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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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ERROR ~ No such variable: outfile #784

Closed Luke-ebbis closed 1 month ago

Luke-ebbis commented 1 month ago

Description of the bug

I am attempting to run the ampliseq pipeline on a single sample to test it on my system. I get an error that says:

ERROR ~ No such variable: outfile

Is there an issue in the configuration that causes this.

Command used and terminal output

$ nextflow run nf-core/ampliseq -r 2.7.1 -params-file config/ampliseq.yaml -profile singularity

N E X T F L O W ~ version 24.04.4

Launching https://github.com/nf-core/ampliseq [stupefied_mendel] DSL2 - revision: 113e90bdff [2.7.1]

WARN: Access to undefined parameter help -- Initialise it to a default value eg. params.help = some_value WARN: Access to undefined parameter validate_params -- Initialise it to a default value eg. params.validate_params = some_value WARN: Access to undefined parameter dada_ref_taxonomy -- Initialise it to a default value eg. params.dada_ref_taxonomy = some_value WARN: Access to undefined parameter sintax_ref_taxonomy -- Initialise it to a default value eg. params.sintax_ref_taxonomy = some_value WARN: Access to undefined parameter qiime_ref_taxonomy -- Initialise it to a default value eg. params.qiime_ref_taxonomy = some_value WARN: Access to undefined parameter version -- Initialise it to a default value eg. params.version = some_value WARN: Access to undefined parameter monochrome_logs -- Initialise it to a default value eg. params.monochrome_logs = some_value WARN: Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | | / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,' null -g113e90b

Core Nextflow options revision : 2.7.1 runName : stupefied_mendel launchDir : /lustre/BIF/nobackup/bakke333/Documents/projects/mursik/analysis workDir : /lustre/BIF/nobackup/bakke333/Documents/projects/mursik/analysis/work projectDir : /home/bakke333/.nextflow/assets/nf-core/ampliseq userName : bakke333 profile : singularity configFiles :

Main arguments input : data/samplesheet_its1_5f.tsv outdir : ./results/ITS1_5F

Sequencing input illumina_novaseq: true

Skipping specific steps skip_cutadapt : true

!! Only displaying parameters that differ from the pipeline defaults !!

If you use null for your analysis please cite:

