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Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics #389

@Renshengjie

Description

@Renshengjie

Dear Juicer teams,

I run juicer meet an error report at the final stage. Here is details:

Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m
Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics
at juicebox.tools.HiCTools.main(HiCTools.java:98)
Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m
Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics
at juicebox.tools.HiCTools.main(HiCTools.java:98)
Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m
Error while reading graphs file: java.io.FileNotFoundException: work/aligned/inter_hists.m (No such file or directory)
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$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1650)
at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1419)
at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:832)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:582)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:346)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:116)
at juicebox.tools.HiCTools.main(HiCTools.java:96)

real 5m2.930s
user 1m21.370s
sys 0m38.045s
Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m
Error reading datasetnull
java.io.EOFException
at htsjdk.tribble.util.LittleEndianInputStream.readFully(LittleEndianInputStream.java:138)
at htsjdk.tribble.util.LittleEndianInputStream.readLong(LittleEndianInputStream.java:80)
at htsjdk.tribble.util.LittleEndianInputStream.readDouble(LittleEndianInputStream.java:100)
at juicebox.data.DatasetReaderV2.readFooter(DatasetReaderV2.java:470)
at juicebox.data.DatasetReaderV2.read(DatasetReaderV2.java:235)
at juicebox.tools.utils.original.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:78)
at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:84)
at juicebox.tools.HiCTools.main(HiCTools.java:96)

real 0m0.834s
user 0m0.342s
sys 0m0.384s
Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m
Error while reading graphs file: java.io.FileNotFoundException: work/aligned/inter_30_hists.m (No such file or directory)
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$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1650)
at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1419)
at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:832)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:582)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:346)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:116)
at juicebox.tools.HiCTools.main(HiCTools.java:96)

real 4m25.574s
user 1m13.627s
sys 0m36.549s
Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m
Error reading datasetnull
java.io.EOFException
at htsjdk.tribble.util.LittleEndianInputStream.readFully(LittleEndianInputStream.java:138)
at htsjdk.tribble.util.LittleEndianInputStream.readLong(LittleEndianInputStream.java:80)
at htsjdk.tribble.util.LittleEndianInputStream.readDouble(LittleEndianInputStream.java:100)
at juicebox.data.DatasetReaderV2.readFooter(DatasetReaderV2.java:470)
at juicebox.data.DatasetReaderV2.read(DatasetReaderV2.java:235)
at juicebox.tools.utils.original.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:78)
at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:84)
at juicebox.tools.HiCTools.main(HiCTools.java:96)

real 0m0.714s
user 0m0.381s
sys 0m0.450s
juicer/scripts/common/juicer_postprocessing.sh: option requires an argument -- g

Would be any help for problems.
Thanks
Henry

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