Shovill Appears to be Not Working

[fugunokaraage]

Hi,

Whenever I run the pipeline, an error always occurs with Shovill. When I check the .nextflow.log file, I see the following message:

10:40:30.287 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=PIPELINE:ASSEMBLY_SHOVILL (sample_name); work-dir=/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65 error [nextflow.exception.ProcessFailedException]: Process PIPELINE:ASSEMBLY_SHOVILL (PC2044) terminated with an error exit status (1) 7月-15 10:40:30.289 [Task monitor] INFO nextflow.processor.TaskProcessor - [ef/b430ea] NOTE: Process PIPELINE:ASSEMBLY_SHOVILL (PC2044) terminated with an error exit status (1) -- Error is ignored

What could be the problem? If there is any log information needed to resolve the issue, I will provide it.

Best regards, Sato

[HarryHung]

Hi, can you please let me know which version of the pipeline you are using, and how much memory (RAM) is available in your system?

Please also provide the hidden file .nextflow.log in the pipeline directory, and the hidden file .command.log in the working directory of Shovill (i.e. /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65).

[fugunokaraage]

Thank you for your response. I'm using v 1.0.0-rc5 and the available RAM is 1008G. (This is based on the RAM display by the htop command.)

I will describe the contents of the .nextflow.log file below, but the first two lines have been omitted because they contain proxy information.

7月-15 10:37:15.802 [main] DEBUG nextflow.cli.Launcher - $> nextflow -C /home/r7_gpc/bin/gps-pipeline/nextflow.config run -w /home/r7_gpc/bin/gps-pipeline/work /home/r7_gpc/bin/gps-pipeline/main.nf --reads /home/r7_gpc/data/nvme2/GPS_test/test --output /home/r7_gpc/data/nvme2/GPS_test/test_res 7月-15 10:37:15.894 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1 7月-15 10:37:15.926 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/r7_gpc/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3 .3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1 7月-15 10:37:15.949 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] 7月-15 10:37:15.951 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] 7月-15 10:37:15.955 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode 7月-15 10:37:15.971 [main] INFO org.pf4j.AbstractPluginManager - No plugins 7月-15 10:37:15.996 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/r7_gpc/bin/gps-pipeline/nextflow.config 7月-15 10:37:16.024 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard 7月-15 10:37:17.507 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from config declaration 7月-15 10:37:17.531 [main] INFO nextflow.cli.CmdRun - Launching /home/r7_gpc/bin/gps-pipeline/main.nf [chaotic_planck] DSL2 - revision: 9ef36daf92 7月-15 10:37:17.532 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] 7月-15 10:37:17.532 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] 7月-15 10:37:17.545 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/r7_gpc/.nextflow/secrets/store.json 7月-15 10:37:17.550 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@14998e21] - activable => nextflow.secret.LocalSecretsProvider@14998e21 7月-15 10:37:17.631 [main] DEBUG nextflow.Session - Session UUID: 5857c160-742a-432a-a8f6-93bd476e99a9 7月-15 10:37:17.631 [main] DEBUG nextflow.Session - Run name: chaotic_planck 7月-15 10:37:17.632 [main] DEBUG nextflow.Session - Executor pool size: 64 7月-15 10:37:17.642 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null 7月-15 10:37:17.648 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false 7月-15 10:37:17.697 [main] DEBUG nextflow.cli.CmdRun - Version: 23.10.1 build 5891 Created: 12-01-2024 22:01 UTC (13-01-2024 07:01 JDT) System: Linux 5.4.0-169-generic Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 11.0.22+7-post-Ubuntu-0ubuntu220.04.1 Encoding: UTF-8 (UTF-8) Process: 2341862@s13 [127.0.1.1] CPUs: 64 - Mem: 1007.6 GB (55.2 GB) - Swap: 16 GB (16 GB) 7月-15 10:37:17.729 [main] DEBUG nextflow.Session - Work-dir: /home/r7_gpc/bin/gps-pipeline/work [xfs] 7月-15 10:37:17.757 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] 7月-15 10:37:17.780 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory 7月-15 10:37:17.828 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory 7月-15 10:37:17.845 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 65; maxThreads: 1000 7月-15 10:37:17.939 [main] DEBUG nextflow.Session - Session start 7月-15 10:37:18.344 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution 7月-15 10:37:22.004 [main] INFO nextflow.Nextflow -

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7月-15 10:37:22.039 [main] INFO nextflow.Nextflow -

The main pipeline workflow has been selected.

Input Directory: /nvme2/GPS_test/test Output Directory: /nvme2/GPS_test/test_res

The workflow started at 2024-07-15 10:37:22 JST.

Current Progress:

7月-15 10:37:22.202 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bwa_container matches labels bwa_container,farm_mid,farm_scratchless for process with name PIPELINE:GET_REF_GENOME_BWA_DB 7月-15 10:37:22.224 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.224 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.231 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local 7月-15 10:37:22.238 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=1007.6 GB; capacity=64; pollInterval=100ms; dumpInterval=5m 7月-15 10:37:22.242 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) 7月-15 10:37:22.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low,farm_scratchless,farm_slow for process with name PIPELINE:GET_KRAKEN2_DB 7月-15 10:37:22.424 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.424 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:seroba_container matches labels seroba_container,farm_low,farm_scratchless,farm_slow for process with name PIPELINE:GET_SEROBA_DB 7月-15 10:37:22.435 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.435 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.443 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low,farm_scratchless,farm_slow for process with name PIPELINE:GET_POPPUNK_DB 7月-15 10:37:22.444 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.444 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.455 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low,farm_scratchless,farm_slow for process with name PIPELINE:GET_POPPUNK_EXT_CLUSTERS 7月-15 10:37:22.458 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.458 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.466 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:ariba_container matches labels ariba_container,farm_low,farm_scratchless,farm_slow for process with name PIPELINE:GET_ARIBA_DB 7月-15 10:37:22.467 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.467 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.547 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name PIPELINE:FILE_VALIDATION 7月-15 10:37:22.550 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.550 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.627 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:fastp_container matches labels fastp_container,farm_mid for process with name PIPELINE:PREPROCESS 7月-15 10:37:22.629 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.629 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.652 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name PIPELINE:READ_QC 7月-15 10:37:22.655 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.656 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.681 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:shovill_container matches labels shovill_container,farm_high_fallible for process with name PIPELINE:ASSEMBLY_SHOVILL 7月-15 10:37:22.682 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.682 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.688 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:quast_container matches labels quast_container,farm_low for process with name PIPELINE:ASSEMBLY_ASSESS 7月-15 10:37:22.689 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.689 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.704 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name PIPELINE:ASSEMBLY_QC 7月-15 10:37:22.706 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.706 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.716 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bwa_container matches labels bwa_container,farm_mid for process with name PIPELINE:MAPPING 7月-15 10:37:22.719 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.719 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.725 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:samtools_container matches labels samtools_container,farm_mid for process with name PIPELINE:SAM_TO_SORTED_BAM 7月-15 10:37:22.726 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.726 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.732 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bcftools_container matches labels bcftools_container,farm_mid for process with name PIPELINE:SNP_CALL 7月-15 10:37:22.733 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.734 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.740 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:python_container matches labels python_container,farm_low for process with name PIPELINE:HET_SNP_COUNT 7月-15 10:37:22.743 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.744 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name PIPELINE:MAPPING_QC 7月-15 10:37:22.762 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.763 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.769 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:kraken2_container matches labels kraken2_container,farm_high for process with name PIPELINE:TAXONOMY 7月-15 10:37:22.769 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.770 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.775 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name PIPELINE:TAXONOMY_QC 7月-15 10:37:22.776 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.776 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.819 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name PIPELINE:OVERALL_QC 7月-15 10:37:22.820 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.820 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.892 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:poppunk_container matches labels poppunk_container,farm_high,farm_slow for process with name PIPELINE:LINEAGE 7月-15 10:37:22.894 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.894 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.903 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:seroba_container matches labels seroba_container,farm_mid for process with name PIPELINE:SEROTYPE 7月-15 10:37:22.903 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.903 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.908 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:mlst_container matches labels mlst_container,farm_low for process with name PIPELINE:MLST 7月-15 10:37:22.910 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.910 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.914 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:spn_pbp_amr_container matches labels spn_pbp_amr_container,farm_low for process with name PIPELINE:PBP_RESISTANCE 7月-15 10:37:22.915 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.915 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.918 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name PIPELINE:PARSE_PBP_RESISTANCE 7月-15 10:37:22.919 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.920 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.924 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:ariba_container matches labels ariba_container,farm_low for process with name PIPELINE:OTHER_RESISTANCE 7月-15 10:37:22.925 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.925 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:22.929 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:python_container matches labels python_container,farm_low for process with name PIPELINE:PARSE_OTHER_RESISTANCE 7月-15 10:37:22.930 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:22.930 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.002 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name PIPELINE:GENERATE_SAMPLE_REPORT 7月-15 10:37:23.003 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.003 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.014 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:python_container matches labels python_container,farm_low for process with name PIPELINE:GENERATE_OVERALL_REPORT 7月-15 10:37:23.014 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.015 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.048 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name SAVE_INFO:GET_VERSION:IMAGES 7月-15 10:37:23.048 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.048 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name SAVE_INFO:GET_VERSION:DATABASES 7月-15 10:37:23.055 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.055 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.059 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:python_container matches labels python_container,farm_low for process with name SAVE_INFO:GET_VERSION:PYTHON_VERSION 7月-15 10:37:23.060 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.060 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.062 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:fastp_container matches labels fastp_container,farm_low for process with name SAVE_INFO:GET_VERSION:FASTP_VERSION 7月-15 10:37:23.063 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.063 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.065 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:unicycler_container matches labels unicycler_container,farm_low for process with name SAVE_INFO:GET_VERSION:UNICYCLER_VERSION 7月-15 10:37:23.066 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.066 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.068 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:shovill_container matches labels shovill_container,farm_low for process with name SAVE_INFO:GET_VERSION:SHOVILL_VERSION 7月-15 10:37:23.069 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.069 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:quast_container matches labels quast_container,farm_low for process with name SAVE_INFO:GET_VERSION:QUAST_VERSION 7月-15 10:37:23.073 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.073 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.075 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bwa_container matches labels bwa_container,farm_low for process with name SAVE_INFO:GET_VERSION:BWA_VERSION 7月-15 10:37:23.076 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.076 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.078 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:samtools_container matches labels samtools_container,farm_low for process with name SAVE_INFO:GET_VERSION:SAMTOOLS_VERSION 7月-15 10:37:23.079 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.079 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.081 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bcftools_container matches labels bcftools_container,farm_low for process with name SAVE_INFO:GET_VERSION:BCFTOOLS_VERSION 7月-15 10:37:23.082 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.082 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.084 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:poppunk_container matches labels poppunk_container,farm_low for process with name SAVE_INFO:GET_VERSION:POPPUNK_VERSION 7月-15 10:37:23.084 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.084 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.087 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:mlst_container matches labels mlst_container,farm_low for process with name SAVE_INFO:GET_VERSION:MLST_VERSION 7月-15 10:37:23.087 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.087 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.089 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:kraken2_container matches labels kraken2_container,farm_low for process with name SAVE_INFO:GET_VERSION:KRAKEN2_VERSION 7月-15 10:37:23.090 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.090 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.092 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:seroba_container matches labels seroba_container,farm_low for process with name SAVE_INFO:GET_VERSION:SEROBA_VERSION 7月-15 10:37:23.093 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.093 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.095 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:ariba_container matches labels ariba_container,farm_low for process with name SAVE_INFO:GET_VERSION:ARIBA_VERSION 7月-15 10:37:23.095 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.095 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.098 