WARN: Access to undefined parameter input_fasta -- Initialise it to a default value eg. params.input_fasta = some_value WARN: Access to undefined parameter FW_primer -- Initialise it to a default value eg. params.FW_primer = some_value WARN: Access to undefined parameter pacbio -- Initialise it to a default value eg. params.pacbio = some_value WARN: Access to undefined parameter iontorrent -- Initialise it to a default value eg. params.iontorrent = some_value WARN: Access to undefined parameter single_end -- Initialise it to a default value eg. params.single_end = some_value WARN: Access to undefined parameter trunclenf -- Initialise it to a default value eg. params.trunclenf = some_value WARN: Access to undefined parameter trunclenr -- Initialise it to a default value eg. params.trunclenr = some_value WARN: Access to undefined parameter double_primer -- Initialise it to a default value eg. params.double_primer = some_value WARN: Access to undefined parameter min_len_asv -- Initialise it to a default value eg. params.min_len_asv = some_value WARN: Access to undefined parameter skip_dada_quality -- Initialise it to a default value eg. params.skip_dada_quality = some_value WARN: Access to undefined parameter tax_agglom_min -- Initialise it to a default value eg. params.tax_agglom_min = some_value WARN: Access to undefined parameter tax_agglom_max -- Initialise it to a default value eg. params.tax_agglom_max = some_value WARN: Access to undefined parameter dada_ref_tax_custom -- Initialise it to a default value eg. params.dada_ref_tax_custom = some_value WARN: Access to undefined parameter dada_ref_tax_custom_sp -- Initialise it to a default value eg. params.dada_ref_tax_custom_sp = some_value WARN: Access to undefined parameter pplace_tree -- Initialise it to a default value eg. params.pplace_tree = some_value WARN: Access to undefined parameter dada_assign_taxlevels -- Initialise it to a default value eg. params.dada_assign_taxlevels = some_value WARN: Access to undefined parameter skip_taxonomy -- Initialise it to a default value eg. params.skip_taxonomy = some_value WARN: Access to undefined parameter skip_dada_taxonomy -- Initialise it to a default value eg. params.skip_dada_taxonomy = some_value WARN: Access to undefined parameter cut_dada_ref_taxonomy -- Initialise it to a default value eg. params.cut_dada_ref_taxonomy = some_value WARN: Access to undefined parameter kraken2_ref_tax_custom -- Initialise it to a default value eg. params.kraken2_ref_tax_custom = some_value WARN: Access to undefined parameter filter_ssu -- Initialise it to a default value eg. params.filter_ssu = some_value WARN: Access to undefined parameter sbdiexport -- Initialise it to a default value eg. params.sbdiexport = some_value WARN: Access to undefined parameter addsh -- Initialise it to a default value eg. params.addsh = some_value WARN: Access to undefined parameter orf_end -- Initialise it to a default value eg. params.orf_end = some_value WARN: Access to undefined parameter multiqc_config -- Initialise it to a default value eg. params.multiqc_config = some_value WARN: Access to undefined parameter multiqc_logo -- Initialise it to a default value eg. params.multiqc_logo = some_value WARN: Access to undefined parameter multiqc_methods_description -- Initialise it to a default value eg. params.multiqc_methods_description = some_value WARN: Access to undefined parameter metadata -- Initialise it to a default value eg. params.metadata = some_value WARN: Access to undefined parameter classifier -- Initialise it to a default value eg. params.classifier = some_value WARN: Access to undefined parameter kraken2_ref_taxonomy -- Initialise it to a default value eg. params.kraken2_ref_taxonomy = some_value WARN: Access to undefined parameter report_template -- Initialise it to a default value eg. params.report_template = some_value WARN: Access to undefined parameter report_css -- Initialise it to a default value eg. params.report_css = some_value WARN: Access to undefined parameter report_logo -- Initialise it to a default value eg. params.report_logo = some_value WARN: Access to undefined parameter report_abstract -- Initialise it to a default value eg. params.report_abstract = some_value WARN: Access to undefined parameter illumina_pe_its -- Initialise it to a default value eg. params.illumina_pe_its = some_value WARN: Access to undefined parameter trunc_qmin -- Initialise it to a default value eg. params.trunc_qmin = some_value WARN: Access to undefined parameter trunc_rmin -- Initialise it to a default value eg. params.trunc_rmin = some_value WARN: No DADA2 cutoffs were specified (--trunclenf & --trunclenr), therefore reads will be truncated where median quality drops below null (defined by --trunc_qmin) but at least a fraction of null (defined by --trunc_rmin) of the reads will be retained. The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.

WARN: Access to undefined parameter kraken2_assign_taxlevels -- Initialise it to a default value eg. params.kraken2_assign_taxlevels = some_value WARN: Access to undefined parameter skip_qiime -- Initialise it to a default value eg. params.skip_qiime = some_value WARN: Access to undefined parameter validationSkipDuplicateCheck -- Initialise it to a default value eg. params.validationSkipDuplicateCheck = some_value WARN: Access to undefined parameter validationS3PathCheck -- Initialise it to a default value eg. params.validationS3PathCheck = some_value [- ] NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES - [- ] NFCORE_AMPLISEQ:AMPLISEQ:FASTQC - [- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 - [- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN - [- ] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM - WARN: Access to undefined parameter skip_fastqc -- Initialise it to a default value eg. params.skip_fastqc = some_value ERROR ~ No such variable: outfile

-- Check script '/home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/ampliseq.nf' at line: 471 or see '.nextflow.log' file for more details

Relevant files

config/ampliseq.yaml

outdir: "results/ITS1_5F"
skip_cutadapt: true
sample_inference: "independent"
input: "data/samplesheet_its1_5f.tsv"
illumina_novaseq: true

data/samplesheet_its1_5f.tsv

I confirmed that both files exist

sampleID forwardReads reverseReads run m1 /lustre/BIF/nobackup/bakke333/Documents/projects/mursik/raw-data/result_X204SC23022204-Z01-F025/01.RawData/M1/M1_1.fastq.gz /lustre/BIF/nobackup/bakke333/Documents/projects/mursik/raw-data/result_X204SC23022204-Z01-F025/01.RawData/M1/M1_2.fastq.gz 1

