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nf-core / circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
https://nf-co.re/circrna
MIT License
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pipeline won't start without filling ref-genome bwa, bowtie, etc... #47

Closed luciazifcakova closed 10 months ago

luciazifcakova commented 2 years ago

Check Documentation

I have checked the following places for your error:

Description of the bug

Pipeline won't start running. I have filled in information to launch the pipeline online but is seems that it won't start without paths to bwa, bowie, bowtie2...

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line: nextflow run nf-core/circrna -r dev -name circRNA_sles -work-dir ./circRNA_sles -resume -params-file nf-params.json
  2. See error: WARN: Access to undefined parameter name -- Initialise it to a default value eg. params.name = some_value WARN: Access to undefined parameter bowtie -- Initialise it to a default value eg. params.bowtie = some_value WARN: Access to undefined parameter bowtie2 -- Initialise it to a default value eg. params.bowtie2 = some_value WARN: Access to undefined parameter bwa -- Initialise it to a default value eg. params.bwa = some_value WARN: Access to undefined parameter hisat -- Initialise it to a default value eg. params.hisat = some_value WARN: Access to undefined parameter star -- Initialise it to a default value eg. params.star = some_value WARN: Access to undefined parameter segemehl -- Initialise it to a default value eg. params.segemehl = some_value [- ] process > SOFTWARE_VERSIONS - [- ] process > BWA_INDEX - [- ] process > SAMTOOLS_INDEX - [- ] process > HISAT2_INDEX - [- ] process > STAR_INDEX - [- ] process > BOWTIE_INDEX - [- ] process > BOWTIE2_INDEX - WARN: Access to undefined parameter circexplorer2_annotation -- Initialise it to a default value eg. params.circexplorer2_annotation = some_value WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /flash/MillerU/circRNA_sles2/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location Pulling Singularity image docker://barryd237/circrna:dev [cache /flash/MillerU/circRNA_sles2/singularity/barryd237-circrna-dev.img] WARN: There's no process matching config selector: get_software_versions -[nf-core/circrna] Pipeline completed with errors-

    Expected behaviour

Start to run pipeline with my genome. I have inputed soft repeat masked multisequnce fasta file. I have inputed gff3 file, which was renamed to gtf file and inputted to pipeline. Only issue, why pipeline is not working I can think of is the gif file. But on the other hand, I have tested the pipeline with iGenome and it was not running with similar warning anyway...

Log files

Have you provided the following extra information/files: The command used to run the pipeline:

!/bin/bash

SBATCH --job-name=nf-core-circ

SBATCH --partition=compute

SBATCH --time=3-0

SBATCH --mem=120G

SBATCH --cpus-per-task=20

SBATCH --mail-user=lucia.zifcakova@oist.jp

SBATCH --mail-type=BEGIN,FAIL,END

SBATCH --output=/flash/MillerU/nf-core-circ.out

ml bioinfo-ugrp-modules ml DebianMed ml singularity ml Nextflow

nextflow run nf-core/circrna -r dev -name circRNA_sles2 -work-dir ./circRNA_sles2 -resume -params-file nf-params.json

