3d-dna/visualize/juicebox_tools.sh: line 3: 180724 be killed
xiaobaiymq opened this issue · 4 comments
Hello sir
my command is “bsub -J 3d-dna -n 5 -R span[hosts=1] -o %J.out -e %J.err -q q2680v2 "module purge ;module load BWA/0.7.17;run-asm-pipeline.sh ../reference/nfmj.asm.hic.hap1.p_ctg.fa ../aligned/merged_nodups.txt" ”
but err is：
/public/home/mqyin/app/3d-dna/visualize/juicebox_tools.sh: 行 3: 180724 已杀死 java -Xms49152m -Xmx49152m -jar dirname $0/juicebox_tools.jar $*
Unable to dump
java.io.IOException: Normalization missing for: assembly_assembly_BP_25000
at juicebox.data.DatasetReaderV2.readNormalizedBlock(DatasetReaderV2.java:719)
at juicebox.data.MatrixZoomData.dump(MatrixZoomData.java:675)
at juicebox.tools.clt.old.Dump.dumpMatrix(Dump.java:282)
at juicebox.tools.clt.old.Dump.run(Dump.java:505)
at juicebox.tools.HiCTools.main(HiCTools.java:86)
已终止
I don't know why，can you help me ?
This suggest that the code wasn't able to build a normalization vector for your hic file. Usually this means that there are some big coverage issues, e.g. due the presence of non-nuclear contaminants, alt haplotypes, other. You can try to pass --editor_coarse_norm NONE when running run-3ddna-pipeline.sh. Best, -Olga
This suggest that the code wasn't able to build a normalization vector for your hic file. Usually this means that there are some big coverage issues, e.g. due the presence of non-nuclear contaminants, alt haplotypes, other. You can try to pass --editor_coarse_norm NONE when running run-3ddna-pipeline.sh. Best, -Olga
Dear developer
I also meet the problem due to the haplotigs in the genome.
When I using the parameter "--editor_coarse_norm NONE", it just shows no this parameter. And I read the file "run-asm-pipeline.sh" , also not find the parameter "--editor_coarse_norm NONE", should I use "--editor_coarse_resolution NONE" ?
Expect for your relpy
Thanks a lot!
@xiaobaiymq Thank you!