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

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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".