Etchevers:Notebook/STRA6 in eye development/2009/07/01

Genetics of human eye development

Main project page Previous entry      Next entry

Reverting to FindPeaks earlier version Matthias Titeux helped me parse some of the language about installing FindPeaks and what the error message might mean. He suggested I not use version 4 which may not be stable and use the earlier one instead. Based on his instructions at the end of yesterday's entry, I did the following: ~/FindPeaks$ tar -xvf findpeaks3-1-9-2-tar 22.test.eland AlignSlice.jar ElandtoBed.jar FindPeaks.jar findpeaksManual.pdf ParseMultipleElands.jar SeparateElandReads.jar VulgartoBed.jar ~/FindPeaks$ time java -Xmx2G -jar FindPeaks -name PAX6-FP -input ~/maq-0.7.1/outdirPAX6/allPAX6.map -output ~/maq-0.7.1/FindPeaksResults/ -maq_read_size 128 -qualityfilter 10 -aligner maq -one_per -saturation -iterations 6 -auto_threshold 0.01 -eff_frac 0.7 -dist_type 1 200 Unable to access jarfile FindPeaks real 0m0.005s user 0m0.000s sys 0m0.008s ~/FindPeaks$ ls 22.test.eland findpeaks3-1-9-2-tar ParseMultipleElands.jar AlignSlice.jar FindPeaks.jar SeparateElandReads.jar ElandtoBed.jar findpeaksManual.pdf VulgartoBed.jar ~/FindPeaks$ java -jar FindPeaks -name PAX6-FP -input ~/maq-0.7.1/outdirPAX6/allPAX6.map -output ~/maq-0.7.1/FindPeaksResults/ -maq_read_size 128 -qualityfilter 10 -aligner maq -one_per -saturation -iterations 6 -auto_threshold 0.01 -eff_frac 0.7 -dist_type 1 200 Unable to access jarfile FindPeaks ~/FindPeaks$ time java -Xmx2G FindPeaks -name PAX6-FP -input ~/maq-0.7.1/outdirPAX6/allPAX6.map -output ~/maq-0.7.1/FindPeaksResults/ -maq_read_size 128 -qualityfilter 10 -aligner maq -one_per -saturation -iterations 6 -auto_threshold 0.01 -eff_frac 0.7 -dist_type 1 200 Exception in thread "main" java.lang.NoClassDefFoundError: FindPeaks Caused by: java.lang.ClassNotFoundException: FindPeaks at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:336) Could not find the main class: FindPeaks. Program will exit. real 0m0.181s user 0m0.116s sys 0m0.032s I'm pretty sure that Matthias just wrote java -jar FindPeaks and he got it to react by telling him he didn't put the flags in. I just get "Unable to access jarfile FindPeaks". Heather 17:32, 30 June 2009 (EDT):