Oct-25 20:45:08.845 [main] DEBUG nextflow.cli.Launcher - $> /usr/local/bin/nextflow run nextflow-scripts/legos/unleashthekraken.nf Oct-25 20:45:08.976 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.22.3 Oct-25 20:45:08.987 [main] INFO nextflow.cli.CmdRun - Launching `nextflow-scripts/legos/unleashthekraken.nf` [berserk_mayer] - revision: 754b0516d7 Oct-25 20:45:09.299 [main] DEBUG nextflow.Session - Session uuid: 49f28bc6-d63d-428e-90c9-5adbae9b27a3 Oct-25 20:45:09.299 [main] DEBUG nextflow.Session - Run name: berserk_mayer Oct-25 20:45:09.301 [main] DEBUG nextflow.Session - Executor pool size: 32 Oct-25 20:45:09.320 [main] DEBUG nextflow.cli.CmdRun - Version: 0.22.3 build 4095 Modified: 12-10-2016 09:31 UTC System: Linux 3.13.0-93-generic Runtime: Groovy 2.4.7 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13 Encoding: UTF-8 (UTF-8) Process: 4050@ip-172-31-22-229 [172.31.22.229] CPUs: 32 - Mem: 240.2 GB (15 GB) - Swap: 0 (0) Oct-25 20:45:09.345 [main] DEBUG nextflow.Session - Work-dir: /data2/work [ext2/ext3] Oct-25 20:45:09.433 [main] DEBUG nextflow.Session - Session start invoked Oct-25 20:45:09.440 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start Oct-25 20:45:09.441 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing Oct-25 20:45:09.599 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Oct-25 20:45:09.624 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider Oct-25 20:45:09.642 [main] DEBUG nextflow.file.FileHelper - AWS S3 config details: {} Oct-25 20:45:11.198 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: atg-datalake-test/acctumorRNA.g1k/tmap/; pattern: *.bam; options: null Oct-25 20:45:11.199 [main] DEBUG nextflow.Session - Session aborted -- Cause: Relative path cannot be made absolute: atg-datalake-test/acctumorRNA.g1k/tmap Oct-25 20:45:11.226 [main] ERROR nextflow.cli.Launcher - @unknown java.lang.IllegalStateException: Relative path cannot be made absolute: atg-datalake-test/acctumorRNA.g1k/tmap at com.upplication.s3fs.S3Path.toAbsolutePath(S3Path.java:435) 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 groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024) at groovy.runtime.metaclass.NextflowDelegatingMetaClass.invokeMethod(NextflowDelegatingMetaClass.java:79) at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117) at nextflow.extension.FilesEx.complete(FilesEx.groovy:1385) 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.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:54) at org.codehaus.groovy.runtime.metaclass.NewInstanceMetaMethod.invoke(NewInstanceMetaMethod.java:56) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024) at groovy.runtime.metaclass.NextflowDelegatingMetaClass.invokeMethod(NextflowDelegatingMetaClass.java:79) at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:47) 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:117) at nextflow.Channel.pathImpl(Channel.groovy:266) 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 org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite$StaticMetaMethodSiteNoUnwrapNoCoerce.invoke(StaticMetaMethodSite.java:151) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:102) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:56) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:194) at nextflow.Channel.fromPathWithMap(Channel.groovy:236) 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 org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite$StaticMetaMethodSiteNoUnwrapNoCoerce.invoke(StaticMetaMethodSite.java:151) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:102) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:56) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:194) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:214) at nextflow.Channel.fromPath0(Channel.groovy:193) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite$StaticMetaMethodSiteNoUnwrapNoCoerce.invoke(StaticMetaMethodSite.java:151) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:102) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:56) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:194) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:214) at nextflow.Channel.fromPath(Channel.groovy:182) at nextflow.Channel.fromPath(Channel.groovy) at nextflow.Channel$fromPath.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:125) at _nf_script_cb9913a7.run(_nf_script_cb9913a7:17) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:322) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:156) at nextflow.cli.CmdRun.run(CmdRun.groovy:204) at nextflow.cli.Launcher.run(Launcher.groovy:406) at nextflow.cli.Launcher.main(Launcher.groovy:554)