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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Unknown config attribute #645

Closed barlavi1 closed 3 years ago

barlavi1 commented 3 years ago

Check Documentation

I have checked the following places for your error:

Description of the bug

After launching nextflow command the run is being terminated after several seconds with the following error

Unknown config attribute params.genomes.GRCh37.projectDir -- check config file: /mnt/data/barA/.nextflow/assets/nf-core/eager/nextflow.config

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line: nextflow run nf-core/eager -r 2.2.2 -name TU_TEST -profile singularity -work-dir /mnt/data/barA/aDNA_TEST/WORK/ -params-file "/mnt/data/barA/aDNA_TEST/nf-params.json"

  2. See error: Unknown config attribute params.genomes.GRCh37.projectDir -- check config file: /mnt/data/barA/.nextflow/assets/nf-core/eager/nextflow.config

Expected behaviour

Run without terminating

Log files

my params file is: { "input": "/mnt/data/barA/aDNA_TEST/RAW//.R{1,2}.fastq.gz", "fasta": "/mnt/data/barA/aDNA_TEST/SVEVO/Svevo.fasta", "bwa_index": "/mnt/data/barA/aDNA_TEST/SVEVO/BWA_INDEX/", "fasta_index": "/mnt/data/barA/aDNA_TEST/SVEVO/Svevo.fasta.fai", "large_ref": "true", "save_reference": "true", "outdir": "/mnt/data/barA/aDNA_TEST/RESULT/", "mapper": "bwamem", "hostremoval_mode": "", "dedup_all_merged": "true", }

Have you provided the following extra information/files:

The next flow .log file: Dec-28 09:18:44.182 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/eager -r 2.2.2 -name TU_TEST -profile singularity -work-dir /mnt/data/barA/aDNA_TEST/WORK/ -params-file /mnt/data/barA/aDNA_TEST/nf-params.json Dec-28 09:18:44.275 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.07.0 Dec-28 09:18:44.409 [main] INFO nextflow.cli.CmdRun - Pulling nf-core/eager ... Dec-28 09:18:44.410 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/eager/contents/nextflow.config Dec-28 09:18:46.515 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/eager/contents/main.nf Dec-28 09:18:47.103 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/eager Dec-28 09:18:47.317 [main] DEBUG nextflow.scm.AssetManager - Pulling nf-core/eager -- Using remote clone url: https://github.com/nf-core/eager.git Dec-28 09:19:09.929 [main] INFO nextflow.cli.CmdRun - downloaded from https://github.com/nf-core/eager.git Dec-28 09:19:10.396 [main] DEBUG nextflow.scm.AssetManager - Git config: /mnt/data/barA/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git Dec-28 09:19:10.396 [main] INFO nextflow.cli.CmdRun - Launching nf-core/eager [TU_TEST] - revision: 85e2e3288a [2.2.2] Dec-28 09:19:10.408 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/data/barA/.nextflow/assets/nf-core/eager/nextflow.config Dec-28 09:19:10.409 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/data/barA/.nextflow/assets/nf-core/eager/nextflow.config Dec-28 09:19:10.418 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: singularity Dec-28 09:19:11.908 [main] DEBUG nextflow.config.ConfigBuilder - In the following config object the attribute params.genomes.GRCh37.projectDir is empty: fasta=s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa bwa=s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa bowtie2=s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/ star=s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ bismark=s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/ gtf=s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf bed12=s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed readme=s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt mito_name='MT' macs_gsize='2.7e9' blacklist=[:]/assets/blacklists/GRCh37-blacklist.bed

Dec-28 09:19:11.914 [main] ERROR nextflow.cli.Launcher - Unknown config attribute params.genomes.GRCh37.projectDir -- check config file: /mnt/data/barA/.nextflow/assets/nf-core/eager/nextflow.config nextflow.exception.ConfigParseException: Unknown config attribute params.genomes.GRCh37.projectDir -- check config file: /mnt/data/barA/.nextflow/assets/nf-core/eager/nextflow.config at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:74) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:237) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:249) at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:400) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrap.invoke(PogoMetaMethodSite.java:179) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184) at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:402) 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.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrap.invoke(PogoMetaMethodSite.java:179) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:63) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184) at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:402) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184) at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:402) at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy) 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.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176) at nextflow.config.ConfigBuilder.merge0(ConfigBuilder.groovy:367) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184) at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:316) 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.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176) at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:282) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:168) at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:627) at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:640) at nextflow.script.ScriptRunner.(ScriptRunner.groovy:88) at nextflow.cli.CmdRun.run(CmdRun.groovy:228) at nextflow.cli.Launcher.run(Launcher.groovy:451) at nextflow.cli.Launcher.main(Launcher.groovy:633)

System

Nextflow Installation

Container engine

Additional context

I hope to solve this quickly. thanks alot, Bar

barlavi1 commented 3 years ago

Bug fixed after using export NXF_VER=20.05.0-edge

apeltzer commented 3 years ago

The latest stable release of Nextflow is 20.10.0 - it's most likely a good idea to upgrade to that one once. There are no drawbacks :-)