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name SAVE_INFO:GET_VERSION:TOOLS 7月-15 10:37:23.099 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.099 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.104 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:bash_container matches labels bash_container,farm_low for process with name SAVE_INFO:GET_VERSION:COMBINE_INFO 7月-15 10:37:23.105 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.105 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.133 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.134 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.141 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local 7月-15 10:37:23.142 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' 7月-15 10:37:23.145 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: PRINT, PIPELINE:GET_SEROBA_DB, PBP_RESISTANCE, FASTP_VERSION, SNP_CALL, PARSE, PIPELINE:OTHER_RESISTANCE, PYTHON_VERSION, MAPPING, GET_POPPUNK_EXT_CLUSTERS, PIPELINE:MAPPING_QC, QUAST_VERSION, SAVE_INFO:GET_VERSION:BCFTOOLS_VERSION, PIPELINE:SAM_TO_SORTED_BAM, FILE_VALIDATION, GET_REF_GENOME_BWA_DB, PIPELINE:PBP_RESISTANCE, OVERALL_QC, PIPELINE:GENERATE_OVERALL_REPORT, PIPELINE:GET_POPPUNK_EXT_CLUSTERS, LINEAGE, PIPELINE:READ_QC, ASSEMBLY_SHOVILL, GENERATE_SAMPLE_REPORT, GENERATE_OVERALL_REPORT, SAVE_INFO:GET_VERSION:IMAGES, TAXONOMY, MLST_VERSION, PIPELINE:GET_KRAKEN2_DB, SEROBA_VERSION, PIPELINE:GET_POPPUNK_DB, PIPELINE:HET_SNP_COUNT, SAVE_INFO:GET_VERSION:SHOVILL_VERSION, SAVE_INFO:GET_VERSION:SEROBA_VERSION, SAVE, PIPELINE:PREPROCESS, MLST, GET_DOCKER_COMPOSE, SAVE_INFO:GET_VERSION:DATABASES, READ_QC, GET_POPPUNK_DB, SAM_TO_SORTED_BAM, SAVE_INFO:GET_VERSION:UNICYCLER_VERSION, SAVE_INFO:GET_VERSION:MLST_VERSION, BCFTOOLS_VERSION, PIPELINE:TAXONOMY_QC, PIPELINE:SNP_CALL, PIPELINE:LINEAGE, PARSE_PBP_RESISTANCE, SAVE_INFO:SAVE, TOOLS, PREPROCESS, MAPPING_QC, PIPELINE:MLST, PIPELINE:GET_ARIBA_DB, PIPELINE:FILE_VALIDATION, POPPUNK_VERSION, COMBINE_INFO, GET_ARIBA_DB, HET_SNP_COUNT, SAVE_INFO:GET_VERSION:QUAST_VERSION, OTHER_RESISTANCE, PIPELINE:PARSE_PBP_RESISTANCE, SAVE_INFO:GET_VERSION:POPPUNK_VERSION, IMAGES, BWA_VERSION, PARSE_OTHER_RESISTANCE, PIPELINE:MAPPING, SAVE_INFO:GET_VERSION:FASTP_VERSION, GET_KRAKEN2_DB, PIPELINE:TAXONOMY, DATABASES, PIPELINE:GET_REF_GENOME_BWA_DB, SAVE_INFO:GET_VERSION:KRAKEN2_VERSION, PIPELINE:SEROTYPE, PIPELINE:OVERALL_QC, SAMTOOLS_VERSION, SEROTYPE, GET_SEROBA_DB, PIPELINE:ASSEMBLY_QC, ASSEMBLY_ASSESS, SHOVILL_VERSION, SAVE_INFO:GET_VERSION:SAMTOOLS_VERSION, SAVE_INFO:GET_VERSION:ARIBA_VERSION, TAXONOMY_QC, PULL_IMAGES, PIPELINE:PARSE_OTHER_RESISTANCE, SAVE_INFO:GET_VERSION:BWA_VERSION, ASSEMBLY_UNICYCLER, PIPELINE:ASSEMBLY_SHOVILL, SAVE_INFO:GET_VERSION:TOOLS, SAVE_INFO:GET_VERSION:COMBINE_INFO, KRAKEN2_VERSION, SAVE_INFO:PARSE, SAVE_INFO:GET_VERSION:PYTHON_VERSION, ASSEMBLY_QC, ARIBA_VERSION, PIPELINE:ASSEMBLY_ASSESS, UNICYCLER_VERSION, PIPELINE:GENERATE_SAMPLE_REPORT 7月-15 10:37:23.146 [main] DEBUG nextflow.Session - Igniting dataflow network (50) 7月-15 10:37:23.146 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:GET_REF_GENOME_BWA_DB 7月-15 10:37:23.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:GET_KRAKEN2_DB 7月-15 10:37:23.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:GET_SEROBA_DB 7月-15 10:37:23.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:GET_POPPUNK_DB 7月-15 10:37:23.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:GET_POPPUNK_EXT_CLUSTERS 7月-15 10:37:23.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:GET_ARIBA_DB 7月-15 10:37:23.197 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:FILE_VALIDATION 7月-15 10:37:23.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:PREPROCESS 7月-15 10:37:23.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:READ_QC 7月-15 10:37:23.200 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:ASSEMBLY_SHOVILL 7月-15 10:37:23.200 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /home/r7_gpc/data/nvme2/GPStest/test/; pattern: *{,R}{1,2}{,_001}.{fq,fastq}{,.gz}; options: [checkIfExists:true] 7月-15 10:37:23.203 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:ASSEMBLY_ASSESS 7月-15 10:37:23.207 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:ASSEMBLY_QC 7月-15 10:37:23.211 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:MAPPING 7月-15 10:37:23.212 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:SAM_TO_SORTED_BAM 7月-15 10:37:23.212 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:SNP_CALL 7月-15 10:37:23.213 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:HET_SNP_COUNT 7月-15 10:37:23.214 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:MAPPING_QC 7月-15 10:37:23.214 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:TAXONOMY 7月-15 10:37:23.214 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:TAXONOMY_QC 7月-15 10:37:23.214 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:OVERALL_QC 7月-15 10:37:23.214 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:LINEAGE 7月-15 10:37:23.214 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:SEROTYPE 7月-15 10:37:23.214 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:MLST 7月-15 10:37:23.219 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:PBP_RESISTANCE 7月-15 10:37:23.220 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:PARSE_PBP_RESISTANCE 7月-15 10:37:23.223 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:OTHER_RESISTANCE 7月-15 10:37:23.223 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:PARSE_OTHER_RESISTANCE 7月-15 10:37:23.224 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:GENERATE_SAMPLE_REPORT 7月-15 10:37:23.224 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PIPELINE:GENERATE_OVERALL_REPORT 7月-15 10:37:23.224 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:IMAGES 7月-15 10:37:23.224 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:DATABASES 7月-15 10:37:23.224 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:PYTHON_VERSION 7月-15 10:37:23.224 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:FASTP_VERSION 7月-15 10:37:23.225 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:UNICYCLER_VERSION 7月-15 10:37:23.225 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:SHOVILL_VERSION 7月-15 10:37:23.225 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:QUAST_VERSION 7月-15 10:37:23.225 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:BWA_VERSION 7月-15 10:37:23.225 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:SAMTOOLS_VERSION 7月-15 10:37:23.228 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:BCFTOOLS_VERSION 7月-15 10:37:23.228 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:POPPUNK_VERSION 7月-15 10:37:23.228 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:MLST_VERSION 7月-15 10:37:23.229 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:KRAKEN2_VERSION 7月-15 10:37:23.229 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:SEROBA_VERSION 7月-15 10:37:23.229 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:ARIBA_VERSION 7月-15 10:37:23.229 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:TOOLS 7月-15 10:37:23.229 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:GET_VERSION:COMBINE_INFO 7月-15 10:37:23.229 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:PARSE 7月-15 10:37:23.229 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SAVE_INFO:SAVE 7月-15 10:37:23.243 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_18b0035d0495eae2: /home/r7_gpc/bin/gps-pipeline/workflows/info_and_version.nf Script_8362d7bf23f59dd4: /home/r7_gpc/bin/gps-pipeline/modules/validate.nf Script_9814d8fd2e43a37b: /home/r7_gpc/bin/gps-pipeline/main.nf Script_ccf11e0d3df379bd: /home/r7_gpc/bin/gps-pipeline/modules/mapping.nf Script_d8c06a1bdd464788: /home/r7_gpc/bin/gps-pipeline/modules/preprocess.nf Script_5e9ce8c457133f72: /home/r7_gpc/bin/gps-pipeline/modules/info.nf Script_7a062f73dd5e06ae: /home/r7_gpc/bin/gps-pipeline/modules/assembly.nf Script_9a4f1dc16030dc70: /home/r7_gpc/bin/gps-pipeline/modules/singularity.nf Script_f1d2ee6c7df6d5d1: /home/r7_gpc/bin/gps-pipeline/modules/docker.nf Script_7787d7715b51a9bc: /home/r7_gpc/bin/gps-pipeline/modules/serotype.nf Script_7861912e11fa354e: /home/r7_gpc/bin/gps-pipeline/modules/overall_qc.nf Script_89b25e70b32b8314: /home/r7_gpc/bin/gps-pipeline/modules/amr.nf Script_5c3eadcff7fe6067: /home/r7_gpc/bin/gps-pipeline/modules/taxonomy.nf Script_82f6ef19113039f3: /home/r7_gpc/bin/gps-pipeline/modules/lineage.nf Script_31fad3a37f7e4fc4: /home/r7_gpc/bin/gps-pipeline/modules/output.nf Script_6fc4fbd00d6149b8: /home/r7_gpc/bin/gps-pipeline/workflows/init.nf Script_e0bc460491f16b40: /home/r7_gpc/bin/gps-pipeline/modules/messages.nf Script_2c92dded4143debc: /home/r7_gpc/bin/gps-pipeline/modules/mlst.nf Script_207632fa7b2fdbb8: /home/r7_gpc/bin/gps-pipeline/workflows/pipeline.nf 7月-15 10:37:23.243 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 7月-15 10:37:23.243 [main] DEBUG nextflow.Session - Session await 7月-15 10:37:23.852 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.856 [Task submitter] INFO nextflow.Session - [b1/4dd027] Submitted process > PIPELINE:GET_POPPUNK_EXT_CLUSTERS 7月-15 10:37:23.862 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.863 [Task submitter] INFO nextflow.Session - [cf/cae1ec] Submitted process > PIPELINE:FILE_VALIDATION (PC2044) 7月-15 10:37:23.873 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.874 [Task submitter] INFO nextflow.Session - [e0/4e4871] Submitted process > PIPELINE:GET_SEROBA_DB 7月-15 10:37:23.898 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.899 [Task submitter] INFO nextflow.Session - [28/d05803] Submitted process > PIPELINE:GET_KRAKEN2_DB 7月-15 10:37:23.906 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.908 [Task submitter] INFO nextflow.Session - [b5/5d1769] Submitted process > PIPELINE:GET_POPPUNK_DB 7月-15 10:37:23.915 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.916 [Task submitter] INFO nextflow.Session - [c5/b4fc57] Submitted process > PIPELINE:GET_ARIBA_DB 7月-15 10:37:23.925 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.926 [Task submitter] INFO nextflow.Session - [18/93bc50] Submitted process > PIPELINE:GET_REF_GENOME_BWA_DB 7月-15 10:37:23.933 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.934 [Task submitter] INFO nextflow.Session - [ba/b36c46] Submitted process > SAVE_INFO:GET_VERSION:FASTP_VERSION 7月-15 10:37:23.940 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.940 [Task submitter] INFO nextflow.Session - [58/17379b] Submitted process > SAVE_INFO:GET_VERSION:SEROBA_VERSION 7月-15 10:37:23.946 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.947 [Task submitter] INFO nextflow.Session - [29/e06e94] Submitted process > SAVE_INFO:GET_VERSION:IMAGES (1) 7月-15 10:37:23.954 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.955 [Task submitter] INFO nextflow.Session - [cc/74277e] Submitted process > SAVE_INFO:GET_VERSION:POPPUNK_VERSION 7月-15 10:37:23.962 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.964 [Task submitter] INFO nextflow.Session - [17/f2faea] Submitted process > SAVE_INFO:GET_VERSION:QUAST_VERSION 7月-15 10:37:23.971 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.972 [Task submitter] INFO nextflow.Session - [0c/9a5a38] Submitted process > SAVE_INFO:GET_VERSION:BWA_VERSION 7月-15 10:37:23.975 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.977 [Task submitter] INFO nextflow.Session - [da/49ec07] Submitted process > SAVE_INFO:GET_VERSION:SAMTOOLS_VERSION 7月-15 10:37:23.986 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.987 [Task submitter] INFO nextflow.Session - [d9/1e8861] Submitted process > SAVE_INFO:GET_VERSION:SHOVILL_VERSION 7月-15 10:37:23.998 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:23.999 [Task submitter] INFO nextflow.Session - [ba/0ccacb] Submitted process > SAVE_INFO:GET_VERSION:PYTHON_VERSION 7月-15 10:37:24.005 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:24.006 [Task submitter] INFO nextflow.Session - [1c/6dbd62] Submitted process > SAVE_INFO:GET_VERSION:KRAKEN2_VERSION 7月-15 10:37:24.012 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:24.013 [Task submitter] INFO nextflow.Session - [cc/745295] Submitted process > SAVE_INFO:GET_VERSION:BCFTOOLS_VERSION 7月-15 10:37:24.021 