.nextflow.log

Oct-16 14:19:13.857 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/ampliseq -r 2.7.1 -params-file config/ampliseq.yaml -profile singularity Oct-16 14:19:13.965 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.4 Oct-16 14:19:13.998 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/bakke333/.nextflow/plugins; core-plugins: nf-amazon@2.5.3,nf-azure@1.6.1,nf-cloudcache@0.4.1,nf-codecommit@0.2.1,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2-patch1,nf-tower@1.9.1,nf-wave@1.4.2-patch1 Oct-16 14:19:14.012 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Oct-16 14:19:14.013 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Oct-16 14:19:14.016 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Oct-16 14:19:14.031 [main] INFO org.pf4j.AbstractPluginManager - No plugins Oct-16 14:19:14.045 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/bakke333/.nextflow/scm Oct-16 14:19:14.079 [main] DEBUG nextflow.scm.AssetManager - Project manifest does not exist: /home/bakke333/.nextflow/assets/nf-core/ampliseq/nextflow.config (No such file or directory) Oct-16 14:19:14.086 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/bakke333/.nextflow/assets/nf-core/ampliseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/ampliseq.git Oct-16 14:19:14.129 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Oct-16 14:19:14.153 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/bakke333/.nextflow/assets/nf-core/ampliseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/ampliseq.git Oct-16 14:19:16.546 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/bakke333/.nextflow/secrets/store.json Oct-16 14:19:16.548 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@65c33b92] - activable => nextflow.secret.LocalSecretsProvider@65c33b92 Oct-16 14:19:16.615 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration Oct-16 14:19:16.616 [main] DEBUG nextflow.cli.CmdRun - Launching https://github.com/nf-core/ampliseq [admiring_celsius] DSL2 - revision: 113e90bdff [2.7.1] Oct-16 14:19:16.618 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Oct-16 14:19:16.618 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Oct-16 14:19:16.673 [main] DEBUG nextflow.Session - Session UUID: 2a89e6b4-9842-4769-babd-ee3205fe672b Oct-16 14:19:16.674 [main] DEBUG nextflow.Session - Run name: admiring_celsius Oct-16 14:19:16.674 [main] DEBUG nextflow.Session - Executor pool size: 96 Oct-16 14:19:16.682 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Oct-16 14:19:16.689 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=288; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Oct-16 14:19:16.777 [main] DEBUG nextflow.cli.CmdRun - Version: 24.04.4 build 5917 Created: 01-08-2024 07:05 UTC (09:05 CEST) System: Linux 5.15.0-88-generic Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.10+7 Encoding: UTF-8 (UTF-8) Process: 2325570@doudna.bioinformatics.nl [10.90.22.7] CPUs: 96 - Mem: 503.3 GB (185.2 GB) - Swap: 8 GB (7.9 GB) Oct-16 14:19:16.837 [main] DEBUG nextflow.Session - Work-dir: /lustre/BIF/nobackup/bakke333/Documents/projects/mursik/analysis/work [lustre] Oct-16 14:19:17.129 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Oct-16 14:19:17.144 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Oct-16 14:19:17.192 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Oct-16 14:19:17.201 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 97; maxThreads: 1000 Oct-16 14:19:17.300 [main] DEBUG nextflow.Session - Session start Oct-16 14:19:17.311 [main] DEBUG nextflow.Session - Using default localLib path: /home/bakke333/.nextflow/assets/nf-core/ampliseq/lib Oct-16 14:19:17.368 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/bakke333/.nextflow/assets/nf-core/ampliseq/lib Oct-16 14:19:17.372 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/bakke333/.nextflow/assets/nf-core/ampliseq/lib/nfcore_external_java_deps.jar Oct-16 14:19:19.897 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Oct-16 14:19:19.912 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: latest Oct-16 14:19:20.846 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.4' resolved Oct-16 14:19:20.847 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.4' Oct-16 14:19:20.997 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.4 Oct-16 14:19:21.000 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsHelp:paramsHelp]; plugin Id: nf-validation Oct-16 14:19:21.276 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter help -- Initialise it to a default value eg. params.help = some_value Oct-16 14:19:21.277 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter validate_params -- Initialise it to a default value eg. params.validate_params = some_value Oct-16 14:19:21.295 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter dada_ref_taxonomy -- Initialise it to a default value eg. params.dada_ref_taxonomy = some_value Oct-16 14:19:21.295 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter sintax_ref_taxonomy -- Initialise it to a default value eg. params.sintax_ref_taxonomy = some_value Oct-16 14:19:21.295 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter qiime_ref_taxonomy -- Initialise it to a default value eg. params.qiime_ref_taxonomy = some_value Oct-16 14:19:21.296 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter version -- Initialise it to a default value eg. params.version = some_value Oct-16 14:19:37.534 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap, fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation Oct-16 14:19:37.537 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter monochrome_logs -- Initialise it to a default value eg. params.monochrome_logs = some_value Oct-16 14:19:37.617 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value Oct-16 14:19:37.632 [main] INFO nextflow.Nextflow - 

