Closed royfrancis closed 4 years ago
Here is the command:
module load conda/2019.10 conda activate nextflow-env nextflow run \ -c params.config \ -profile nbis,conda ~/bower/resources/pipelines-nextflow/AbinitioTraining/AbinitioTraining.nf
Here is the params.config
Here is the error log from .nextflow.log.
Here is the command:
Here is the params.config
params.config
``` // Workflow parameters params.maker_evidence_gff = "evidence.gff" params.genome = "genome_clean.fa" params.outdir = "results" params.species_label = 'ailuroedus_buccoides' // e.g. 'asecodes_parviclava' params.model_selection_value = 0.3 params.locus_distance = 3000 params.codon_table = 1 params.test_size = 100 params.flank_region_size = 1000 params.maker_species_publishdir = '/projects/references/augustus/config/species/ailuroedus_buccoides/' // Nextflow parameters resume = true workDir = '/scratch/roy/augustus' conda.cacheDir = "$HOME/.nextflow/conda" singularity.cacheDir = "$HOME/.nextflow/singularity" ```Here is the error log from .nextflow.log.
.nextflow.log
``` Jun-22 09:26:07.233 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -c params.config -profile nbis,conda /home/roy/bower/resources/pipelines-nextflow/AbinitioTraining/AbinitioTraining.nf Jun-22 09:26:07.383 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.01.0 Jun-22 09:26:07.403 [main] INFO nextflow.cli.CmdRun - Launching `/home/roy/bower/resources/pipelines-nextflow/AbinitioTraining/AbinitioTraining.nf` [confident_dubinsky] - revision: 3402b15e08 Jun-22 09:26:07.431 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/roy/bower/resources/pipelines-nextflow/AbinitioTraining/nextflow.config Jun-22 09:26:07.434 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /projects/annotation/3_bower_birds/ailuroedus_buccoides/augustus/params.config Jun-22 09:26:07.435 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/roy/bower/resources/pipelines-nextflow/AbinitioTraining/nextflow.config Jun-22 09:26:07.435 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /projects/annotation/3_bower_birds/ailuroedus_buccoides/augustus/params.config Jun-22 09:26:07.462 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `nbis,conda` Jun-22 09:26:08.086 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `nbis,conda` Jun-22 09:26:08.126 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bils, debug, test, conda, uppmax, singularity, nbis, docker] Jun-22 09:26:08.191 [main] DEBUG nextflow.Session - Session uuid: b086f2b3-4b07-43a2-8339-0798ce408f82 Jun-22 09:26:08.192 [main] DEBUG nextflow.Session - Run name: confident_dubinsky Jun-22 09:26:08.192 [main] DEBUG nextflow.Session - Executor pool size: 32 Jun-22 09:26:08.239 [main] DEBUG nextflow.cli.CmdRun - Version: 20.01.0 build 5264 Created: 12-02-2020 10:14 UTC (11:14 CEST) System: Linux 4.15.0-88-generic Runtime: Groovy 2.5.8 on OpenJDK 64-Bit Server VM 11.0.1-internal+0-adhoc..src Encoding: UTF-8 (UTF-8) Process: 35974@nac-login [192.168.11.35] CPUs: 32 - Mem: 62.9 GB (1.9 GB) - Swap: 8 GB (7.5 GB) Jun-22 09:26:08.278 [main] DEBUG nextflow.Session - Work-dir: /scratch/roy/augustus [ext2/ext3] Jun-22 09:26:08.279 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/roy/bower/resources/pipelines-nextflow/AbinitioTraining/bin Jun-22 09:26:08.307 [main] DEBUG nextflow.Session - Observer factory: TowerFactory Jun-22 09:26:08.309 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jun-22 09:26:08.524 [main] DEBUG nextflow.Session - Session start invoked Jun-22 09:26:08.529 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /projects/annotation/3_bower_birds/ailuroedus_buccoides/augustus/pipeline_report/execution_trace.txt Jun-22 09:26:09.024 [main] WARN nextflow.NextflowMeta$Preview - DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE Jun-22 09:26:09.028 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jun-22 09:26:09.052 [main] INFO nextflow.Nextflow - NBIS _ _ ____ _____ _____ | \ | | _ \_ _|/ ____| | \| | |_) || | | (___ | . ` | _ < | | \___ \ | |\ | |_) || |_ ____) | |_| \_|____/_____|_____/ Annotation Service Abintio training dataset workflow =================================== General Parameters maker_evidence_gff : evidence.gff genome : genome_clean.fa outdir : results species_label : ailuroedus_buccoides Model selection by AED model_selection_value : 0.3 Filter by locus distance locus_distance : 3000 Protein Sequence extraction parameters codon_table : 1 Augustus training parameters test_size : 100 flank_region_size : 1000 Jun-22 09:26:09.092 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: gff2gbk, snap_training, split_maker_evidence, blast_makeblastdb, model_selection_by_AED, gbk2augustus, blast_recursive, gff_filter_by_blast, remove_incomplete_gene_models, filter_by_locus_distance, retain_longest_isoform, augustus_training, convert_gff2zff, extract_protein_sequence Jun-22 09:26:09.272 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AGAT` matches label `AGAT` for process with name abinitio_training:split_maker_evidence Jun-22 09:26:09.279 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.280 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.291 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Jun-22 09:26:09.302 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Jun-22 09:26:09.307 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Jun-22 09:26:09.368 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:split_maker_evidence -- maxForks: 20; blocking: true Jun-22 09:26:09.398 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AGAT` matches label `AGAT` for process with name abinitio_training:model_selection_by_AED Jun-22 09:26:09.400 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.400 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.437 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:model_selection_by_AED -- maxForks: 20; blocking: true Jun-22 09:26:09.444 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AGAT` matches label `AGAT` for process with name abinitio_training:retain_longest_isoform Jun-22 09:26:09.447 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.447 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.449 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:retain_longest_isoform -- maxForks: 20; blocking: true Jun-22 09:26:09.470 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AGAT` matches label `AGAT` for process with name abinitio_training:remove_incomplete_gene_models Jun-22 09:26:09.471 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.471 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.476 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:remove_incomplete_gene_models -- maxForks: 20; blocking: true Jun-22 09:26:09.