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:24.022 [Task submitter] INFO nextflow.Session - [f6/954e6f] Submitted process > SAVE_INFO:GET_VERSION:MLST_VERSION 7月-15 10:37:24.026 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:24.029 [Task submitter] INFO nextflow.Session - [af/2e6bbb] Submitted process > SAVE_INFO:GET_VERSION:UNICYCLER_VERSION 7月-15 10:37:24.034 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:24.037 [Task submitter] INFO nextflow.Session - [b8/660104] Submitted process > SAVE_INFO:GET_VERSION:ARIBA_VERSION 7月-15 10:37:25.829 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: PIPELINE:GET_POPPUNK_EXT_CLUSTERS; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/b1/4dd0278b3099b68ce4b5b71de7a491] 7月-15 10:37:26.545 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: PIPELINE:GET_SEROBA_DB; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/e0/4e487169e1785733256782dbb5cfdb] 7月-15 10:37:27.601 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: PIPELINE:GET_KRAKEN2_DB; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/28/d05803b1d8ac0aed30c7b47c51d2b2] 7月-15 10:37:27.831 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: PIPELINE:GET_REF_GENOME_BWA_DB; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/18/93bc50ba6654e4a07438410f5befd1] 7月-15 10:37:28.228 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: SAVE_INFO:GET_VERSION:FASTP_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/ba/b36c4623d4785e8f126e71a1ad364e] 7月-15 10:37:28.513 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: SAVE_INFO:GET_VERSION:QUAST_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/17/f2faea3dddfe9ef36bfe8876a7b8cc] 7月-15 10:37:28.642 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: PIPELINE:GET_POPPUNK_DB; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/b5/5d176961eb44e48964c24120a6a1f5] 7月-15 10:37:28.833 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: PIPELINE:GET_ARIBA_DB; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/c5/b4fc572dbfa21b0023c0eb6a6f0f3c] 7月-15 10:37:28.894 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:28.896 [Task submitter] INFO nextflow.Session - [c5/6b552b] Submitted process > SAVE_INFO:GET_VERSION:DATABASES 7月-15 10:37:28.924 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: SAVE_INFO:GET_VERSION:SHOVILL_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/d9/1e8861c860e15d47a106c15ad6ff2a] 7月-15 10:37:29.081 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: SAVE_INFO:GET_VERSION:BWA_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/0c/9a5a38f0ee2d813511d82a1e746e66] 7月-15 10:37:29.177 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: SAVE_INFO:GET_VERSION:SAMTOOLS_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/da/49ec07093d0b59446b1824a9d5af49] 7月-15 10:37:29.278 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: SAVE_INFO:GET_VERSION:POPPUNK_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/cc/74277eef18335bd1ebf9a51b000376] 7月-15 10:37:29.389 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: SAVE_INFO:GET_VERSION:IMAGES (1); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/29/e06e948fd1ce31a211a753141ae411] 7月-15 10:37:29.472 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: SAVE_INFO:GET_VERSION:KRAKEN2_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/1c/6dbd62cf09d0419857fee7569f235d] 7月-15 10:37:29.573 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: SAVE_INFO:GET_VERSION:BCFTOOLS_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/cc/745295f7cf03fa3ef1b710deba9384] 7月-15 10:37:29.641 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: SAVE_INFO:GET_VERSION:MLST_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/f6/954e6f4432670b7d5f9574f3e2064c] 7月-15 10:37:29.741 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: SAVE_INFO:GET_VERSION:SEROBA_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/58/17379b0c743a14201cc6842bb9bae1] 7月-15 10:37:29.820 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: SAVE_INFO:GET_VERSION:PYTHON_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/ba/0ccacb19af46e8fab17ae41445d43f] 7月-15 10:37:29.906 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: SAVE_INFO:GET_VERSION:UNICYCLER_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/af/2e6bbb7179c17b25ae577bbf8c37a1] 7月-15 10:37:30.674 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: SAVE_INFO:GET_VERSION:ARIBA_VERSION; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/b8/66010463e175686c2a2ec9ad6a49cb] 7月-15 10:37:30.697 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:30.698 [Task submitter] INFO nextflow.Session - [ec/c1a557] Submitted process > SAVE_INFO:GET_VERSION:TOOLS 7月-15 10:37:31.528 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: SAVE_INFO:GET_VERSION:DATABASES; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/c5/6b552b2c7fd5280c5c03cc18bced57] 7月-15 10:37:32.057 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: SAVE_INFO:GET_VERSION:TOOLS; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/ec/c1a5572eb6934bc5d6df76cd84ded1] 7月-15 10:37:32.070 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:37:32.071 [Task submitter] INFO nextflow.Session - [7c/e6ea05] Submitted process > SAVE_INFO:GET_VERSION:COMBINE_INFO (1) 7月-15 10:37:32.967 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: SAVE_INFO:GET_VERSION:COMBINE_INFO (1); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/7c/e6ea05478c0e6193d2027d8c49c4f2] 7月-15 10:37:33.014 [Task submitter] INFO nextflow.Session - [84/45c49d] Submitted process > SAVE_INFO:PARSE (1) 7月-15 10:37:33.046 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: SAVE_INFO:PARSE (1); status: COMPLETED; exit: -; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/84/45c49d698b82cac9ee9ca5e16e59dd] 7月-15 10:37:33.193 [Task submitter] INFO nextflow.Session - [30/c724c6] Submitted process > SAVE_INFO:SAVE (1) 7月-15 10:37:33.225 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: SAVE_INFO:SAVE (1); status: COMPLETED; exit: -; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/30/c724c6b623e2f2a63272bc2688fad3] 7月-15 10:37:33.243 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false 7月-15 10:38:17.816 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: PIPELINE:FILE_VALIDATION (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/cf/cae1ecdd6ff4d62d059ea19bb9f9f3] 7月-15 10:38:17.859 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:38:17.860 [Task submitter] INFO nextflow.Session - [3b/90fdf4] Submitted process > PIPELINE:PREPROCESS (PC2044) 7月-15 10:38:39.533 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: PIPELINE:PREPROCESS (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/3b/90fdf4770a30d9acd03b51e385b464] 7月-15 10:38:39.558 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:38:39.559 [Task submitter] INFO nextflow.Session - [c9/cbe577] Submitted process > PIPELINE:READ_QC (PC2044) 7月-15 10:38:40.389 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: PIPELINE:READ_QC (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/c9/cbe577b5199b48ea75886548ad2db3] 7月-15 10:38:40.422 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:38:40.423 [Task submitter] INFO nextflow.Session - [22/e99678] Submitted process > PIPELINE:MAPPING (PC2044) 7月-15 10:38:40.428 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:38:40.429 [Task submitter] INFO nextflow.Session - [23/35839c] Submitted process > PIPELINE:TAXONOMY (PC2044) 7月-15 10:38:40.433 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:38:40.434 [Task submitter] INFO nextflow.Session - [ef/b430ea] Submitted process > PIPELINE:ASSEMBLY_SHOVILL (PC2044) 7月-15 10:39:03.240 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: PIPELINE:TAXONOMY (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/23/35839cf1866991f51adfc5331b3b67] 7月-15 10:39:03.268 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:39:03.270 [Task submitter] INFO nextflow.Session - [4a/2b17b4] Submitted process > PIPELINE:TAXONOMY_QC (PC2044) 7月-15 10:39:04.133 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: PIPELINE:TAXONOMY_QC (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/4a/2b17b40fed0950ee6d1e226f2c6925] 7月-15 10:39:17.724 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: PIPELINE:MAPPING (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/22/e9967864b67c52158d5883254090b4] 7月-15 10:39:17.758 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:39:17.759 [Task submitter] INFO nextflow.Session - [46/dd2d9c] Submitted process > PIPELINE:SAM_TO_SORTED_BAM (PC2044) 7月-15 10:39:46.575 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: PIPELINE:SAM_TO_SORTED_BAM (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/46/dd2d9c05c4eee588c86b70ebffc9e8] 7月-15 10:39:46.604 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:39:46.605 [Task submitter] INFO nextflow.Session - [36/1d70ee] Submitted process > PIPELINE:SNP_CALL (PC2044) 7月-15 10:40:30.283 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: PIPELINE:ASSEMBLY_SHOVILL (PC2044); status: COMPLETED; exit: 1; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65] 7月-15 10:40:30.287 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=PIPELINE:ASSEMBLY_SHOVILL (PC2044); work-dir=/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65 error [nextflow.exception.ProcessFailedException]: Process PIPELINE:ASSEMBLY_SHOVILL (PC2044) terminated with an error exit status (1) 7月-15 10:40:30.289 [Task monitor] INFO nextflow.processor.TaskProcessor - [ef/b430ea] NOTE: Process PIPELINE:ASSEMBLY_SHOVILL (PC2044) terminated with an error exit status (1) -- Error is ignored 7月-15 10:41:23.614 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: PIPELINE:SNP_CALL (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/36/1d70ee16da7c508da574339aab4b35] 7月-15 10:41:23.632 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:41:23.633 [Task submitter] INFO nextflow.Session - [d9/6a4e7e] Submitted process > PIPELINE:HET_SNP_COUNT (PC2044) 7月-15 10:41:24.538 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: PIPELINE:HET_SNP_COUNT (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/d9/6a4e7e6f5f5d99c0675fcfdf9a7f46] 7月-15 10:41:24.559 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:41:24.560 [Task submitter] INFO nextflow.Session - [87/193197] Submitted process > PIPELINE:MAPPING_QC (PC2044) 7月-15 10:41:25.399 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: PIPELINE:MAPPING_QC (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/87/193197c09497e64be3f2b7299b4837] 7月-15 10:41:25.422 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:41:25.423 [Task submitter] INFO nextflow.Session - [20/582979] Submitted process > PIPELINE:OVERALL_QC (PC2044) 7月-15 10:41:26.148 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: PIPELINE:OVERALL_QC (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/20/5829797f5b24c7abc0239b3cd5e951] 7月-15 10:41:26.165 [Actor Thread 50] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null 7月-15 10:41:26.191 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:41:26.192 [Task submitter] INFO nextflow.Session - [dc/38e3ac] Submitted process > PIPELINE:GENERATE_SAMPLE_REPORT (PC2044) 7月-15 10:41:26.994 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: PIPELINE:GENERATE_SAMPLE_REPORT (PC2044); status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/dc/38e3ac549cc37023ad308e182c4bc1] 7月-15 10:41:27.013 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run 7月-15 10:41:27.014 [Task submitter] INFO nextflow.Session - [2d/4a19c7] Submitted process > PIPELINE:GENERATE_OVERALL_REPORT 7月-15 10:41:28.241 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: PIPELINE:GENERATE_OVERALL_REPORT; status: COMPLETED; exit: 0; error: -; workDir: /home/r7_gpc/bin/gps-pipeline/work/2d/4a19c7a982ee2a33a477abb6753ec7] 7月-15 10:41:28.247 [main] DEBUG nextflow.Session - Session await > all processes finished 7月-15 10:41:28.251 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop 7月-15 10:41:28.255 [main] DEBUG nextflow.Session - Session await > all barriers passed 7月-15 10:41:28.265 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) 7月-15 10:41:28.271 [main] INFO nextflow.Nextflow - The workflow ended at 2024-07-15 10:41:28 JST. The duration was 4m 10s