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | | / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,' null -g113e90b

Core Nextflow options revision : 2.7.1 runName : admiring_celsius launchDir : /lustre/BIF/nobackup/bakke333/Documents/projects/mursik/analysis workDir : /lustre/BIF/nobackup/bakke333/Documents/projects/mursik/analysis/work projectDir : /home/bakke333/.nextflow/assets/nf-core/ampliseq userName : bakke333 profile : singularity configFiles :

Main arguments input : data/samplesheet_its1_5f.tsv outdir : results/ITS1_5F

Sequencing input illumina_novaseq: true

Skipping specific steps skip_cutadapt : true

!! Only displaying parameters that differ from the pipeline defaults !!

If you use null for your analysis please cite:

Oct-16 14:19:37.650 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter input_fasta -- Initialise it to a default value eg. params.input_fasta = some_value Oct-16 14:19:37.651 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter FW_primer -- Initialise it to a default value eg. params.FW_primer = some_value Oct-16 14:19:37.652 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter pacbio -- Initialise it to a default value eg. params.pacbio = some_value Oct-16 14:19:37.653 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter iontorrent -- Initialise it to a default value eg. params.iontorrent = some_value Oct-16 14:19:37.654 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter single_end -- Initialise it to a default value eg. params.single_end = some_value Oct-16 14:19:37.654 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter trunclenf -- Initialise it to a default value eg. params.trunclenf = some_value Oct-16 14:19:37.655 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter trunclenr -- Initialise it to a default value eg. params.trunclenr = some_value Oct-16 14:19:37.657 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter double_primer -- Initialise it to a default value eg. params.double_primer = some_value Oct-16 14:19:37.657 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter min_len_asv -- Initialise it to a default value eg. params.min_len_asv = some_value Oct-16 14:19:37.658 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter skip_dada_quality -- Initialise it to a default value eg. params.skip_dada_quality = some_value Oct-16 14:19:37.658 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter tax_agglom_min -- Initialise it to a default value eg. params.tax_agglom_min = some_value Oct-16 14:19:37.659 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter tax_agglom_max -- Initialise it to a default value eg. params.tax_agglom_max = some_value Oct-16 14:19:37.659 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter dada_ref_tax_custom -- Initialise it to a default value eg. params.dada_ref_tax_custom = some_value Oct-16 14:19:37.660 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter dada_ref_tax_custom_sp -- Initialise it to a default value eg. params.dada_ref_tax_custom_sp = some_value Oct-16 14:19:37.661 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter pplace_tree -- Initialise it to a default value eg. params.pplace_tree = some_value Oct-16 14:19:37.661 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter dada_assign_taxlevels -- Initialise it to a default value eg. params.dada_assign_taxlevels = some_value Oct-16 14:19:37.662 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter skip_taxonomy -- Initialise it to a default value eg. params.skip_taxonomy = some_value Oct-16 14:19:37.662 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter skip_dada_taxonomy -- Initialise it to a default value eg. params.skip_dada_taxonomy = some_value Oct-16 14:19:37.663 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter cut_dada_ref_taxonomy -- Initialise it to a default value eg. params.cut_dada_ref_taxonomy = some_value Oct-16 14:19:37.663 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter kraken2_ref_tax_custom -- Initialise it to a default value eg. params.kraken2_ref_tax_custom = some_value Oct-16 14:19:37.664 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter filter_ssu -- Initialise it to a default value eg. params.filter_ssu = some_value Oct-16 14:19:37.664 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter sbdiexport -- Initialise it to a default value eg. params.sbdiexport = some_value Oct-16 14:19:37.664 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter addsh -- Initialise it to a default value eg. params.addsh = some_value Oct-16 14:19:37.665 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter orf_end -- Initialise it to a default value eg. params.orf_end = some_value Oct-16 14:19:37.697 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter multiqc_config -- Initialise it to a default value eg. params.multiqc_config = some_value Oct-16 14:19:37.702 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter multiqc_logo -- Initialise it to a default value eg. params.multiqc_logo = some_value Oct-16 14:19:37.702 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter multiqc_methods_description -- Initialise it to a default value eg. params.multiqc_methods_description = some_value Oct-16 14:19:37.714 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter metadata -- Initialise it to a default value eg. params.metadata = some_value Oct-16 14:19:37.715 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter classifier -- Initialise it to a default value eg. params.classifier = some_value Oct-16 14:19:37.718 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter kraken2_ref_taxonomy -- Initialise it to a default value eg. params.kraken2_ref_taxonomy = some_value Oct-16 14:19:37.719 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter report_template -- Initialise it to a default value eg. params.report_template = some_value Oct-16 14:19:37.720 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter report_css -- Initialise it to a default value eg. params.report_css = some_value Oct-16 14:19:37.721 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter report_logo -- Initialise it to a default value eg. params.report_logo = some_value Oct-16 14:19:37.722 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter report_abstract -- Initialise it to a default value eg. params.report_abstract = some_value Oct-16 14:19:37.723 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter illumina_pe_its -- Initialise it to a default value eg. params.illumina_pe_its = some_value Oct-16 14:19:37.725 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter trunc_qmin -- Initialise it to a default value eg. params.trunc_qmin = some_value Oct-16 14:19:37.725 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter trunc_rmin -- Initialise it to a default value eg. params.trunc_rmin = some_value Oct-16 14:19:37.725 [main] WARN nextflow.Nextflow - No DADA2 cutoffs were specified (--trunclenf & --trunclenr), therefore reads will be truncated where median quality drops below null (defined by --trunc_qmin) but at least a fraction of null (defined by --trunc_rmin) of the reads will be retained. The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.

