bdm-lab/mogen

The software for modeling the 3D structure of a genome using Hi-C chromosome conformation capturing data

mogen's Issues

The first non-comment line of the file pos_max_dist_weight.txt must contain one number for pairs(i,j) where i <> j

Here is my command and error
`$java -jar /annoroad/data1/bioinfo/PMO/yuanzan/MOGEN/MOGEN-master/bin/3DGenerator.jar parameters_normal.txt

Reading parameters for genome..........................

The first non-comment line of the file pos_max_dist_weight.txt must contain one number for pairs(i,j) where i <> j

Subsequent lines of the file pos_max_dist_weight.txt must contain 2 numbers in format: chromosome value

java.lang.NullPointerException
at java.util.regex.Matcher.toMatchResult(libgcj.so.10)
at java.util.Scanner.myCoreNext(libgcj.so.10)
at java.util.Scanner.myPrepareForNext(libgcj.so.10)
at java.util.Scanner.myNextLine(libgcj.so.10)
at java.util.Scanner.hasNextLine(libgcj.so.10)
at utility.Helper.readMatrix(Helper.java:601)
at genomeReconstruction.GenomeGenerator.readGenomeParameters(GenomeGenerator.java:548)
at genomeReconstruction.GenomeGenerator.initialization(GenomeGenerator.java:157)
at genomeReconstruction.GenomeGenerator.generateStructure(GenomeGenerator.java:247)
at genomeReconstruction.GenomeGenerator.main(GenomeGenerator.java:1022)
at java.lang.reflect.Method.invoke(libgcj.so.10)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
java.lang.NullPointerException
at java.util.regex.Matcher.toMatchResult(libgcj.so.10)
at java.util.Scanner.myCoreNext(libgcj.so.10)
at java.util.Scanner.myPrepareForNext(libgcj.so.10)
at java.util.Scanner.myNextLine(libgcj.so.10)
at java.util.Scanner.hasNextLine(libgcj.so.10)
at utility.Helper.readMatrix(Helper.java:601)
at genomeReconstruction.GenomeGenerator.readGenomeParameters(GenomeGenerator.java:548)
at genomeReconstruction.GenomeGenerator.initialization(GenomeGenerator.java:157)
at genomeReconstruction.GenomeGenerator.generateStructure(GenomeGenerator.java:247)
at genomeReconstruction.GenomeGenerator.main(GenomeGenerator.java:1022)
at java.lang.reflect.Method.invoke(libgcj.so.10)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
No structure is generated !
Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.lang.reflect.Method.invoke(libgcj.so.10)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NullPointerException
at java.util.regex.Matcher.toMatchResult(libgcj.so.10)
at java.util.Scanner.myCoreNext(libgcj.so.10)
at java.util.Scanner.myPrepareForNext(libgcj.so.10)
at java.util.Scanner.myNextLine(libgcj.so.10)
at java.util.Scanner.hasNextLine(libgcj.so.10)
at utility.Helper.readMatrix(Helper.java:601)
at genomeReconstruction.GenomeGenerator.readGenomeParameters(GenomeGenerator.java:548)
at genomeReconstruction.GenomeGenerator.initialization(GenomeGenerator.java:157)
at genomeReconstruction.GenomeGenerator.generateStructure(GenomeGenerator.java:247)
at genomeReconstruction.GenomeGenerator.main(GenomeGenerator.java:1022)
at java.lang.reflect.Method.invoke(libgcj.so.10)
...1 more
`

my pos_max_dist_weight.txt is this:
#the first coefficient is for all (chr1,chr2) where chr1 != chr2 1.0 ##coefficients for intrachromosomal contacts of chromosomes 1 1.0 2 1.0 3 1.0 4 1.0 5 1.0
pos_min_dist_weight.txt
#the first coefficient is for all (chr1,chr2) where chr1 != chr2 2.0 #coefficients for intrachromosomal contacts of chromosomes 1 4.0 2 4.0 3 4.0 4 4.0 5 4.0
neg_max_dist_weight.txt
#the first coefficient is for all (chr1,chr2) where chr1 != chr2 0.5 #coefficients for intrachromosomal contacts of chromosome 1 5.0 2 5.0 3 5.0 4 5.0 5 5.0

neg_min_dist_weight.txt
#the first coefficient is for all (chr1,chr2) where chr1 != chr2 0.5 #coefficients for intrachromosomal contacts of chromosomes 1 1.2 2 1.35 3 2.2 4 2.2 5 2.0
chr_upper_bound_id.txt
1 31 2 51 3 75 4 94 5 121

what should I do?

Building from source?

I would like to build MOGEN from source. Could you provide a build file?

How to adjust the weight parameters?

I use the MOGEN to reconstruct the 3D model of xenopus tropicalis using the default parameters. The resulting evaluation file are as follows. But I am confused that how to adjust the weight parameters to improve the contact score to keep both of contact and non-contact scores for chromosomes to be maximized.

Looking forward to your reply, Thanks !

How to use this program?

Dear the author:

Thanks for developing such an useful tool. But I am confused about the parameters set for this tool.

I do not know how to generate the input files for the program. I seems that the tool need a detialed

manual.

I will be very grateful if you could give me some valuable advice.

I am looking forward to your help.

Very thanks.