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

{| width="800"
 * style="background-color: #EEE"|[[Image:C14.jpg|128px]] Genetics of human eye development
 * style="background-color: #F2F2F2" align="center"|  |Main project page
 * style="background-color: #F2F2F2" align="center"|  |Main project page


 * colspan="2"|
 * colspan="2"|

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 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

mkdir Findpeaks
 * Heather 03:30, 30 June 2009 (EDT):
 * 1) create working directory

mv findpeaks3-1-9-2-tar.gz Findpeaks/
 * 1) move tarball into working directory

cd Findpeaks
 * 1) change directory

tar -xvzf findpeaks3-1-9-2-tar.gz
 * 1) extract files form tarball

java -jar ......
 * 1) launch program


 * }