Oct-16 14:19:37.726 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter kraken2_assign_taxlevels -- Initialise it to a default value eg. params.kraken2_assign_taxlevels = some_value Oct-16 14:19:37.730 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter skip_qiime -- Initialise it to a default value eg. params.skip_qiime = some_value Oct-16 14:21:08.774 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter validationSkipDuplicateCheck -- Initialise it to a default value eg. params.validationSkipDuplicateCheck = some_value Oct-16 14:21:08.786 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'data/samplesheet_its1_5f.tsv' with '/home/bakke333/.nextflow/assets/nf-core/ampliseq/assets/schema_input.json' Oct-16 14:21:08.932 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter validationS3PathCheck -- Initialise it to a default value eg. params.validationS3PathCheck = some_value Oct-16 14:21:09.801 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'data/samplesheet_its1_5f.tsv' with '/home/bakke333/.nextflow/assets/nf-core/ampliseq/assets/schema_input.json' Oct-16 14:21:10.023 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.023 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.028 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Oct-16 14:21:10.033 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=96; memory=503.3 GB; capacity=96; pollInterval=100ms; dumpInterval=5m Oct-16 14:21:10.035 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Oct-16 14:21:10.091 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter skip_fastqc -- Initialise it to a default value eg. params.skip_fastqc = some_value Oct-16 14:21:10.097 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.097 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.124 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.124 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.137 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.137 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.169 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.169 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.207 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.207 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.242 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.242 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.255 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.256 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.282 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.282 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.298 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.298 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.314 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.314 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.328 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.328 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.333 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter vsearch_cluster -- Initialise it to a default value eg. params.vsearch_cluster = some_value Oct-16 14:21:10.437 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter skip_barrnap -- Initialise it to a default value eg. params.skip_barrnap = some_value Oct-16 14:21:10.447 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.447 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.456 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-16 14:21:10.457 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-16 14:21:10.465 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter max_len_asv -- Initialise it to a default value eg. params.max_len_asv = some_value Oct-16 14:21:10.465 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter filter_codons -- Initialise it to a default value eg. params.filter_codons = some_value Oct-16 14:21:10.465 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter cut_its -- Initialise it to a default value eg. params.cut_its = some_value Oct-16 14:21:10.469 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_c3294b34a2f7ac7e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/nf-core/vsearch/sintax/main.nf Script_400265f1f06bb13b: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/filter_clusters.nf Script_32685eb5242f257f: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/hmmer/hmmbuild/main.nf Script_d6a860896b1130af: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_diversity_betaord.nf Script_b32bf3cb38b5442b: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/summary_report.nf Script_e823e4eb2f5b147d: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/phyloseq_inasv.nf Script_a905a6ee23f4721e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/sbdiexport.nf Script_01b711320c66b785: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/sintax_taxonomy_wf.nf Script_703e9ffb29f90163: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/merge_stats.nf Script_b479605552f338c7: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/metadata_pairwise.nf Script_d1832e11b9029ac2: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/format_taxresults_sintax.nf Script_fd346d4733ba514c: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_featuretable_group.nf Script_cbc7460cd104f644: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/dada2_stats.nf Script_417c08a3efda3115: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_tree.nf Script_84779c0760c63586: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/filter_ssu.nf Script_5a7a67a92ad637b6: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/filter_stats.nf Script_9cdd81671bb883c1: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/cutadapt_summary_merge.nf Script_8a63379aa5b62352: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_classify.nf Script_7c6e32bf61d6e6b5: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/phyloseq_workflow.nf Script_5b2bde79f9128ec2: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/dada2_filtntrim.nf Script_62a38cb1cb9ccd74: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_export_absolute.nf Script_1b31bc7102b58240: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/filter_len_asv.nf Script_731c0f86bc8b6167: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/qiime2_barplotavg.nf Script_d5212239962deb88: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/format_taxonomy.nf Script_2f5099b0637a136f: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/hmmer/eslreformat/main.nf Script_e910ede3611aba72: /home/bakke333/.nextflow/assets/nf-core/ampliseq/main.nf Script_6cef970678748707: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/nf-core/vsearch/usearchglobal/main.nf Script_b564cbbf0598379e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/kraken2_taxonomy_wf.nf Script_eb9d0450a65129bd: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/nf-core/multiqc/main.nf Script_9810fb02b6bdfc6e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/epang/split/main.nf Script_34c88151768aebf0: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/dada2_err.nf Script_b68acfcd6baa18f7: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/qiime2_ancom.nf Script_5907ea1d27d70511: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_train.nf Script_81ccecb09b477085: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/nf-core/vsearch/cluster/main.nf Script_80c31cb1ff3bd881: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/combine_table.nf Script_31fd35dd6d89b098: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/novaseq_err.nf