The .nextflow.log file Apr-05 15:21:54.801 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/circrna -r dev -name circRNA_sles2 -work-dir ./circRNA_sles2 -resume -params-file nf-params.json Apr-05 15:21:55.044 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.10.6 Apr-05 15:21:56.349 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/circrna.git Apr-05 15:21:56.361 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/circrna.git Apr-05 15:21:56.739 [main] INFO nextflow.cli.CmdRun - Launching nf-core/circrna [circRNA_sles2] - revision: 5e17f6cbbc [dev] Apr-05 15:21:57.488 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/nextflow.config Apr-05 15:21:57.488 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /flash/MillerU/nextflow.config Apr-05 15:21:57.489 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/nextflow.config Apr-05 15:21:57.489 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /flash/MillerU/nextflow.config Apr-05 15:21:57.514 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard Apr-05 15:21:57.971 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager Apr-05 15:21:57.985 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Apr-05 15:21:57.987 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Apr-05 15:21:57.990 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Apr-05 15:21:58.095 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager Apr-05 15:21:58.705 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard Apr-05 15:21:58.792 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/l/lucia-zifcakova/.nextflow/plugins Apr-05 15:21:58.794 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Apr-05 15:21:58.799 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Apr-05 15:21:58.800 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Apr-05 15:21:58.802 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Apr-05 15:21:58.815 [main] INFO org.pf4j.AbstractPluginManager - No plugins Apr-05 15:21:58.882 [main] DEBUG nextflow.Session - Session uuid: 0eb81af5-8ec3-475b-848a-68da4f2d4258 Apr-05 15:21:58.882 [main] DEBUG nextflow.Session - Run name: circRNA_sles2 Apr-05 15:21:58.883 [main] DEBUG nextflow.Session - Executor pool size: 20 Apr-05 15:21:58.908 [main] DEBUG nextflow.cli.CmdRun - Version: 21.10.6 build 5661 Created: 21-12-2021 17:01 UTC (22-12-2021 02:01 JDT) System: Linux 4.18.0-348.2.1.el8_5.x86_64 Runtime: Groovy 3.0.9 on OpenJDK 64-Bit Server VM 1.8.0_312-b07 Encoding: UTF-8 (ANSI_X3.4-1968) Process: 3854499@deigo011109.oist.jp [10.145.2.81] CPUs: 20 - Mem: 120 GB (119.2 GB) - Swap: 8 GB (7.4 GB) Apr-05 15:21:58.998 [main] DEBUG nextflow.Session - Work-dir: /flash/MillerU/circRNA_sles2 [lustre] Apr-05 15:21:59.090 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, AwsBatchExecutor, IgExecutor] Apr-05 15:21:59.107 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Apr-05 15:21:59.133 [main] DEBUG nextflow.Session - Observer factory: TowerFactory Apr-05 15:21:59.261 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 21; maxThreads: 1000 Apr-05 15:21:59.379 [main] DEBUG nextflow.Session - Session start invoked Apr-05 15:21:59.386 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /flash/MillerU/results_circRNA_sles2/pipeline_info/execution_trace_2022-04-05_15-21-58.txt Apr-05 15:21:59.405 [main] DEBUG nextflow.Session - Using default localLib path: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/lib Apr-05 15:21:59.411 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/lib Apr-05 15:21:59.412 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/lib/nfcore_external_java_deps.jar Apr-05 15:22:02.515 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Apr-05 15:22:02.532 [main] INFO nextflow.Nextflow -

------------------------------------------------------ ,--./,-.  _ _ /,-..--~'  |\ | | / ` / \ |) | } {  | | | _, __/ | \ |__ `-.,--, .,.,'  nf-core/circrna v1.0.0 ------------------------------------------------------

Apr-05 15:22:02.682 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter genomes -- Initialise it to a default value eg. params.genomes = some_value Apr-05 15:22:02.749 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 21; maxThreads: 1000 Apr-05 15:22:02.771 [Actor Thread 2] ERROR nextflow.extension.DataflowHelper - @unknown java.nio.charset.MalformedInputException: Input length = 1 at java.nio.charset.CoderResult.throwException(CoderResult.java:281) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:339) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at nextflow.splitter.CsvSplitter.parseHeader(CsvSplitter.groovy:136) at nextflow.splitter.CsvSplitter.process(CsvSplitter.groovy:124) at nextflow.splitter.CsvSplitter.process(CsvSplitter.groovy) at nextflow.splitter.AbstractSplitter.apply(AbstractSplitter.groovy:155) at nextflow.extension.SplitOp$_applySplittingOperator_closure1.doCall(SplitOp.groovy:190) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139) at nextflow.extension.DataflowHelper$_subscribeImpl_closure2.doCall(DataflowHelper.groovy:285) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108) at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43) at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293) at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30) at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93) at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Apr-05 15:22:02.787 [Actor Thread 2] DEBUG nextflow.Session - Session aborted -- Cause: Input length = 1 Apr-05 15:22:02.795 [main] INFO nextflow.Nextflow - Core Nextflow options revision : dev runName : circRNA_sles2 containerEngine : singularity container : barryd237/circrna:dev launchDir : /flash/MillerU workDir : /flash/MillerU/circRNA_sles2 projectDir : /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna userName : lucia-zifcakova profile : standard configFiles : /home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/nextflow.config, /flash/MillerU/nextflow.config

Input/output options input : /bucket/MillerU/Zifcakova/circ_rna_samples.csv input_type : fastq outdir : ./results_circRNA_sles2

Pipeline Options tool : ciriquant,circexplorer2,find_circ,circrna_finder,mapsplice,dcc,segemehl module : circrna_discovery,mirna_prediction

Reference genome files fasta : /bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/PO1788_Sepioteuthis_lessoniana_RepeatMasked.fasta gtf : /bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/PO1788_Sepioteuthis_lessoniana_RepeatMasked.gtf mature : /bucket/MillerU/Zifcakova/databases/mature.fa species : Sepiotheusis lessoniana fasta_fai : /bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/PO1788_Sepioteuthis_lessoniana_RepeatMasked.fasta.fai igenomes_ignore : true

