Etchevers:Notebook/STRA6 in eye development/2009/06/30

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Building FindPeaks

I hate the way OWW will automatically log you out after a finite, arbitrary amount of time and NOT SAVE DRAFTS. Or at least I don't know where to find them. Make sure to apt-get install subversion first.

~$ svn co http://vancouvershortr.svn.sourceforge.net/svnroot/vancouvershortr/trunk

U trunk/Changelog.txt U trunk/src/lib/analysisTools/Exon_Overlap.java U trunk/src/lib/analysisTools/Process_Exons.java U trunk/src/lib/Ensembl.java D trunk/src/projects/findFeatues A trunk/src/projects/findFeatures A trunk/src/projects/findFeatures/FindFeatures.java U trunk/src/projects/findPeaks/filewriters/PeakWriter.java U trunk/src/projects/findPeaks/PeakDataSetParent.java U trunk/src/projects/findPeaks/FPConstants.java U trunk/src/projects/findPeaks/FindPeaks.java U trunk/src/projects/findPeaks/objects/SaturationDataHolder.java U trunk/src/projects/findPeaks/objects/Parameters.java U trunk/src/projects/findPeaks/objects/LinearRegressionPerpendicular.java U trunk/src/projects/findPeaks/PeakDataSetChild.java U trunk/src/projects/findPeaks/FDR/MC_Simulation.java U trunk/src/projects/findPeaks/FDR/ApplyControl.java U trunk/src/fileUtilities/MaqPetToBedFormat.java U trunk/src/transcriptome_analysis/SNP_Detection/PSNPAnalysisPipeline.java U trunk/build.xml Checked out revision 1309.

~$ ls

calib-36.dat Documents hg18 maqview Pictures Templates Videos Desktop examples.desktop maq-0.7.1 Music Public trunk

~$ ant fpsuite

Buildfile: build.xml does not exist! Build failed

(Oops. One was forewarned.)

~$ cd trunk
~/trunk$ ls

build.xml Changelog.txt classes jars lib src testdata

~$ ant fpsuite

Buildfile: build.xml

cleanfp:

initfp:

   [mkdir] Created dir: /home/heather/trunk/jars/fp4

compile:

   [javac] Compiling 137 source files to /home/heather/trunk/classes

FindPeaks:

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/FindPeaks.jar
  [delete] Deleting directory /home/heather/trunk/tmp

SeparateReads:

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/SeparateReads.jar
  [delete] Deleting directory /home/heather/trunk/tmp

SortFiles:

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/SortFiles.jar
  [delete] Deleting directory /home/heather/trunk/tmp

GenomeViewer:

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/AlignSlice.jar
  [delete] Deleting directory /home/heather/trunk/tmp

ConvertToBed:

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/ConvertToBed.jar
  [delete] Deleting directory /home/heather/trunk/tmp

MaqPetToBed:

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/MaqPetToBed.jar
  [delete] Deleting directory /home/heather/trunk/tmp

buildfp:

fptestdata:

    [copy] Copying 1 file to /home/heather/trunk/jars/fp4

changelog:

    [copy] Copying 1 file to /home/heather/trunk/jars

fpsuite:

BUILD SUCCESSFUL Total time: 7 seconds

I've elided the few attempts where I messed up the pathnames, but here is the last one and I don't see why it can't find MaqPetToBedFormat, as the fileUtilities folder contains:

BowtieToBedFormat.java MapHeaderInfo.java RegionToBed.java CombineFiles.java MaqPetToBedFormat.java SeparateReads.java ConvertToAce.java MaqToReadFormat.java SortFiles.java ConvertToBed.java RegionToAberations.java


~$ time java -Xmx4G ~/trunk/src/fileUtilities/MaqPetToBedFormat -output ~/maq-0.7.1/PetToBeds/ -name PAX6 -input ~/maq-0.7.1/outdirPAX6/allPAX6.map -maq_read_size 128 -bridge

Exception in thread "main" java.lang.NoClassDefFoundError: ~/trunk/src/fileUtilities/MaqPetToBedFormat Caused by: java.lang.ClassNotFoundException: .(~/).trunk.src.fileUtilities.MaqPetToBedFormat 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: ~/trunk/src/fileUtilities/MaqPetToBedFormat. Program will exit.

real 0m0.194s user 0m0.140s sys 0m0.020s

Since I don't know what a class is, I can't fix the problem. I also wonder if I can use single-end tags rather than paired-end, and what it will do with the bridge flag if so. Then again, it seems like anything that hasn't been paired (everything in principle) will end up in :

  • "paired(map)-SET.bed.gz: this bed file contains all reads that could not be paired - either because their mate pair was unmappable by Maq, or because their mate pair was below the minimum quality filter." Write Anthony and ask for help here.
  • Heather 02:48, 30 June 2009 (EDT):

On the Workflows page for FindPeaks, as a neophyte I would have found it really useful if Anthony added in the expected output. I will give it a try and see.

I keep aborting this entry by accident - it's really frustrating. Anyhow, will try -qualityfilter 10 since recommended 10-20 and 30 was used in example. All parameter/flags are here and -saturation is particularly interesting.

I also don't know whether the Monte Carlo or the Lander-Waterman false detection rate calculations are more adapted, when I don't have a control file (want to use ISL1 but that is an ELAND format).

The LW FDR seems to more resemble the concept used in CisGenome. I suppose I could try one then the other? First the MC, then. -iterations 6 -auto_threshold 0.01 -eff_frac 0.7 (Uh-oh, what does <float> mean? Should I specify something after the -flag or not? Can't figure out what it would be for -auto_threshold - an example on the Workflows page is 0.01 -, perhaps automatic for -eff_frac then - no, specify as 0.7).

And after "time java" (why time?) there is a flag that is sometimes given as -Xmx8g and sometimes as -Xmx2G - what is that about?

Ah, I think I missed the subfolder "classes" earlier. However, this still doesn't resolve my problem:

~$ time java -Xmx2G ~/trunk/classes/src/projects/findPeaks/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: /home/heather/trunk/classes/src/projects/findPeaks/FindPeaks Caused by: java.lang.ClassNotFoundException: .home.heather.trunk.classes.src.projects.findPeaks.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: /home/heather/trunk/classes/src/projects/findPeaks/FindPeaks. Program will exit.

real 0m0.186s user 0m0.144s sys 0m0.020s

  • Heather 03:30, 30 June 2009 (EDT):
  1. create working directory

mkdir Findpeaks

  1. move tarball into working directory

mv findpeaks3-1-9-2-tar.gz Findpeaks/

  1. change directory

cd Findpeaks

  1. extract files form tarball

tar -xvzf findpeaks3-1-9-2-tar.gz

  1. launch program

java -jar ......

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