Apr-09 14:29:18.699 [main] DEBUG nextflow.cli.Launcher - $> /clusterfs/jgi/groups/gentech/homes/amoralescruz/venv/misc/bin/nextflow run nextflow-pacbio-demux-bbduk/pacbio_demux_bbduk.nf -c nextflow-pacbio-demux-bbduk/nextflow.config --samples /clusterfs/jgi/groups/gentech/homes/amoralescruz/custom_gentech_qc/pb_seqwell/bam/pbio-2959-31062.hifi_reads.bc31062.bam --barcodes_i7 nextflow-pacbio-demux-bbduk/LongPlex_set3_i7_trimmed_adapters.fa --barcodes_i5 nextflow-pacbio-demux-bbduk/LongPlex_set3_i5_trimmed_adapters.fa -bg -resume -work-dir nexflow_dir Apr-09 14:29:18.759 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.24.2 Apr-09 14:29:18.767 [main] INFO nextflow.cli.CmdRun - Launching `nextflow-pacbio-demux-bbduk/pacbio_demux_bbduk.nf` [fervent_boyd] - revision: 7d58681210 Apr-09 14:29:18.774 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /clusterfs/jgi/groups/gentech/homes/amoralescruz/custom_gentech_qc/pb_seqwell/nextflow-pacbio-demux-bbduk/nextflow.config Apr-09 14:29:18.775 [main] DEBUG nextflow.config.ConfigBuilder - User config file: nextflow-pacbio-demux-bbduk/nextflow.config Apr-09 14:29:18.776 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /clusterfs/jgi/groups/gentech/homes/amoralescruz/custom_gentech_qc/pb_seqwell/nextflow-pacbio-demux-bbduk/nextflow.config Apr-09 14:29:18.776 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /clusterfs/jgi/groups/gentech/homes/amoralescruz/custom_gentech_qc/pb_seqwell/nextflow-pacbio-demux-bbduk/nextflow.config Apr-09 14:29:18.937 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'standard' Apr-09 14:29:18.987 [main] DEBUG nextflow.Session - Session uuid: 113f8ead-1220-45cd-9757-5691367f5f30 Apr-09 14:29:18.988 [main] DEBUG nextflow.Session - Run name: fervent_boyd Apr-09 14:29:18.989 [main] DEBUG nextflow.Session - Executor pool size: 32 Apr-09 14:29:19.002 [main] DEBUG nextflow.cli.CmdRun - Version: 0.24.2 build 4271 Modified: 05-04-2017 16:50 UTC (09:50 PDT) System: Linux 4.18.0-425.3.1.el8.x86_64 Runtime: Groovy 2.4.10 on OpenJDK 64-Bit Server VM 1.8.0_92-b15 Encoding: UTF-8 (UTF-8) Process: 1584273@ln004.jgi [10.0.7.4] CPUs: 32 - Mem: 503.8 GB (25 GB) - Swap: 8 GB (0) Apr-09 14:29:19.030 [main] DEBUG nextflow.Session - Work-dir: /clusterfs/jgi/groups/gentech/homes/amoralescruz/custom_gentech_qc/pb_seqwell/nexflow_dir [nfs] Apr-09 14:29:19.103 [main] DEBUG nextflow.Session - Session start invoked Apr-09 14:29:19.105 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start Apr-09 14:29:19.105 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing Apr-09 14:29:19.231 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Apr-09 14:29:19.368 [main] WARN nextflow.processor.ProcessFactory - Unknown directive `lima` for process `reads_count` Apr-09 14:29:19.373 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown variable 'pair_id' Apr-09 14:29:19.423 [main] ERROR nextflow.cli.Launcher - @unknown groovy.lang.MissingPropertyException: Unknown variable 'pair_id' 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:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:60) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:235) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:263) at nextflow.processor.ProcessConfig.getProperty(ProcessConfig.groovy:217) at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:174) at groovy.lang.Closure.getPropertyTryThese(Closure.java:312) at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:302) at groovy.lang.Closure.getProperty(Closure.java:287) at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:50) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:307) at _nf_script_7fa1e634$_run_closure2.doCall(_nf_script_7fa1e634:34) 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:93) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1027) at groovy.lang.Closure.call(Closure.java:414) at groovy.lang.Closure.call(Closure.java:430) at org.codehaus.groovy.runtime.DefaultGroovyMethods.with(DefaultGroovyMethods.java:242) at org.codehaus.groovy.runtime.dgm$757.invoke(Unknown Source) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoMetaMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:251) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.call(PogoMetaMethodSite.java:71) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at nextflow.processor.ProcessFactory.createProcessor(ProcessFactory.groovy:236) at nextflow.processor.ProcessFactory.createProcessor(ProcessFactory.groovy) at nextflow.processor.ProcessFactory$createProcessor.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133) at nextflow.script.BaseScript.process(BaseScript.groovy:132) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174) at _nf_script_7fa1e634.run(_nf_script_7fa1e634:27) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:322) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:156) at nextflow.cli.CmdRun.run(CmdRun.groovy:223) at nextflow.cli.Launcher.run(Launcher.groovy:410) at nextflow.cli.Launcher.main(Launcher.groovy:564)