Script_d2c3aa9d408cd884: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/dada2_merge.nf Script_bf2da8225c4393f0: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/qiime2_taxonomy.nf Script_c83a536e5ec8de8d: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/assignsh.nf Script_2e17524c73600c60: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/metadata_all.nf Script_f5fca7dd0b32f992: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/barrnapsummary.nf Script_042518d1a5640704: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/rename_raw_data_files.nf Script_77090ceba634ea38: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/itsx_cutasv.nf Script_f1759350f3c06308: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/dada2_rmchimera.nf Script_6b85f5cc795f2b67: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/format_taxonomy_qiime.nf Script_de809e122889e39c: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_diversity_beta.nf Script_5f77d66bd35f559e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/dada2_addspecies.nf Script_09147e8eac3f06f9: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/nf-core/custom/dumpsoftwareversions/main.nf Script_de05469192f3f9c9: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/hmmer/hmmalign/main.nf Script_283337d83f5fb1ed: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/nf-core/kraken2/kraken2/main.nf Script_e1b5ef1bfd1317aa: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_diversity_alpha.nf Script_ecde45584081a12d: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/format_taxresults.nf Script_33cce904e823a970: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/parse_input.nf Script_1255045e448f2fbb: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/sbdiexportreannotate.nf Script_0eb3912402269429: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/format_fastainput.nf Script_e331621de682cf28: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/format_taxonomy_sintax.nf Script_8cbc9496fa7aa09e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/qiime2_preptax.nf Script_77977f62e8918a77: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/qiime2_intree.nf Script_893ba4a8cb5dd8d4: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/nf-core/untar/main.nf Script_fca9e2502549eb7e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/gappa/examinegraft/main.nf Script_4b9aabd37da23602: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/format_pplacetax.nf Script_1e9963d02d3e2abf: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/cutadapt_workflow.nf Script_be9a2ca8b607ed75: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/ampliseq.nf Script_dfc9986abf5c42c1: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_export_reltax.nf Script_89c5323769e82834: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/qiime2_filtertaxa.nf Script_d0137300da460cf1: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/dada2_taxonomy.nf Script_656bb79ae7dc5dd0: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_ancom_asv.nf Script_bfcc8d85b9b6fafd: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_alphararefaction.nf Script_3c1d4f49752899c0: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/phyloseq_intax.nf Script_cc3922f216d60538: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/filter_codons.nf Script_daf15d4dcf58301b: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/qiime2_intax.nf Script_30bad2d84b84bd98: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/dada2_taxonomy_wf.nf Script_5c6b7a4674b37e42: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_export_relasv.nf Script_7b7bad1cdf4f918a: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/nf-core/cutadapt/main.nf Script_edeb91dba9a29767: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/phyloseq.nf Script_749a41f83d8c7921: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_barplot.nf Script_b4f46c577a80128e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/barrnap.nf Script_8b90fea6f8226527: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_diversity_adonis.nf Script_991aa06870337525: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/picrust.nf Script_2fcf1c087396bee7: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/qiime2_export.nf Script_11d1d725eceddc4e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/qiime2_inseq.nf Script_bbfc43bf273ae640: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/local/dada2_denoising.nf Script_810c50b2736f1a5b: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../modules/nf-core/fastqc/main.nf Script_afb137a2b7f62538: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/hmmer/eslalimask/main.nf Script_303b0afddbbee6ae: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_extract.nf Script_ae6f6ce09b0e041e: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/dada2_quality.nf Script_2c346cb9627f3770: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/dada2_preprocessing.nf Script_5e7003a9b5f06c92: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_diversity_core.nf Script_10b347658d044afc: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/cutadapt_summary.nf Script_e67541561a418848: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/trunclen.nf Script_3f1cc491c25fbe1b: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/format_taxresults_kraken2.nf Script_688c3abfe6f890e5: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/gappa/examineassign/main.nf Script_8fe478f54e9c597b: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/main.nf Script_87ec82fd16bc4741: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_filtersamples.nf Script_22a37cceed1dfd43: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/gappa/examineheattree/main.nf Script_9dd71d0404207e5f: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/qiime2_diversity.nf Script_30e1dcc7772952ae: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/epang/place/main.nf Script_d7cb9987ee8d27bd: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_ancom_tax.nf Script_3b4bf68fd22a9eaf: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/local/../../modules/local/qiime2_inasv.nf Script_b7acbd417602eae4: /home/bakke333/.nextflow/assets/nf-core/ampliseq/./workflows/../subworkflows/nf-core/fasta_newick_epang_gappa/../../../modules/nf-core/mafft/main.nf Oct-16 14:21:10.470 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: outfile for class: nextflow.script.WorkflowBinding Oct-16 14:21:10.493 [main] DEBUG nextflow.Session - The following nodes are still active: [operator] map [operator] branch [operator] map [operator] collect [operator] subscribe [operator] mix [operator] mix [operator] map [operator] collect [operator] map [operator] map [operator] collect [operator] map [operator] mix [operator] mix [operator] subscribe [operator] toSortedList [operator] mix [operator] subscribe [operator] combine [operator] mix [operator] branch [operator] map [operator] collect [operator] subscribe [operator] map [operator] map [operator] map [operator] map [operator] collect [operator] map [operator] map [operator] collect [operator] map [operator] mix [operator] subscribe [operator] map [operator] groupTuple [operator] map [operator] map [operator] groupTuple [operator] map [operator] collect [operator] collect [operator] mix [operator] join [operator] mix [operator] join [operator] join [operator] join [operator] map [operator] collect [operator] map [operator] collect [operator] collect [operator] subscribe [operator] ifEmpty [operator] mix

