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

[vinitamehlawat]

Dear Authors,

Thanks for the great tool. I am using this tool to assemble de novo vertebrate genome. I got the following file after running
juicer pre -a -o out_JBAT hic-to-contigs.bin scaffolds_final.agp contigs.fa.fai >out_JBAT.log 2>&1 ' and got 5 files: out_JBAT.txt
out_JBAT.liftover.agp
out_JBAT.assembly
out_JBAT.assembly.agp
out_JBAT.log `

After running ` java -jar -Xmx32G juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part <(cat out_JBAT.log | grep PRE_C_SIZE | awk '{print $2" "$3}')) && (mv out_JBAT.hic.part out_JBAT.hic ' I got following error

Skipping PRE_C_SIZE: assembly 553400379 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)

Could you please suggest any solution for this

Thank you
Vinita

[c-zhou]

Hi Vinita,

It looks to me like the command cat out_JBAT.log | grep PRE_C_SIZE | awk '{print $2" "$3}' in your system generated output PRE_C_SIZE: assembly 553400379 instead of assembly 553400379 for which I am not sure why. You can double-check if this is the case.

A clearer way to run the command is to generate a chromosome size file and feed it into juicerbox, i.e., cat out_JBAT.log | grep PRE_C_SIZE | awk '{print $2" "$3}' >chrom.sizes and then (java -jar -Xmx32G juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part chrom.sizes) && (mv out_JBAT.hic.part out_JBAT.hic). Make sure the content of the chrom.sizes file is assembly 553400379. If awk does not work in your system, you can simply do echo "assembly 553400379" >chrom.sizes.

Best,
Chenxi

[vinitamehlawat]

Hi @c-zhou

Thanks for your prompt respose. I tried what you have suggest in above thread and I guess it worked. Could you please confirm if this looks fine or something is not correct in this step.

I got following print message:
java -jar -Xmx32G /home/vlamba/juicer/PBS/scripts/juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part chrom.sizes && mv out_JBAT.hic.part out_JBAT.hic

Not including fragment map
Start preprocess
Writing header
Writing body
..
Writing footer

Finished preprocess

Calculating norms for zoom BP_2500000
Calculating norms for zoom BP_1000000
Calculating norms for zoom BP_500000
Calculating norms for zoom BP_250000
Calculating norms for zoom BP_100000
Calculating norms for zoom BP_50000
Calculating norms for zoom BP_25000
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Writing expected
Writing norms
Finished writing norms