/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java -agentlib:jdwp=transport=dt_socket,address=127.0.0.1:64843,suspend=y,server=n -Xmx4G -javaagent:/Users/micha/Library/Caches/IdeaIC11/groovyHotSwap/gragent.jar -Dfile.encoding=UTF-8 -classpath "/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/deploy.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/dt.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/javaws.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/jce.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/jconsole.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/management-agent.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/plugin.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/sa-jdi.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/charsets.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsse.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/ui.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/apple_provider.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/dnsns.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/localedata.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/sunjce_provider.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext/sunpkcs11.jar:/Users/micha/git_idea/barna/out/production/barna.simulator:/Users/micha/.gradle/caches/artifacts-13/filestore/jdbm/jdbm/2.3/jar/db56efad7261a81b90b6966f220cc3994775398a/jdbm-2.3.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/org.codehaus.groovy/groovy-all/1.8.4/jar/b5e7c2a5e6af43ccccf643ad656d6fe4b773be2b/groovy-all-1.8.4.jar:/Users/micha/git_idea/barna/out/production/barna.model:/Users/micha/git_idea/barna/out/production/barna.commons:/Users/micha/.gradle/caches/artifacts-13/filestore/org.apache.commons/commons-math/2.2/jar/4877b85d388275f994a5cfc7eceb73a8045d3006/commons-math-2.2.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/commons-cli/commons-cli/1.2/jar/2bf96b7aa8b611c177d329452af1dc933e14501c/commons-cli-1.2.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/jfree/jfreechart/1.0.0/jar/7776a5e3f555643720415a47e022daac9cca32b1/jfreechart-1.0.0.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/com.lowagie/itext/2.0.7/jar/84175e0669d88fc44e5ca0bd9bd5f170aa7ca27f/itext-2.0.7.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/org.reflections/reflections/0.9.5/jar/12d5bb5c74b486c133e3de9899a692e67f71642c/reflections-0.9.5.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/org.slf4j/slf4j-nop/1.6.1/jar/70249094d4e5653b6bdfea46f3a1a4165c1e1993/slf4j-nop-1.6.1.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/com.martiansoftware/jsap/2.1/jar/d17c260c8f5eb6e7d6bd75449a57edfeb53d2305/jsap-2.1.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/xpp3/xpp3_min/1.1.3.4.O/jar/cbb9d21eed484a16e0c0bd712830a80c75970753/xpp3_min-1.1.3.4.O.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/com.thoughtworks.xstream/xstream/1.2.2/jar/40c19ec03a2063bcc04d7066f4b607d5aa336192/xstream-1.2.2.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/jfree/jcommon/1.0.0/jar/25b1bfc1bb224a270e30cc8c19c4b8f63108ada0/jcommon-1.0.0.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/com.google.guava/guava/r08/jar/b024b674b64bea7bcb214c3eee005d1a9168097d/guava-r08.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/javassist/javassist/3.12.1.GA/jar/526633327faa61aee448a519e8a4d53ec3057885/javassist-3.12.1.GA.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/org.slf4j/slf4j-api/1.6.1/jar/6f3b8a24bf970f17289b234284c94f43eb42f0e4/slf4j-api-1.6.1.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/xml-apis/xml-apis/1.0.b2/jar/3136ca936f64c9d68529f048c2618bd356bf85c9/xml-apis-1.0.b2.jar:/Users/micha/.gradle/caches/artifacts-13/filestore/dom4j/dom4j/1.6.1/jar/5d3ccc056b6f056dbf0dddfdf43894b9065a8f94/dom4j-1.6.1.jar:/Users/micha/git_idea/barna/out/production/barna.io:/Applications/IntelliJ IDEA 11 CE.app/lib/idea_rt.jar" barna.flux.simulator.SimulationPipeline /Users/micha/Desktop/hg19_no_tails.par Connected to the target VM, address: '127.0.0.1:64843', transport: 'socket' [INFO] I am collecting information on the run. initializing profiler ********** [INFO] Checking GTF file ********** OK (00:00:03) [INFO] you did not ask for expression, I skip it. [LIBRARY] creating the cDNA libary Initializing Fragmentation File ********** OK (00:00:06) 4999444 mol initialized [LIBRARY] Fragmentation UR [LIBRARY] Configuration D0: 1.0 Delta: Not specified, depends on sequence length Eta: 350.0 Processing Fragments ********** OK (00:01:34) 49367248 mol: in 4999444, new 44367804, out 49367248 avg Len 315.80347, maxLen 1088 preparing transcript sequences ********** OK (00:01:17) [INFO] Initializing PWM cache [INFO] Done [LIBRARY] Reverse Transcription [LIBRARY] Configuration Mode: RH PWM: default RT MIN: 500 RT MAX: 5500 Processing Fragments ********** OK (00:10:37) 49424196 mol: in 49367248, new 56948, out 49424196 avg Len 182.07387, maxLen 1149 start amplification [INFO] Loading default PCR distribution [INFO] Initializing PWM cache [INFO] Done [LIBRARY] Amplification [LIBRARY] Configuration Rounds: 15 PCR Probability: 0.05 Processing Fragments ********** OK (00:02:13) Amplification done. In: 49424196 Out: 1333074525 49424196 mol: in 49424196, new 0, out 1333074525 avg Len 182.04697, maxLen 1139 Copied results to /Users/micha/Desktop/hg19_no_tails.lib Updating .pro file ********** OK (00:00:00) [SEQUENCING] getting the reads Initializing Fragment Index Indexing ********** OK (00:00:56) 26523788 lines indexed (1333074525 fragments, 18766 entries) sequencing ********** OK (00:52:11) 1333074525 fragments found (26523788 without PCR duplicates) 299993998 reads sequenced 17478242 reads fall in poly-A tail 107232752 truncated reads Moving temporary BED file Updating .pro file ********** OK (00:00:00) Updating .pro file ********** OK (00:00:00) Updating .pro file ********** OK (00:00:00) Updating .pro file ********** OK (00:00:00) [END] I finished, took me 4313 sec.