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AGAT` matches label `AGAT` for process with name abinitio_training:filter_by_locus_distance Jun-22 09:26:09.481 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.481 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.484 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:filter_by_locus_distance -- maxForks: 20; blocking: true Jun-22 09:26:09.489 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AGAT` matches label `AGAT` for process with name abinitio_training:extract_protein_sequence Jun-22 09:26:09.490 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.490 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.492 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:extract_protein_sequence -- maxForks: 20; blocking: true Jun-22 09:26:09.496 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:Blast` matches label `Blast` for process with name abinitio_training:blast_makeblastdb Jun-22 09:26:09.497 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.497 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.500 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:blast_makeblastdb -- maxForks: 20; blocking: true Jun-22 09:26:09.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:Blast` matches label `Blast` for process with name abinitio_training:blast_recursive Jun-22 09:26:09.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:blast_recursive` matches process abinitio_training:blast_recursive Jun-22 09:26:09.508 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.508 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.511 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:blast_recursive -- maxForks: 20; blocking: true Jun-22 09:26:09.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AGAT` matches label `AGAT` for process with name abinitio_training:gff_filter_by_blast Jun-22 09:26:09.519 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.520 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.521 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:gff_filter_by_blast -- maxForks: 20; blocking: true Jun-22 09:26:09.528 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:Augustus` matches label `Augustus` for process with name abinitio_training:gff2gbk Jun-22 09:26:09.529 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.529 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.530 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:gff2gbk -- maxForks: 20; blocking: true Jun-22 09:26:09.536 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:Augustus` matches label `Augustus` for process with name abinitio_training:gbk2augustus Jun-22 09:26:09.537 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.537 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.539 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:gbk2augustus -- maxForks: 20; blocking: true Jun-22 09:26:09.562 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:Augustus` matches label `Augustus` for process with name abinitio_training:augustus_training Jun-22 09:26:09.564 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.564 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.566 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:augustus_training -- maxForks: 20; blocking: true Jun-22 09:26:09.574 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:AGAT` matches label `AGAT` for process with name abinitio_training:convert_gff2zff Jun-22 09:26:09.575 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.575 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.577 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:convert_gff2zff -- maxForks: 20; blocking: true Jun-22 09:26:09.584 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:snap_training` matches process abinitio_training:snap_training Jun-22 09:26:09.585 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-22 09:26:09.585 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-22 09:26:09.587 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > abinitio_training:snap_training -- maxForks: 20; blocking: true Jun-22 09:26:09.590 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot emit a multi-channel output: augustus Jun-22 09:26:09.625 [main] DEBUG nextflow.Session - The following nodes are still active: [operator] ifEmpty [operator] ifEmpty [operator] collect [operator] collect [operator] collect [operator] collect [operator] collect [operator] collect Jun-22 09:26:09.630 [Actor Thread 3] DEBUG nextflow.Nextflow - Ignore exit because execution is already aborted -- message=Cannot find genome matching genome_clean.fa! Jun-22 09:26:09.630 [Actor Thread 2] DEBUG nextflow.Nextflow - Ignore exit because execution is already aborted -- message=Cannot find gff file matching evidence.gff! Jun-22 09:26:09.634 [main] ERROR nextflow.cli.Launcher - Cannot emit a multi-channel output: augustus java.lang.IllegalArgumentException: Cannot emit a multi-channel output: augustus at nextflow.script.WorkflowDef.collectOutputs(WorkflowDef.groovy:149) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:206) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:191) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:87) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:397) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:339) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:64) 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 Script_bd931283$_runScript_closure1$_closure18.doCall(Script_bd931283:67) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at groovy.lang.Closure.call(Closure.java:405) at groovy.lang.Closure.call(Closure.java:399) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:191) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ChainableDef$invoke_a.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:127) at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:180) at nextflow.script.BaseScript.run(BaseScript.groovy:189) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:225) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:218) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:126) at nextflow.cli.CmdRun.run(CmdRun.groovy:273) at nextflow.cli.Launcher.run(Launcher.groovy:460) at nextflow.cli.Launcher.main(Launcher.groovy:642) ```