 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.402 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.404 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:make_tiles
Feb-02 00:00:08.405 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.405 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.407 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:coverage_summary
Feb-02 00:00:08.408 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.409 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.419 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:get_on_target_reads
Feb-02 00:00:08.420 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.420 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.424 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:get_on_target_bams
Feb-02 00:00:08.425 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.425 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.428 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:target_summary
Feb-02 00:00:08.428 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.429 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.431 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:target_coverage
Feb-02 00:00:08.432 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.432 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:background
Feb-02 00:00:08.435 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.435 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.540 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:build_tables
Feb-02 00:00:08.540 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.541 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.543 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:makeReport
Feb-02 00:00:08.544 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.544 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.551 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name pipeline:pack_files_into_sample_dirs
Feb-02 00:00:08.552 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.553 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.558 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cas9` matches labels `cas9` for process with name output
Feb-02 00:00:08.559 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-02 00:00:08.560 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-02 00:00:08.563 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: pipeline:getParams, get_on_target_reads, validate_sample_sheet, pipeline:makeReport, pipeline:target_summary, output, coverage_summary, pipeline:align_reads, pipeline:build_tables, pipeline:background, makeReport, getVersions, pipeline:make_tiles, pack_files_into_sample_dirs, target_coverage, make_tiles, pipeline:coverage_summary, pipeline:build_index, get_on_target_bams, pipeline:getVersions, align_reads, target_summary, move_or_compress, build_index, fastcat, background, build_tables, pipeline:get_on_target_bams, pipeline:pack_files_into_sample_dirs, pipeline:get_on_target_reads, getParams, pipeline:target_coverage
Feb-02 00:00:08.564 [main] DEBUG nextflow.Session - Igniting dataflow network (17)
Feb-02 00:00:08.565 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastcat
Feb-02 00:00:08.567 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:build_index
Feb-02 00:00:08.567 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getVersions
Feb-02 00:00:08.568 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getParams
Feb-02 00:00:08.569 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:align_reads
Feb-02 00:00:08.570 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:make_tiles
Feb-02 00:00:08.571 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:coverage_summary
Feb-02 00:00:08.571 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:get_on_target_reads
Feb-02 00:00:08.572 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:get_on_target_bams
Feb-02 00:00:08.573 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:target_summary
Feb-02 00:00:08.574 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:target_coverage
Feb-02 00:00:08.574 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:background
Feb-02 00:00:08.575 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:build_tables
Feb-02 00:00:08.575 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:makeReport
Feb-02 00:00:08.576 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:pack_files_into_sample_dirs
Feb-02 00:00:08.578 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output
Feb-02 00:00:08.580 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Feb-02 00:00:08.580 [main] DEBUG nextflow.Session - Session await
Feb-02 00:00:08.722 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-02 00:00:08.725 [Task submitter] INFO  nextflow.Session - [4d/b04b4c] Submitted process > pipeline:getParams
Feb-02 00:00:08.733 [Actor Thread 23] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:08.741 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-02 00:00:08.742 [Task submitter] INFO  nextflow.Session - [c0/641aaf] Submitted process > fastcat (1)
Feb-02 00:00:08.746 [Actor Thread 24] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:08.758 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-02 00:00:08.759 [Task submitter] INFO  nextflow.Session - [d8/3a01bb] Submitted process > pipeline:getVersions
Feb-02 00:00:08.764 [Actor Thread 24] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:08.806 [Actor Thread 24] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:08.808 [Actor Thread 24] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:08.810 [Actor Thread 24] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:10.016 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: pipeline:getParams; status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work/4d/b04b4cb225d55ff00362efad9d1da9]
Feb-02 00:00:10.044 [Actor Thread 23] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:10.169 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: pipeline:getVersions; status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work/d8/3a01bb6fa8adf89369cba9d22c8502]
Feb-02 00:00:10.176 [Actor Thread 22] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:11.686 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: fastcat (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work/c0/641aaf233bd6c65d57e767691fe655]
Feb-02 00:00:11.703 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-02 00:00:11.704 [Task submitter] INFO  nextflow.Session - [35/950c26] Submitted process > pipeline:build_index
Feb-02 00:00:11.708 [Actor Thread 24] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:11.712 [Actor Thread 17] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:11.776 [Actor Thread 24] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.013 s; total time: 0.015 s
Feb-02 00:00:11.787 [Actor Thread 25] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:00:11.824 [Actor Thread 24] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work/collect-file/de4f2514eacf34cf21f9eed49731d90c
Feb-02 00:00:11.834 [Actor Thread 24] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-13500011448549269933
Feb-02 00:01:47.995 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: pipeline:build_index; status: COMPLETED; exit: 1; error: -; workDir: /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work/35/950c267e218bd1d1bb1a9e9379e3a3]
Feb-02 00:01:47.997 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=pipeline:build_index; work-dir=/mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work/35/950c267e218bd1d1bb1a9e9379e3a3
  error [nextflow.exception.ProcessFailedException]: Process `pipeline:build_index` terminated with an error exit status (1)
Feb-02 00:01:48.008 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'pipeline:build_index'

Caused by:
  Process `pipeline:build_index` terminated with an error exit status (1)

