sa501428 / hic-emt Goto Github PK

Hi hic-emt dev team,

Thanks for the nice tools!
I've got an error when I want to extract chromosome 1-22 (straw.getChromosomes() shows it has: All,1-22,X,Y,MT) using the following code:

java -Xmx15g -jar hic_emt.jar excise -r 5000 -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 --cleanup GM12878_combined.hic GM_22chr_emt

Output was like:

Reading file: GM12878_combined.hic
HiC file version: 7
Exception in thread "main" java.lang.NullPointerException
        at javastraw.reader.basics.ChromosomeHandler.inferGenomeId(ChromosomeHandler.java:287)
        at javastraw.reader.basics.ChromosomeHandler.<init>(ChromosomeHandler.java:53)
        at javastraw.reader.basics.ChromosomeHandler.<init>(ChromosomeHandler.java:47)
        at javastraw.tools.HiCFileTools.stringToChromosomes(HiCFileTools.java:191)
        at emt.clt.tools.Excise.run(Excise.java:58)
        at emt.Tools.main(Tools.java:75)

Seems like it can't detect -c input? Cause when I run without -c, it works perfectly.

Another question, how can I know the number of Hi-C contacts from a .hic file? Sry it's not hic-emt related, it would be of great help if you can drop me some hints.

Thanks
Yiling

Hello,

Thanks for this great tool.

I keep getting an error that I'm not sure how to address:

java -Xmx20g -jar /home/braulio/lab/analisis/hic/Hi-C_EMT/hic_emt.jar excise --subsample 1312476019 /media/braulio/Braulio/hic/juicer/GFP/GFP/mega/inter_30.hic subsample_folder inter_30_1.3.hic WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. Aiming to retain ~1312476019/2414513412 Ratio: 0.5435778540210486 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ...WARN [2023-07-15T20:21:39,752] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) for primary task Using 1 CPU thread(s) for secondary task Exception in thread "main" java.lang.NoSuchFieldError: useIteratorDontPutAllInRAM at hic.HiCGlobals.setMatrixZoomDataRAMUsage(HiCGlobals.java:75) at hic.tools.clt.old.PreProcessing.readArguments(PreProcessing.java:154) at hic.tools.HiCTools.main(HiCTools.java:82) at emt.main.FileBuildingMethod.buildNewHiCFile(FileBuildingMethod.java:52) at emt.main.FileBuildingMethod.tryToBuild(FileBuildingMethod.java:58) at emt.clt.tools.Excise.run(Excise.java:71) at emt.Tools.main(Tools.java:75)
The files that I am using are V9 and they do have SCALE. Do you know what could cause this?
I tried the cluster using module load java/1.8.0_121 with the same result

Thank you!
Braulio

Hi,

Thank you for the development of this tool.

I'm getting an error when trying to use the excise function to subsample a .hic file. My code and the error message looks like this:

(base) $ java -Xmx5g -jar hic_emt.jar excise -r 5000 --subsample 500 inter.hic test

Reading file: inter.hic
HiC file version: 8
Aiming to retain ~500/259758692
Ratio: 1.9248634036084537E-6
..........
..........
..........
..........
..........
.....WARN [2023-08-02T16:41:36,521]  [Globals.java:138] [main]  Development mode is enabled
Using 1 CPU thread(s) for primary task
Using 1 CPU thread(s) for secondary task
Not including fragment map
Start preprocess
Writing header
Writing body
java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.
        at hic.tools.utils.original.MatrixZoomDataPP.mergeAndWriteBlocks(MatrixZoomDataPP.java:337)
        at hic.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:839)
        at hic.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:583)
        at hic.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:370)
        at hic.tools.clt.old.PreProcessing.run(PreProcessing.java:165)
        at hic.tools.HiCTools.main(HiCTools.java:83)
        at emt.main.FileBuildingMethod.buildNewHiCFile(FileBuildingMethod.java:51)
        at emt.main.FileBuildingMethod.tryToBuild(FileBuildingMethod.java:57)
        at emt.clt.tools.Excise.run(Excise.java:69)
        at emt.Tools.main(Tools.java:75)

However, the input .hic file looks fine in Juicebox. Do you know what is causing this error?

Thanks,
Josephine

https://github.com/sa501428/hic-equals