Oct-16 14:21:10.497 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Oct-16 14:21:10.504 [main] ERROR nextflow.cli.Launcher - @unknown groovy.lang.MissingPropertyException: No such property: outfile for class: nextflow.script.WorkflowBinding at groovy.lang.Binding.getVariable(Binding.java:61) at nextflow.script.WorkflowBinding.getVariable(WorkflowBinding.groovy:141) at groovy.lang.Binding.getProperty(Binding.java:117) at nextflow.script.WorkflowBinding.getProperty(WorkflowBinding.groovy:130) at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:167) at groovy.lang.Closure.getPropertyTryThese(Closure.java:325) at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:315) at groovy.lang.Closure.getProperty(Closure.java:301) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_be9a2ca8b607ed75$_runScript_closure5$_closure7.doCall(Script_be9a2ca8b607ed75:471) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at groovy.lang.Closure.call(Closure.java:433) at groovy.lang.Closure.call(Closure.java:412) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:103) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:651) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:391) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:330) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_e910ede3611aba72$_runScript_closure1$_closure3.doCall(Script_e910ede3611aba72:50) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at groovy.lang.Closure.call(Closure.java:433) at groovy.lang.Closure.call(Closure.java:412) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:103) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:651) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:391) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:330) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_e910ede3611aba72$_runScript_closure2$_closure4.doCall(Script_e910ede3611aba72:64) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at groovy.lang.Closure.call(Closure.java:433) at groovy.lang.Closure.call(Closure.java:412) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.script.BaseScript.run0(BaseScript.groovy:198) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.script.BaseScript.run(BaseScript.groovy:209) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) at nextflow.cli.CmdRun.run(CmdRun.groovy:372) at nextflow.cli.Launcher.run(Launcher.groovy:503) at nextflow.cli.Launcher.main(Launcher.groovy:657)