Command executed:

  minimap2 -t 8 -x map-ont -d genome_index.mmi reference
  samtools faidx reference
  cut -f 1,2 reference.fai >> chrom.sizes

Command exit status:
  1

Command output:
  (empty)

Command error:
  [M::mm_idx_gen::31.005*1.78] collected minimizers
  [M::mm_idx_gen::35.155*2.47] sorted minimizers
  [M::main::94.293*1.01] loaded/built the index for 61 target sequence(s)
  [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 61
  [M::mm_idx_stat::94.995*1.01] distinct minimizers: 97791701 (39.85% are singletons); average occurrences: 5.142; average spacing: 5.426; total length: 2728222451
  [M::main] Version: 2.24-r1122
  [M::main] CMD: minimap2 -t 8 -x map-ont -d genome_index.mmi reference
  [M::main] Real time: 95.117 sec; CPU: 95.673 sec; Peak RSS: 10.618 GB
  [E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip
  [faidx] Could not build fai index reference.fai

Work dir:
  /mnt/c/Users/Claire Herrington/epi2melabs/instances/wf-cas9_01HNKHTT4Y0WERFXHH8PPA2XMV/work/35/950c267e218bd1d1bb1a9e9379e3a3

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Feb-02 00:01:48.019 [Actor Thread 19] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Feb-02 00:01:48.021 [Actor Thread 22] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Feb-02 00:01:48.019 [Actor Thread 18] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Feb-02 00:01:48.021 [Actor Thread 16] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Feb-02 00:01:48.023 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `pipeline:build_index` terminated with an error exit status (1)
Feb-02 00:01:48.021 [Actor Thread 21] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Feb-02 00:01:48.022 [Actor Thread 23] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Feb-02 00:01:48.027 [Actor Thread 15] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:01:48.040 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] pipeline:pack_files_into_sample_dirs
  status=ACTIVE
  port 0: (queue) closed; channel: -
  port 1: (cntrl) -     ; channel: $

[process] output
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: fname
  port 1: (cntrl) -     ; channel: $

Feb-02 00:01:48.043 [Actor Thread 15] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:01:48.464 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-02 00:01:48.467 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-02 00:01:48.627 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=3; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=1; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=5.2s; failedDuration=12m 50s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=8; peakMemory=0; ]
Feb-02 00:01:48.628 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Feb-02 00:01:48.634 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Feb-02 00:01:48.668 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  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(1)","maxLabel":"fastcat (1)","q1Label":"fastcat (1)","q2Label":"fastcat (1)","q3Label":"fastcat (1)"},"process":"fastcat","mem":{"mean":10608640,"min":10608640,"q1":10608640,"q2":10608640,"q3":10608640,"max":10608640,"minLabel":"fastcat (1)","maxLabel":"fastcat (1)","q1Label":"fastcat (1)","q2Label":"fastcat (1)","q3Label":"fastcat (1)"},"memUsage":null,"timeUsage":null,"vmem":{"mean":385576960,"min":385576960,"q1":385576960,"q2":385576960,"q3":385576960,"max":385576960,"minLabel":"fastcat (1)","maxLabel":"fastcat (1)","q1Label":"fastcat (1)","q2Label":"fastcat (1)","q3Label":"fastcat (1)"},"reads":{"mean":154674439,"min":154674439,"q1":154674439,"q2":154674439,"q3":154674439,"max":154674439,"minLabel":"fastcat (1)","maxLabel":"fastcat (1)","q1Label":"fastcat (1)","q2Label":"fastcat (1)","q3Label":"fastcat (1)"},"cpu":{"mean":272,"min":272,"q1":272,"q2":272,"q3":272,"max":272,"minLabel":"fastcat (1)","maxLabel":"fastcat (1)","q1Label":"fastcat (1)","q2Label":"fastcat (1)","q3Label":"fastcat (1)"},"time":{"mean":1668,"min":1668,"q1":1668,"q2":1668,"q3":1668,"max":1668,"minLabel":"fastcat (1)","maxLabel":"fastcat (1)","q1Label":"fastcat (1)","q2Label":"fastcat (1)","q3Label":"fastcat (1)"},"writes":{"mean":148260567,"min":148260567,"q1":148260567,"q2":148260567,"q3":148260567,"max":148260567,"minLabel":"fastcat (1)","maxLabel":"fastcat (1)","q1Label":"fastcat (1)","q2Label":"fastcat (1)","q3Label":"fastcat (1)"}},{"cpuUsage":null,"process":"build_index","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":96209,"min":96209,"q1":96209,"q2":96209,"q3":96209,"max":96209,"minLabel":"pipeline:build_index","maxLabel":"pipeline:build_index","q1Label":"pipeline:build_index","q2Label":"pipeline:build_index","q3Label":"pipeline:build_index"},"writes":null}]
Feb-02 00:01:49.103 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Feb-02 00:01:49.221 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.24.32.1:50343 -- received status code 200.
Feb-02 00:01:49.231 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-02 00:01:49.259 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Application activity log entry

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@nrhorner
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nrhorner commented Apr 5, 2024

Hi @claireherrington

Apologies for the late reply.

Your reference genome sequence appears to have been compressed with gzip. It will need decompressing for it to work, after which you can optionally compress with bgzip. Please let me know if this does not solve your issue.

Neil

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@nrhorner @claireherrington