3d-dna: errors

[Zhichao]

I run 3d-dna pipeline as:

sh $soft/run-pipeline.sh -m diploid -s 2 -c 24 -t 10000 genome.fa p1.nodups.txt

gawk: software/3d-dna/scaffold/merge-scores.awk:42: fatal: division by zero attempted

java.lang.NumberFormatException: For input string: "ST-E00310:387:H3VFCCCXY:3:1105:9374:23811/2"

        at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

        at java.lang.Integer.parseInt(Integer.java:580)

        at java.lang.Integer.parseInt(Integer.java:615)

        at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:148)

        at juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:194)

        at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:493)

        at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:371)

        at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:283)

        at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:108)

        at juicebox.tools.HiCTools.main(HiCTools.java:86)

Could not read hic file: null

:( Juicebox dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!

Could not read hic file: null

:( Juicebox coverage dump is empty! Perhaps something is wrong with the hic file or the requested resolution is too high. Exiting!

mv: cannot stat 'depletion_score_wide.wig': No such file or directory

mv: cannot stat 'depletion_score_narrow.wig': No such file or directory

mv: cannot stat 'mismatch_wide.bed': No such file or directory

mv: cannot stat 'mismatch_narrow.bed': No such file or directory

mv: cannot stat 'coverage_wide.wig': No such file or directory

mv: cannot stat 'repeats_wide.bed': No such file or directory

cat: mismatch_narrow.at.step.0.bed: No such file or directory

cat: repeats_wide.at.step.0.bed: No such file or directory

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

Signal 18 (CONT) caught by ps (procps version 3.2.8).

gawk: /public/agis/ruanjue_group/wuzhichao/software/3d-dna/scaffold/merge-scores.awk:42: fatal: division by zero attempted

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

Can you help me? What made the pipeline cannot read hic file ? and why mv and cat cannot find files ?

What should I do now?

Thank you very much !

[Olga Dudchenko]

Hello Zhichao,

It is difficult with so little information to infer what is going on. The division by zero is not an error but a poorly handled exit scenario that occasionally happens, so it by itself does not necessarily point to a problem. What round of editing is this happening at? is what you are showing the full output or just a subset around the occurring error? If it is the full output this suggest that the even the scaffolder does not launch. What does your mnd file? The mv errors do not matter: these are consequences of the .hic file not being created and editor failing to execute. You can ignore the warnings: these are listed for the unlikely chance that your read names contain strings like these in the original names which would mess us with keeping track of the edits.

Best,
Olga