Various warning and error messages

Hi,

I'm trying to run Juicer in order to use 3d-dna. Everything seems to work fine with the data you provide, but when I execute it on my data I get a number or warning messages and some errors. The main file for 3d-dna merged_nodups.txt is there but for same reasons the run has problems.

Skipping Scf0008823 1000    538299569   1000    1001
Skipping Scf0008824 1000    538300582   1000    1001
Skipping Scf0008825 1000    538301595   1000    1001
Skipping Scf0008826 1000    538302608   1000    1001
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 juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1762)
    at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1531)
    at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:944)
    at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:661)
    at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:419)
    at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:122)
    at juicebox.tools.HiCTools.main(HiCTools.java:96)
./scripts/common/juicer_tools is post-processing Hi-C for Diul
Data read from /home/fc464/rds/rds-shm37-helixmbodyw/HeliconiiniProg/Diul.Assembly-Supernova10x/Diul.Juicer/aligned/inter_30.hic.
Motifs read from ./references/motif

ARROWHEAD:

Picked up _JAVA_OPTIONS: -Xmx16384m
WARN [2019-07-03T09:26:01,051]  [Globals.java:138] [main]  Development mode is enabled
Reading file: /home/fc464/rds/rds-shm37-helixmbodyw/HeliconiiniProg/Diul.Assembly-Supernova10x/Diul.Juicer/aligned/inter_30.hic
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
    at juicebox.data.DatasetReaderV2.readFooter(DatasetReaderV2.java:474)
    at juicebox.data.DatasetReaderV2.read(DatasetReaderV2.java:236)
    at juicebox.data.HiCFileTools.extractDatasetForCLT(HiCFileTools.java:60)
    at juicebox.tools.clt.juicer.Arrowhead.readJuicerArguments(Arrowhead.java:135)
    at juicebox.tools.clt.JuicerCLT.readArguments(JuicerCLT.java:66)
    at juicebox.tools.HiCTools.main(HiCTools.java:95)
***! Problem while running Arrowhead
(-: Pipeline successfully completed (-:

Attached the entire log file Thanks for your help F Juicer.Diul.log

aidenlab / juicer

Various warning and error messages #120