pipeline won't start without filling ref-genome bwa, bowtie, etc...

[luciazifcakova]

Check Documentation

I have checked the following places for your error:

• [yes ] nf-core website: troubleshooting
• [ yes] nf-core/circrna pipeline documentation

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: 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: 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 -

-�[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 BioinfoUgrp@oist.jp�[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

• Version: 21.10.6

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

[xnr13]

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]

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