The pipeline has been completed successfully. The output is located at /nvme2/GPS_test/test_res.

7月-15 10:41:28.277 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=38; failedCount=1; ignoredCount=1; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=6m 8s; failedDuration=1m 50s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=21; peakCpus=21; peakMemory=0; ] 7月-15 10:41:28.468 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done 7月-15 10:41:28.487 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) 7月-15 10:41:28.490 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Next, I found a .command.log file in the folder you mentioned, so I will copy and paste its contents here.

[shovill] Hello stranger [shovill] You ran: /shovill-1.1.0/bin/shovill --R1 processed-PC2044_1.fastq.gz --R2 processed-PC2044_2.fastq.gz --outdir results --cpus 64 --minlen 500 --force [shovill] This is shovill 1.1.0 [shovill] Written by Torsten Seemann [shovill] Homepage is https://github.com/tseemann/shovill [shovill] Operating system is linux [shovill] Perl version is v5.22.1 [shovill] Machine has 64 CPU cores and 1007.59 GB RAM [shovill] Using bwa - /bwa/bwa-0.7.17/bwa | Version: 0.7.17-r1188 [shovill] Using flash - /flash/FLASH-1.2.11/flash | FLASH v1.2.11 [shovill] Using java - /usr/bin/java | openjdk version "9-internal" [shovill] Using kmc - /kmc/kmc | K-Mer Counter (KMC) ver. 3.1.1 (2019-05-19) [shovill] Using lighter - /Lighter-1.1.1/lighter | Lighter v1.1.1 [shovill] Using megahit - /megahit/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit | MEGAHIT v1.1.3 [shovill] Using megahit_toolkit - /megahit/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_toolkit | v1.1.3 [shovill] Using pigz - /usr/bin/pigz | pigz 2.3.1 [shovill] Using pilon - /pilon/pilon | Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500 [shovill] Using samclip - /samclip/samclip | samclip 0.4.0 [shovill] Using samtools - /usr/local/bin/samtools | Version: 1.16.1 (using htslib 1.16) [shovill] Using seqtk - /usr/local/bin/seqtk | Version: 1.3-r106 [shovill] Using skesa - /skesa/skesa | SKESA v.2.3.0 [shovill] Using spades.py - /SPAdes-3.15.5-Linux/bin/spades.py | SPAdes genome assembler v3.15.5 [shovill] Using trimmomatic - /trimmomatic/trimmomatic | 0.39 [shovill] Using velvetg - /velvet/velvet-1.2.10/velvetg | Version 1.2.10 [shovill] Using velveth - /velvet/velvet-1.2.10/velveth | Version 1.2.10 [shovill] Found spades version: 003015000 [shovill] Will use spades 003015000 options: --isolate and --merged [shovill] Using tempdir: /tmp/Lh94HN77sL [shovill] Changing into folder: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results [shovill] Collecting raw read statistics with 'seqtk' [shovill] Running: seqtk fqchk -q3 \/home\/r7_gpc\/bin\/gps-pipeline\/work\/3b\/90fdf4770a30d9acd03b51e385b464\/processed-PC2044_1.fastq.gz >/tmp/vkje15bqb4 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Read stats: min_len = 31 [shovill] Read stats: total_bp = 861042064 [shovill] Read stats: max_len = 151 [shovill] Read stats: avg_len = 151 [shovill] Estimating genome size by counting unqiue 21-mers > frequency 10 [shovill] Running: kmc -sm -m8 -t64 -k21 -ci10 \/home\/r7_gpc\/bin\/gps-pipeline\/work\/3b\/90fdf4770a30d9acd03b51e385b464\/processed-PC2044_1.fastq.gz /tmp/yZdPfHfPv4/kmc /tmp/yZdPfHfPv4 2>&1 | sed 's/^/[kmc] /' | tee -a shovill.log [kmc] * Stage 1: 100% Stage 2: 100% [kmc] [kmc] 1st stage: 7.6442s [kmc] 2nd stage: 0.843276s [kmc] 3rd stage: 0.113799s [kmc] Total : 8.60127s [kmc] Tmp size : 459MB [kmc] Tmp size strict memory : 0MB [kmc] Tmp total: 459MB [kmc] [kmc] Stats: [kmc] No. of k-mers below min. threshold : 8897764 [kmc] No. of k-mers above max. threshold : 0 [kmc] No. of unique k-mers : 10968005 [kmc] No. of unique counted k-mers : 2070241 [kmc] Total no. of k-mers : 373471494 [kmc] Total no. of reads : 2852473 [kmc] Total no. of super-k-mers : 56178924 [shovill] Using genome size 2070241 bp [shovill] Estimated sequencing depth: 415 x [shovill] Subsampling reads by factor 0.361 to get from 415x to 150x [shovill] Running: seqtk sample \/home\/r7_gpc\/bin\/gps-pipeline\/work\/3b\/90fdf4770a30d9acd03b51e385b464\/processed-PC2044_1.fastq.gz 0.361 | pigz --fast -c -p 64 > R1.sub.fq.gz 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Running: seqtk sample \/home\/r7_gpc\/bin\/gps-pipeline\/work\/3b\/90fdf4770a30d9acd03b51e385b464\/processed-PC2044_2.fastq.gz 0.361 | pigz --fast -c -p 64 > R2.sub.fq.gz 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Appending -Xmx16g to _JAVA_OPTIONS [shovill] Running: ln -sf R1.sub.fq.gz R1.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log [shovill] Running: ln -sf R2.sub.fq.gz R2.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log [shovill] Average read length looks like 151 bp [shovill] Setting k-mer range to (31 .. 113) [shovill] Estimated K-mers: 31 51 71 91 111 [kn=5, ks=20, kmin=31, kmax=113] [shovill] Using kmers: 31,51,71,91,111 [shovill] Correcting reads with 'Lighter' [shovill] Running: lighter -od . -r R1.fq.gz -r R2.fq.gz -K 32 2070241 -t 64 -maxcor 1 2>&1 | sed 's/^/[lighter] /' | tee -a shovill.log [lighter] [2024-07-15 01:39:17] =============Start==================== [lighter] [2024-07-15 01:39:17] Scanning the input files to infer alpha(sampling rate) [lighter] [2024-07-15 01:39:22] Average coverage is 150.023 and alpha is 0.047 [lighter] [2024-07-15 01:39:25] Bad quality threshold is "-" [lighter] [2024-07-15 01:39:39] Finish sampling kmers [lighter] [2024-07-15 01:39:39] Bloom filter A's false positive rate: 0.007551 [lighter] [2024-07-15 01:39:45] Finish storing trusted kmers [lighter] [2024-07-15 01:40:02] Finish error correction [lighter] Processed 2057808 reads: [lighter] 1646985 are error-free [lighter] Corrected 591079 bases(1.438768 corrections for reads with errors) [lighter] Trimmed 0 reads with average trimmed bases 0.000000 [lighter] Discard 0 reads [shovill] Overlapping/stitching PE reads with 'FLASH' [shovill] Running: flash -m 20 -M 151 -d . -o flash -z -t 64 R1.cor.fq.gz R2.cor.fq.gz 2>&1 | sed 's/^//' | tee -a shovill.log [FLASH] Starting FLASH v1.2.11 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] R1.cor.fq.gz [FLASH] R2.cor.fq.gz [FLASH] [FLASH] Output files: [FLASH] ./flash.extendedFrags.fastq.gz [FLASH] ./flash.notCombined_1.fastq.gz [FLASH] ./flash.notCombined_2.fastq.gz [FLASH] ./flash.hist [FLASH] ./flash.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 20 [FLASH] Max overlap: 151 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: false [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 64 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 64 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 200000 read pairs [FLASH] Processed 225000 read pairs [FLASH] Processed 250000 read pairs [FLASH] Processed 275000 read pairs [FLASH] Processed 300000 read pairs [FLASH] Processed 325000 read pairs [FLASH] Processed 350000 read pairs [FLASH] Processed 375000 read pairs [FLASH] Processed 400000 read pairs [FLASH] Processed 425000 read pairs [FLASH] Processed 450000 read pairs [FLASH] Processed 475000 read pairs [FLASH] Processed 500000 read pairs [FLASH] Processed 525000 read pairs [FLASH] Processed 550000 read pairs [FLASH] Processed 575000 read pairs [FLASH] Processed 600000 read pairs [FLASH] Processed 625000 read pairs [FLASH] Processed 650000 read pairs [FLASH] Processed 675000 read pairs [FLASH] Processed 700000 read pairs [FLASH] Processed 725000 read pairs [FLASH] Processed 750000 read pairs [FLASH] Processed 775000 read pairs [FLASH] Processed 800000 read pairs [FLASH] Processed 825000 read pairs [FLASH] Processed 850000 read pairs [FLASH] Processed 875000 read pairs [FLASH] Processed 900000 read pairs [FLASH] Processed 925000 read pairs [FLASH] Processed 950000 read pairs [FLASH] Processed 975000 read pairs [FLASH] Processed 1000000 read pairs [FLASH] Processed 1025000 read pairs [FLASH] Processed 1028904 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 1028904 [FLASH] Combined pairs: 344559 [FLASH] Uncombined pairs: 684345 [FLASH] Percent combined: 33.49% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v1.2.11 complete! [FLASH] 19.058 seconds elapsed [shovill] Assembling reads with 'spades' [shovill] Running: spades.py -1 flash.notCombined_1.fastq.gz -2 flash.notCombined_2.fastq.gz --isolate --threads 64 --memory 16 -o spades --tmp-dir /tmp/Lh94HN77sL -k 31,51,71,91,111 --merged flash.extendedFrags.fastq.gz 2>&1 | sed 's/^/[spades] /' | tee -a shovill.log [spades] Command line: /SPAdes-3.15.5-Linux/bin/spades.py -1 /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_1.fastq.gz -2 /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_2.fastq.gz --isolate --threads 64 --memory 16 -o /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades --tmp-dir /tmp/Lh94HN77sL -k 31,51,71,91,111 --merged /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.extendedFrags.fastq.gz [spades] [spades] System information: [spades] SPAdes version: 3.15.5 [spades] Python version: 2.7.12 [spades] OS: Linux-5.4.0-169-generic-x86_64-with-Ubuntu-16.04-xenial [spades] [spades] Output dir: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades [spades] Mode: ONLY assembling (without read error correction) [spades] Debug mode is turned OFF [spades] [spades] Dataset parameters: [spades] Isolate mode [spades] Reads: [spades] Library number: 1, library type: paired-end [spades] orientation: fr [spades] left reads: ['/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_1.fastq.gz'] [spades] right reads: ['/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_2.fastq.gz'] [spades] interlaced reads: not specified [spades] single reads: not specified [spades] merged reads: ['/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.extendedFrags.fastq.gz'] [spades] Assembly parameters: [spades] k: [31, 51, 71, 91, 111] [spades] Repeat resolution is enabled [spades] Mismatch careful mode is turned OFF [spades] MismatchCorrector will be SKIPPED [spades] Coverage cutoff is turned OFF [spades] Other parameters: [spades] Dir for temp files: /tmp/Lh94HN77sL [spades] Threads: 64 [spades] Memory limit (in Gb): 16 [spades] [spades] [spades] ======= SPAdes pipeline started. Log can be found here: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/spades.log [spades] [spades] Files with merged reads were