System information

Pipeline version

2.7.1

Nextflow version

  N E X T F L O W
  version 24.04.4 build 5917
  created 01-08-2024 07:05 UTC (09:05 CEST)
  cite doi:10.1038/nbt.3820
  http://nextflow.io

Container

singularity

Executor

Local

Hardware

Linux server

Operating system

cat /etc/os-release NAME="Ubuntu" VERSION="20.04.6 LTS (Focal Fossa)" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 20.04.6 LTS" VERSION_ID="20.04" HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" VERSION_CODENAME=focal UBUNTU_CODENAME=focal

d4straub commented 1 month ago

Hi here, can you confirm that the folder "results" exists in your directory?

Luke-ebbis commented 1 month ago

Hey @d4straub , results/ITS1_5F/ exist and is empty

d4straub commented 1 month ago

Could you use the most up to date version, i.e. 2.11.0?

Luke-ebbis commented 1 month ago

Hey @d4straub that seemed to do it!

~ $ nextflow run nf-core/ampliseq -r 2.11.0 -params-file config/ampliseq.yaml -profile singularity

Now it seems to behave better. Can I suggest a change in the documentation to change this to the latest version?

Image

or at least make it clear that the differences between pipeline versions have different CLI inputs?

d4straub commented 1 month ago

There is no difference in cli inputs. I assume that was a combination of nextflow version and pipeline version. I assumed the "please use the most recent release" will do it, but was wrong in that case, I try to keep in mind to keep that snippet updated ;)