Read trimming & adapter removal adapters : 

STAR chimScoreSeparation : 10

Generic options max_multiqc_email_size : 25 MB

Max job request options max_cpus : 20 max_memory : 500 GB max_time : 3d 18h

Institutional config options config_profile_description: The Okinawa Institute of Science and Technology Graduate University (OIST) HPC cluster profile provided by nf-core/configs. config_profile_contact : OISTs Bioinformatics User Group BioinfoUgrp@oist.jp config_profile_url : https://github.com/nf-core/configs/blob/master/docs/oist.md

------------------------------------------------------ Only displaying parameters that differ from defaults. ------------------------------------------------------ Apr-05 15:22:02.796 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter name -- Initialise it to a default value eg. params.name = some_value Apr-05 15:22:02.797 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter bowtie -- Initialise it to a default value eg. params.bowtie = some_value Apr-05 15:22:02.797 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter bowtie2 -- Initialise it to a default value eg. params.bowtie2 = some_value Apr-05 15:22:02.797 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter bwa -- Initialise it to a default value eg. params.bwa = some_value Apr-05 15:22:02.798 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter hisat -- Initialise it to a default value eg. params.hisat = some_value Apr-05 15:22:02.798 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter star -- Initialise it to a default value eg. params.star = some_value Apr-05 15:22:02.798 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter segemehl -- Initialise it to a default value eg. params.segemehl = some_value Apr-05 15:22:02.818 [Actor Thread 2] DEBUG nextflow.Session - The following nodes are still active: [operator] splitCsv [operator] map [operator] into