ignored. [spades] /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_2.fastq.gz: max reads length: 151 [spades] /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_1.fastq.gz: max reads length: 151 [spades] [spades] Reads length: 151 [spades] [spades] [spades] ===== Before start started. [spades] [spades] [spades] ===== Assembling started. [spades] [spades] [spades] ===== K31 started. [spades] [spades] [spades] == Running: /SPAdes-3.15.5-Linux/bin/spades-core /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/config.info /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/isolate_mode.info [spades] [spades] 0:00:00.000 1M / 14M INFO General (main.cpp : 99) Loaded config from /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/config.info [spades] 0:00:00.024 1M / 14M INFO General (main.cpp : 99) Loaded config from /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/isolate_mode.info [spades] 0:00:00.038 1M / 14M INFO General (memory_limit.cpp : 54) Memory limit set to 16 Gb [spades] 0:00:00.051 1M / 14M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.5, git revision e757b8216f9a038fb616e9551a2d4891b2d19ad7 [spades] 0:00:00.064 1M / 14M INFO General (main.cpp : 108) Maximum k-mer length: 128 [spades] 0:00:00.076 1M / 14M INFO General (main.cpp : 109) Assembling dataset (/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/dataset.info) with K=31 [spades] 0:00:00.089 1M / 14M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 64 [spades] 0:00:00.102 1M / 14M INFO General (pipeline.cpp : 212) SPAdes started [spades] 0:00:00.115 1M / 14M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion [spades] 0:00:00.128 1M / 14M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled [spades] 0:00:00.141 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 [spades] 0:00:00.154 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 [spades] 0:00:00.166 1M / 14M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 [spades] 0:00:00.179 1M / 14M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) [spades] 0:00:00.194 1M / 14M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) [spades] 0:00:00.205 1M / 14M INFO General (read_converter.cpp : 73) Converting paired reads [spades] 0:00:00.943 21M / 75M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:00.967 21M / 77M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:00.999 21M / 81M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:01.310 12M / 107M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:01.825 3M / 154M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:02.759 0M / 247M INFO General (binary_converter.cpp : 96) 524288 reads processed [spades] 0:00:03.438 0M / 269M INFO General (binary_converter.cpp : 111) 684345 reads written [spades] 0:00:03.449 0M / 269M INFO General (read_converter.cpp : 86) Converting single reads [spades] 0:00:03.464 0M / 269M INFO General (binary_converter.cpp : 111) 0 reads written [spades] 0:00:03.477 0M / 269M INFO General (read_converter.cpp : 92) Converting merged reads [spades] 0:00:03.830 0M / 299M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:03.852 0M / 301M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:03.879 0M / 303M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:04.358 0M / 331M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:05.024 0M / 359M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:05.377 0M / 359M INFO General (binary_converter.cpp : 111) 344559 reads written [spades] 0:00:05.476 1M / 360M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) [spades] 0:00:05.571 2M / 360M INFO General (construction.cpp : 153) Max read length 282 [spades] 0:00:05.578 2M / 360M INFO General (construction.cpp : 156) Max read length without merged 151 [spades] 0:00:05.591 2M / 360M INFO General (construction.cpp : 159) Average read length 170.268 [spades] 0:00:05.604 2M / 360M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) [spades] 0:00:05.617 2M / 360M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 640 files using 64 threads. This might take a while. [spades] 0:00:05.630 3M / 360M INFO General (file_limit.hpp : 42) Open file limit set to 1048576 [spades] 0:00:05.656 3M / 360M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.083323 Gb [spades] 0:00:05.668 3M / 360M INFO General (kmer_splitter.hpp : 101) Using cell size of 17474 [spades] mimalloc: error: unable to allocate OS memory (268435456 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1) [spades] mimalloc: process info: [spades] elapsed: 6.282 s [spades] process: user: 61.153 s, system: 3.002 s, faults: 0 [spades] rss: current: 16381898752, peak: 2206056448 [spades] commit: current: 16381898752, peak: 16381898752 [spades] [spades] [spades] == Error == system call for: "['/SPAdes-3.15.5-Linux/bin/spades-core', '/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/config.info', '/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/isolate_mode.info']" finished abnormally, OS return value: -6 [spades] None [spades] [spades] In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru [spades] or report an issue on our GitHub repository github.com/ablab/spades [spades] Please provide us with params.txt and spades.log files from the output directory. [spades] [spades] SPAdes log can be found here: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/spades.log [spades] [spades] Thank you for using SPAdes! [shovill] Assembly failed - spades.fasta has zero contigs! r7_gpc@s13:~/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65$ r7_gpc@s13:~/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65$ cat .command.log [shovill] Hello stranger [shovill] You ran: /shovill-1.1.0/bin/shovill --R1 processed-PC2044_1.fastq.gz --R2 processed-PC2044_2.fastq.gz --outdir results --cpus 64 --minlen 500 --force [shovill] This is shovill 1.1.0 [shovill] Written by Torsten Seemann [shovill] Homepage is https://github.com/tseemann/shovill [shovill] Operating system is linux [shovill] Perl version is v5.22.1 [shovill] Machine has 64 CPU cores and 1007.59 GB RAM [shovill] Using bwa - /bwa/bwa-0.7.17/bwa | Version: 0.7.17-r1188 [shovill] Using flash - /flash/FLASH-1.2.11/flash | FLASH v1.2.11 [shovill] Using java - /usr/bin/java | openjdk version "9-internal" [shovill] Using kmc - /kmc/kmc | K-Mer Counter (KMC) ver. 3.1.1 (2019-05-19) [shovill] Using lighter - /Lighter-1.1.1/lighter | Lighter v1.1.1 [shovill] Using megahit - /megahit/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit | MEGAHIT v1.1.3 [shovill] Using megahit_toolkit - /megahit/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit_toolkit | v1.1.3 [shovill] Using pigz - /usr/bin/pigz | pigz 2.3.1 [shovill] Using pilon - /pilon/pilon | Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500 [shovill] Using samclip - /samclip/samclip | samclip 0.4.0 [shovill] Using samtools - /usr/local/bin/samtools | Version: 1.16.1 (using htslib 1.16) [shovill] Using seqtk - /usr/local/bin/seqtk | Version: 1.3-r106 [shovill] Using skesa - /skesa/skesa | SKESA v.2.3.0 [shovill] Using spades.py - /SPAdes-3.15.5-Linux/bin/spades.py | SPAdes genome assembler v3.15.5 [shovill] Using trimmomatic - /trimmomatic/trimmomatic | 0.39 [shovill] Using velvetg - /velvet/velvet-1.2.10/velvetg | Version 1.2.10 [shovill] Using velveth - /velvet/velvet-1.2.10/velveth | Version 1.2.10 [shovill] Found spades version: 003015000 [shovill] Will use spades 003015000 options: --isolate and --merged [shovill] Using tempdir: /tmp/Lh94HN77sL [shovill] Changing into folder: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results [shovill] Collecting raw read statistics with 'seqtk' [shovill] Running: seqtk fqchk -q3 \/home\/r7_gpc\/bin\/gps-pipeline\/work\/3b\/90fdf4770a30d9acd03b51e385b464\/processed-PC2044_1.fastq.gz >/tmp/vkje15bqb4 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Read stats: min_len = 31 [shovill] Read stats: total_bp = 861042064 [shovill] Read stats: max_len = 151 [shovill] Read stats: avg_len = 151 [shovill] Estimating genome size by counting unqiue 21-mers > frequency 10 [shovill] Running: kmc -sm -m8 -t64 -k21 -ci10 \/home\/r7_gpc\/bin\/gps-pipeline\/work\/3b\/90fdf4770a30d9acd03b51e385b464\/processed-PC2044_1.fastq.gz /tmp/yZdPfHfPv4/kmc /tmp/yZdPfHfPv4 2>&1 | sed 's/^/[kmc] /' | tee -a shovill.log [kmc] * Stage 1: 100% Stage 2: 100% [kmc] [kmc] 1st stage: 7.6442s [kmc] 2nd stage: 0.843276s [kmc] 3rd stage: 0.113799s [kmc] Total : 8.60127s [kmc] Tmp size : 459MB [kmc] Tmp size strict memory : 0MB [kmc] Tmp total: 459MB [kmc] [kmc] Stats: [kmc] No. of k-mers below min. threshold : 8897764 [kmc] No. of k-mers above max. threshold : 0 [kmc] No. of unique k-mers : 10968005 [kmc] No. of unique counted k-mers : 2070241 [kmc] Total no. of k-mers : 373471494 [kmc] Total no. of reads : 2852473 [kmc] Total no. of super-k-mers : 56178924 [shovill] Using genome size 2070241 bp [shovill] Estimated sequencing depth: 415 x [shovill] Subsampling reads by factor 0.361 to get from 415x to 150x [shovill] Running: seqtk sample \/home\/r7_gpc\/bin\/gps-pipeline\/work\/3b\/90fdf4770a30d9acd03b51e385b464\/processed-PC2044_1.fastq.gz 0.361 | pigz --fast -c -p 64 > R1.sub.fq.gz 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Running: seqtk sample \/home\/r7_gpc\/bin\/gps-pipeline\/work\/3b\/90fdf4770a30d9acd03b51e385b464\/processed-PC2044_2.fastq.gz 0.361 | pigz --fast -c -p 64 > R2.sub.fq.gz 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Appending -Xmx16g to _JAVA_OPTIONS [shovill] Running: ln -sf R1.sub.fq.gz R1.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log [shovill] Running: ln -sf R2.sub.fq.gz R2.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log [shovill] Average read length looks like 151 bp [shovill] Setting k-mer range to (31 .. 