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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:
- Command line: nextflow run nf-core/circrna -r dev -name circRNA_sles -work-dir ./circRNA_sles -resume -params-file nf-params.json
- 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=[email protected]
#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: 5e17f6c [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: [email protected] [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 -
-�[2m----------------------------------------------------�[0m-
�[0;32m,--.�[0;30m/�[0;32m,-.�[0m
�[0;34m ___ __ __ __ ___ �[0;32m/,-..--~'�[0m
�[0;34m |\ | |__ __ / / \ |__) |__ �[0;33m} {�[0m �[0;34m | \| | \__, \__/ | \ |___ �[0;32m\
-.,--,�[0m �[0;32m
.,.,'�[0m
�[0;35m nf-core/circrna v1.0.0�[0m
-�[2m----------------------------------------------------�[0m-
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 - �[1mCore Nextflow options�[0m
�[0;34mrevision : �[0;32mdev�[0m
�[0;34mrunName : �[0;32mcircRNA_sles2�[0m
�[0;34mcontainerEngine : �[0;32msingularity�[0m
�[0;34mcontainer : �[0;32mbarryd237/circrna:dev�[0m
�[0;34mlaunchDir : �[0;32m/flash/MillerU�[0m
�[0;34mworkDir : �[0;32m/flash/MillerU/circRNA_sles2�[0m
�[0;34mprojectDir : �[0;32m/home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna�[0m
�[0;34muserName : �[0;32mlucia-zifcakova�[0m
�[0;34mprofile : �[0;32mstandard�[0m
�[0;34mconfigFiles : �[0;32m/home/l/lucia-zifcakova/.nextflow/assets/nf-core/circrna/nextflow.config, /flash/MillerU/nextflow.config�[0m
�[1mInput/output options�[0m
�[0;34minput : �[0;32m/bucket/MillerU/Zifcakova/circ_rna_samples.csv�[0m
�[0;34minput_type : �[0;32mfastq�[0m
�[0;34moutdir : �[0;32m./results_circRNA_sles2�[0m
�[1mPipeline Options�[0m
�[0;34mtool : �[0;32mciriquant,circexplorer2,find_circ,circrna_finder,mapsplice,dcc,segemehl�[0m
�[0;34mmodule : �[0;32mcircrna_discovery,mirna_prediction�[0m
�[1mReference genome files�[0m
�[0;34mfasta : �[0;32m/bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/PO1788_Sepioteuthis_lessoniana_RepeatMasked.fasta�[0m
�[0;34mgtf : �[0;32m/bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/PO1788_Sepioteuthis_lessoniana_RepeatMasked.gtf�[0m
�[0;34mmature : �[0;32m/bucket/MillerU/Zifcakova/databases/mature.fa�[0m
�[0;34mspecies : �[0;32mSepiotheusis lessoniana�[0m
�[0;34mfasta_fai : �[0;32m/bucket/MillerU/Zifcakova/Dovetail_ika_genomes/Dovetail_annotated_v_3_01_2022/PO1788_Sepioteuthis_lessoniana_RepeatMasked.fasta.fai�[0m
�[0;34migenomes_ignore : �[0;32mtrue�[0m
�[1mRead trimming & adapter removal�[0m
�[0;34madapters : �[0;32m�[0m
�[1mSTAR�[0m
�[0;34mchimScoreSeparation : �[0;32m10�[0m
�[1mGeneric options�[0m
�[0;34mmax_multiqc_email_size : �[0;32m25 MB�[0m
�[1mMax job request options�[0m
�[0;34mmax_cpus : �[0;32m20�[0m
�[0;34mmax_memory : �[0;32m500 GB�[0m
�[0;34mmax_time : �[0;32m3d 18h�[0m
�[1mInstitutional config options�[0m
�[0;34mconfig_profile_description: �[0;32mThe Okinawa Institute of Science and Technology Graduate University (OIST) HPC cluster profile provided by nf-core/configs.�[0m
�[0;34mconfig_profile_contact : �[0;32mOISTs Bioinformatics User Group [email protected]�[0m
�[0;34mconfig_profile_url : �[0;32mhttps://github.com/nf-core/configs/blob/master/docs/oist.md�[0m
-�[2m----------------------------------------------------�[0m-�[2m
Only displaying parameters that differ from defaults.
�[0m-�[2m----------------------------------------------------�[0m-
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 - -�[0;35m[nf-core/circrna]�[0;31m Pipeline completed with errors�[0m-
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
- Hardware:HPC Deigo, OIST
- Executor: slurm
- OS: CentOS Linux
- Version
Nextflow Installation
Container engine
- Engine: Singularity
- version: 3.5.2
- Image tag: docker://barryd237/circrna:dev [cache /flash/MillerU/circRNA_sles2/singularity/barryd237-circrna-dev.img
Additional context