Apr-05 15:22:02.865 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:02.865 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:02.872 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Apr-05 15:22:02.876 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Apr-05 15:22:02.880 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Apr-05 15:22:02.949 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:02.949 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:02.957 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name SAMTOOLS_INDEX Apr-05 15:22:02.958 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:02.958 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:02.969 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name HISAT2_INDEX Apr-05 15:22:02.969 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:02.969 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:02.978 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name STAR_INDEX Apr-05 15:22:02.979 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:02.979 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:02.987 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name BOWTIE_INDEX Apr-05 15:22:02.987 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:02.987 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:02.997 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name BOWTIE2_INDEX Apr-05 15:22:02.998 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:02.999 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.010 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name SEGEMEHL_INDEX Apr-05 15:22:03.011 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.011 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.018 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.018 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.059 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.060 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.069 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.070 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.072 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter circexplorer2_annotation -- Initialise it to a default value eg. params.circexplorer2_annotation = some_value Apr-05 15:22:03.076 [Actor Thread 4] DEBUG n.splitter.AbstractTextSplitter - Splitter Fasta collector path: nextflow.splitter.TextFileCollector$CachePath(/flash/MillerU/circRNA_sles2/46/c92957289d11a17261b909334d3350/PO1788_Sepioteuthis_lessoniana_RepeatMasked.fasta, null) Apr-05 15:22:03.089 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name BAM_TO_FASTQ Apr-05 15:22:03.093 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.093 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.102 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low,py3 for process with name FASTQC_RAW Apr-05 15:22:03.103 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:py3 matches labels process_low,py3 for process with name FASTQC_RAW Apr-05 15:22:03.103 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.103 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.108 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name BBDUK Apr-05 15:22:03.109 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.109 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.111 [Actor Thread 38] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /flash/MillerU/circRNA_sles2/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location Apr-05 15:22:03.112 [Actor Thread 38] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://barryd237/circrna:dev [cache /flash/MillerU/circRNA_sles2/singularity/barryd237-circrna-dev.img] Apr-05 15:22:03.118 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low,py3 for process with name FASTQC_BBDUK Apr-05 15:22:03.119 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:py3 matches labels process_low,py3 for process with name FASTQC_BBDUK Apr-05 15:22:03.119 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.119 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.129 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name CIRIQUANT Apr-05 15:22:03.131 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.131 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.145 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name STAR_1PASS Apr-05 15:22:03.146 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.146 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.153 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.153 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.171 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name STAR_2PASS Apr-05 15:22:03.172 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.172 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.182 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name CIRCEXPLORER2 Apr-05 15:22:03.183 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.183 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.192 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name CIRCRNA_FINDER Apr-05 15:22:03.192 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.192 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.199 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name DCC_MATE1 Apr-05 15:22:03.200 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.201 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.207 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name DCC_MATE2 Apr-05 15:22:03.207 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.207 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.226 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels py3,process_medium for process with name DCC Apr-05 15:22:03.226 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:py3 matches labels py3,process_medium for process with name DCC Apr-05 15:22:03.227 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.227 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.235 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name FIND_ANCHORS Apr-05 15:22:03.235 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.235 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.244 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name FIND_CIRC Apr-05 15:22:03.245 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.245 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.251 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name MAPSPLICE_ALIGN Apr-05 15:22:03.252 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.252 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.261 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name MAPSPLICE_PARSE Apr-05 15:22:03.261 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.261 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.300 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name SEGEMEHL_ALIGN Apr-05 15:22:03.301 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.301 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.313 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name ANNOTATION Apr-05 15:22:03.314 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.314 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.318 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name FASTA Apr-05 15:22:03.319 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.319 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.329 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.330 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.334 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.334 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.337 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.337 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.349 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name MIRNA_PREDICTION Apr-05 15:22:03.350 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.350 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.355 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name MIRNA_TARGETS Apr-05 15:22:03.356 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.356 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.361 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name HISAT_ALIGN Apr-05 15:22:03.361 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.361 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.366 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name STRINGTIE Apr-05 15:22:03.366 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.367 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.372 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name DEA Apr-05 15:22:03.373 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.373 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.408 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels py3,process_low for process with name MULTIQC Apr-05 15:22:03.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:py3 matches labels py3,process_low for process with name MULTIQC Apr-05 15:22:03.409 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-05 15:22:03.409 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-05 15:22:03.416 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: BOWTIE2_INDEX, MULTIQC, COUNT_MATRIX_SINGLE, SJDB_FILE, MAPSPLICE_PARSE, FASTQC_BBDUK, TARGETSCAN_DATABASE, ANNOTATION, FILTER_GTF, BWA_INDEX, BBDUK, FASTA, HISAT2_INDEX, GENE_ANNOTATION, SEGEMEHL_ALIGN, FASTQC_RAW, SEGEMEHL_INDEX, DEA, COUNT_MATRIX_COMBINED, DCC_MATE2, MIRNA_PREDICTION, DCC, STAR_2PASS, DCC_MATE1, BOWTIE_INDEX, CIRIQUANT, FIND_CIRC, MAPSPLICE_ALIGN, STRINGTIE, STAR_INDEX, FIND_ANCHORS, MIRNA_TARGETS, CIRIQUANT_YML, CIRCEXPLORER2, CIRCRNA_FINDER, HISAT_ALIGN, STAR_1PASS, SOFTWARE_VERSIONS, MERGE_TOOLS, BAM_TO_FASTQ, SAMTOOLS_INDEX Apr-05 15:22:03.429 [main] WARN nextflow.Session - There's no process matching config selector: get_software_versions Apr-05 15:22:03.431 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Apr-05 15:22:03.431 [main] DEBUG nextflow.Session - Session await Apr-05 15:22:03.431 [main] DEBUG nextflow.Session - Session await > all process finished Apr-05 15:22:03.431 [main] DEBUG nextflow.Session - Session await > all barriers passed Apr-05 15:22:03.534 [Actor Thread 45] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.021 s; total time: 0.022 s Apr-05 15:22:03.535 [Actor Thread 45] DEBUG nextflow.file.FileCollector - >> temp file exists? false Apr-05 15:22:03.536 [Actor Thread 45] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /scratch/b0fa46d8336bb20794c7a1e468467e4d.collect-file Apr-05 15:22:03.543 [Actor Thread 45] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /scratch/b0fa46d8336bb20794c7a1e468467e4d.collect-file Apr-05 15:22:03.554 [Actor Thread 45] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/nxf-4044264932371346223 Apr-05 15:22:03.632 [main] INFO nextflow.Nextflow - -[nf-core/circrna] Pipeline completed with errors- Apr-05 15:22:03.638 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] Apr-05 15:22:03.639 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Apr-05 15:22:03.642 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Apr-05 15:22:03.643 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [] Apr-05 15:22:05.392 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline Apr-05 15:22:05.583 [main] DEBUG nextflow.CacheDB - Closing CacheDB done Apr-05 15:22:05.636 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System

Nextflow Installation

Container engine

Additional context

xnr13 commented 2 years ago

same here, the images pulled by circrna do not provide those tools?

My run fails at the very beginning with missing fastqc, but the rest is also not there, nor in barryd237/circrna:dev.

nictru commented 10 months ago

Hey, I think these problems should be fixed by now - if not, feel free to reopen this issue