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.

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

  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 ......