113) [shovill] Estimated K-mers: 31 51 71 91 111 [kn=5, ks=20, kmin=31, kmax=113] [shovill] Using kmers: 31,51,71,91,111 [shovill] Correcting reads with 'Lighter' [shovill] Running: lighter -od . -r R1.fq.gz -r R2.fq.gz -K 32 2070241 -t 64 -maxcor 1 2>&1 | sed 's/^/[lighter] /' | tee -a shovill.log [lighter] [2024-07-15 01:39:17] =============Start==================== [lighter] [2024-07-15 01:39:17] Scanning the input files to infer alpha(sampling rate) [lighter] [2024-07-15 01:39:22] Average coverage is 150.023 and alpha is 0.047 [lighter] [2024-07-15 01:39:25] Bad quality threshold is "-" [lighter] [2024-07-15 01:39:39] Finish sampling kmers [lighter] [2024-07-15 01:39:39] Bloom filter A's false positive rate: 0.007551 [lighter] [2024-07-15 01:39:45] Finish storing trusted kmers [lighter] [2024-07-15 01:40:02] Finish error correction [lighter] Processed 2057808 reads: [lighter] 1646985 are error-free [lighter] Corrected 591079 bases(1.438768 corrections for reads with errors) [lighter] Trimmed 0 reads with average trimmed bases 0.000000 [lighter] Discard 0 reads [shovill] Overlapping/stitching PE reads with 'FLASH' [shovill] Running: flash -m 20 -M 151 -d . -o flash -z -t 64 R1.cor.fq.gz R2.cor.fq.gz 2>&1 | sed 's/^//' | tee -a shovill.log [FLASH] Starting FLASH v1.2.11 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] R1.cor.fq.gz [FLASH] R2.cor.fq.gz [FLASH] [FLASH] Output files: [FLASH] ./flash.extendedFrags.fastq.gz [FLASH] ./flash.notCombined_1.fastq.gz [FLASH] ./flash.notCombined_2.fastq.gz [FLASH] ./flash.hist [FLASH] ./flash.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 20 [FLASH] Max overlap: 151 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: false [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 64 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 64 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 200000 read pairs [FLASH] Processed 225000 read pairs [FLASH] Processed 250000 read pairs [FLASH] Processed 275000 read pairs [FLASH] Processed 300000 read pairs [FLASH] Processed 325000 read pairs [FLASH] Processed 350000 read pairs [FLASH] Processed 375000 read pairs [FLASH] Processed 400000 read pairs [FLASH] Processed 425000 read pairs [FLASH] Processed 450000 read pairs [FLASH] Processed 475000 read pairs [FLASH] Processed 500000 read pairs [FLASH] Processed 525000 read pairs [FLASH] Processed 550000 read pairs [FLASH] Processed 575000 read pairs [FLASH] Processed 600000 read pairs [FLASH] Processed 625000 read pairs [FLASH] Processed 650000 read pairs [FLASH] Processed 675000 read pairs [FLASH] Processed 700000 read pairs [FLASH] Processed 725000 read pairs [FLASH] Processed 750000 read pairs [FLASH] Processed 775000 read pairs [FLASH] Processed 800000 read pairs [FLASH] Processed 825000 read pairs [FLASH] Processed 850000 read pairs [FLASH] Processed 875000 read pairs [FLASH] Processed 900000 read pairs [FLASH] Processed 925000 read pairs [FLASH] Processed 950000 read pairs [FLASH] Processed 975000 read pairs [FLASH] Processed 1000000 read pairs [FLASH] Processed 1025000 read pairs [FLASH] Processed 1028904 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 1028904 [FLASH] Combined pairs: 344559 [FLASH] Uncombined pairs: 684345 [FLASH] Percent combined: 33.49% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v1.2.11 complete! [FLASH] 19.058 seconds elapsed [shovill] Assembling reads with 'spades' [shovill] Running: spades.py -1 flash.notCombined_1.fastq.gz -2 flash.notCombined_2.fastq.gz --isolate --threads 64 --memory 16 -o spades --tmp-dir /tmp/Lh94HN77sL -k 31,51,71,91,111 --merged flash.extendedFrags.fastq.gz 2>&1 | sed 's/^/[spades] /' | tee -a shovill.log [spades] Command line: /SPAdes-3.15.5-Linux/bin/spades.py -1 /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_1.fastq.gz -2 /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_2.fastq.gz --isolate --threads 64 --memory 16 -o /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades --tmp-dir /tmp/Lh94HN77sL -k 31,51,71,91,111 --merged /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.extendedFrags.fastq.gz [spades] [spades] System information: [spades] SPAdes version: 3.15.5 [spades] Python version: 2.7.12 [spades] OS: Linux-5.4.0-169-generic-x86_64-with-Ubuntu-16.04-xenial [spades] [spades] Output dir: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades [spades] Mode: ONLY assembling (without read error correction) [spades] Debug mode is turned OFF [spades] [spades] Dataset parameters: [spades] Isolate mode [spades] Reads: [spades] Library number: 1, library type: paired-end [spades] orientation: fr [spades] left reads: ['/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_1.fastq.gz'] [spades] right reads: ['/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_2.fastq.gz'] [spades] interlaced reads: not specified [spades] single reads: not specified [spades] merged reads: ['/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.extendedFrags.fastq.gz'] [spades] Assembly parameters: [spades] k: [31, 51, 71, 91, 111] [spades] Repeat resolution is enabled [spades] Mismatch careful mode is turned OFF [spades] MismatchCorrector will be SKIPPED [spades] Coverage cutoff is turned OFF [spades] Other parameters: [spades] Dir for temp files: /tmp/Lh94HN77sL [spades] Threads: 64 [spades] Memory limit (in Gb): 16 [spades] [spades] [spades] ======= SPAdes pipeline started. Log can be found here: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/spades.log [spades] [spades] Files with merged reads were ignored. [spades] /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_2.fastq.gz: max reads length: 151 [spades] /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/flash.notCombined_1.fastq.gz: max reads length: 151 [spades] [spades] Reads length: 151 [spades] [spades] [spades] ===== Before start started. [spades] [spades] [spades] ===== Assembling started. [spades] [spades] [spades] ===== K31 started. [spades] [spades] [spades] == Running: /SPAdes-3.15.5-Linux/bin/spades-core /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/config.info /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/isolate_mode.info [spades] [spades] 0:00:00.000 1M / 14M INFO General (main.cpp : 99) Loaded config from /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/config.info [spades] 0:00:00.024 1M / 14M INFO General (main.cpp : 99) Loaded config from /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/isolate_mode.info [spades] 0:00:00.038 1M / 14M INFO General (memory_limit.cpp : 54) Memory limit set to 16 Gb [spades] 0:00:00.051 1M / 14M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.5, git revision e757b8216f9a038fb616e9551a2d4891b2d19ad7 [spades] 0:00:00.064 1M / 14M INFO General (main.cpp : 108) Maximum k-mer length: 128 [spades] 0:00:00.076 1M / 14M INFO General (main.cpp : 109) Assembling dataset (/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/dataset.info) with K=31 [spades] 0:00:00.089 1M / 14M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 64 [spades] 0:00:00.102 1M / 14M INFO General (pipeline.cpp : 212) SPAdes started [spades] 0:00:00.115 1M / 14M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion [spades] 0:00:00.128 1M / 14M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled [spades] 0:00:00.141 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 [spades] 0:00:00.154 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 [spades] 0:00:00.166 1M / 14M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 [spades] 0:00:00.179 1M / 14M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) [spades] 0:00:00.194 1M / 14M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) [spades] 0:00:00.205 1M / 14M INFO General (read_converter.cpp : 73) Converting paired reads [spades] 0:00:00.943 21M / 75M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:00.967 21M / 77M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:00.999 21M / 81M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:01.310 12M / 107M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:01.825 3M / 154M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:02.759 0M / 247M INFO General (binary_converter.cpp : 96) 524288 reads processed [spades] 0:00:03.438 0M / 269M INFO General (binary_converter.cpp : 111) 684345 reads written [spades] 0:00:03.449 0M / 269M INFO General (read_converter.cpp : 86) Converting single reads [spades] 0:00:03.464 0M / 269M INFO General (binary_converter.cpp : 111) 0 reads written [spades] 0:00:03.477 0M / 269M INFO General (read_converter.cpp : 92) Converting merged reads [spades] 0:00:03.830 0M / 299M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:03.852 0M / 301M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:03.879 0M / 303M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:04.358 0M / 331M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:05.024 0M / 359M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:05.377 0M / 359M INFO General (binary_converter.cpp : 111) 344559 reads written [spades] 0:00:05.476 1M / 360M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) [spades] 0:00:05.571 2M / 360M INFO General (construction.cpp : 153) Max read length 282 [spades] 0:00:05.578 2M / 360M INFO General (construction.cpp : 156) Max read length without merged 151 [spades] 0:00:05.591 2M / 360M INFO General (construction.cpp : 159) Average read length 170.268 [spades] 0:00:05.604 2M / 360M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) [spades] 0:00:05.617 2M / 360M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 640 files using 64 threads. This might take a while. [spades] 0:00:05.630 3M / 360M INFO General (file_limit.hpp : 42) Open file limit set to 1048576 [spades] 0:00:05.656 3M / 360M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 0.083323 Gb [spades] 0:00:05.668 3M / 360M INFO General (kmer_splitter.hpp : 101) Using cell size of 17474 [spades] mimalloc: error: unable to allocate OS memory (268435456 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1) [spades] mimalloc: process info: [spades] elapsed: 6.282 s [spades] process: user: 61.153 s, system: 3.002 s, faults: 0 [spades] rss: current: 16381898752, peak: 2206056448 [spades] commit: current: 16381898752, peak: 16381898752 [spades] [spades] [spades] == Error == system call for: "['/SPAdes-3.15.5-Linux/bin/spades-core', '/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/config.info', '/home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/K31/configs/isolate_mode.info']" finished abnormally, OS return value: -6 [spades] None [spades] [spades] In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru [spades] or report an issue on our GitHub repository github.com/ablab/spades [spades] Please provide us with params.txt and spades.log files from the output directory. [spades] [spades] SPAdes log can be found here: /home/r7_gpc/bin/gps-pipeline/work/ef/b430ea5af438e5f12a05df0985cf65/results/spades/spades.log [spades] [spades] Thank you for using SPAdes! [shovill] Assembly failed - spades.fasta has zero contigs!

Best, Sato

[HarryHung]

Hi

This line should be the root cause of the error:

[spades] mimalloc: error: unable to allocate OS memory (268435456 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1)

Can you check whether all or at least a sufficient amount of system memory is made available to Docker?

Another potential fix would be this: https://github.com/ablab/spades/issues/442#issuecomment-593606697

If all fail, please try to use the alternative assembler unicycler.

As I will have no Internet access for the rest of the week, I will get back to you next week. Please let me know how things work out for you.

[fugunokaraage]

Thank you for your response. I tried what you suggested. First, I monitored the RAM usage allocated to Docker during the pipeline execution using the docker stats command. I have attached a screenshot of that.

According to this, it seems that 1008G is allocated to Docker. Then, following the instructions in ablab/spades#442 (comment), I ran the ulimit -n 200000 command before executing the pipeline, but the same error occurred again.

Finally, I changed the assembler to unicycler by running ./run_pipeline --reads /home/r7_gpc/data/nvme2/GPS_test/test/ --output /home/r7_gpc/data/nvme2/GPS_test/test3 --assembler unicycler.

The run completed successfully-like, but it took more than 10 minutes despite being for just one strain. In addition, there was no file found in assemblies directory.

[HarryHung]

@fugunokaraage

Thank you for waiting.

Unicycler is considerably slower than Shovill, hence the slower runtime is acceptable if it was not terminated by error.

If no output file is found in the assemblies directory, please check whether the pipeline directory is located within the same file system as the output directory? If not, add the option --assembly_publish copy when you run the pipeline to avoid the usage of hard links.

You can also try to run things manually in Docker on a single read pair without the pipeline to isolate the issue:

1. Set the read filenames (change the names into your test read pair)

   READ_ONE="READ1_NAME_HERE"
   READ_TWO="READ2_NAME_HERE"

2. Preprocess the reads using fastp

   docker run --rm -it -u $(id -u):$(id -g) -v $PWD:/data staphb/fastp:0.23.4 fastp --thread $(nproc) --in1 "$READ_ONE" --in2 "$READ_TWO" --out1 "processed_1.fastq.gz" --out2 "processed_2.fastq.gz" --unpaired1 "processed_unpair.fastq.gz" --unpaired2 "processed_unpair.fastq.gz"

3. Assembly the processed reads using Shovill

   docker run --rm -it -u $(id -u):$(id -g) -v $PWD:/data staphb/shovill:1.1.0-2022Dec shovill --R1 "processed_1.fastq.gz" --R2 "processed_2.fastq.gz" --outdir results --cpus $(nproc) --minlen "500" --force

   If Shovill is able to complete successfully, you should be able to view the resulting file contigs.fa in results directory.

If it still crashes, I would suggest trying to use Singularity instead of Docker as your container engine. Please install Singularity/Apptainer if not already installed, then run the pipeline with the option -profile singularity

Please me know how it goes.