Syntax error - awk

[ddelgadillod]

Hi

I tried to run 3d-dna/visualize/run-assembly-visualizer.sh script in order to generate.hic file, input files like .assembly an .pairs were generated following Method II here specified, after it is running, appear an awk syntax error:

:) -p flag was triggered. Running with GNU Parallel support parameter set to false. ...Remapping contact data from the original contig set to assembly ...Building track files awk: Software/3d-dna/lift/lift-input-annotations-to-asm-annotations.awk: line 108: regular expression compile failed (syntax error ^* or ^+) ^+ ...Building the hic file Not including fragment map java.lang.ArithmeticException: / by zero at juicebox.tools.utils.original.ExpectedValueCalculation.<init>(ExpectedValueCalculation.java:130) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:247) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:108) at juicebox.tools.HiCTools.main(HiCTools.java:86)

Does anyone have an idea how to solve this?

[dudcha]

3D-DNA does not take “pairs" as input. Please see Genome Assembly Cookbook for instructions on how to use the tools. -Olga

On Apr 5, 2022, at 2:12 PM, ddelgadillod @.***> wrote:

Hi

I tried to run 3d-dna/visualize/run-assembly-visualizer.sh script in order to generate.hic file, input files like .assembly an .pairs were generated following Method II here specified, after it is running, appear an awk syntax error:

:) -p flag was triggered. Running with GNU Parallel support parameter set to false. ...Remapping contact data from the original contig set to assembly ...Building track files awk: Software/3d-dna/lift/lift-input-annotations-to-asm-annotations.awk: line 108: regular expression compile failed (syntax error ^* or ^+) ^+ ...Building the hic file Not including fragment map java.lang.ArithmeticException: / by zero at juicebox.tools.utils.original.ExpectedValueCalculation.(ExpectedValueCalculation.java:130) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:247) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:108) at juicebox.tools.HiCTools.main(HiCTools.java:86)

Does anyone have an idea how to solve this?

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[ddelgadillod]

Hi I used the following to convert pairs to link files:

`

Convert .pair file to merged_nodups.txt formats

grep -v '#' aln.pairs | \ awk '{if($6!="+") $6=16; else $6=0; if($7!="+") $7=16; else $7=0} \ $2<=$4{print $6, $2, $3, 0, $7, $4, $5, 1, "1 - - 1 - - -" } \ $4<$2{print $7, $4, $5, 0, $6, $2, $3, 1, "1 - - 1 - - -" }' > out.links.txt `

Is the last procedure correct?

[dudcha]

The pair file is not our file format, I do not know it’s structure and a such cannot help with the conversion. Please see the cookbook for instructions on how to prepare the input. Thanks, -Olga

On Apr 5, 2022, at 2:19 PM, ddelgadillod @.***> wrote:

Hi I used the following to convert pairs to link files:

`

Convert .pair file to merged_nodups.txt formats

grep -v '#' aln.pairs | awk '{if($6!="+") $6=16; else $6=0; if($7!="+") $7=16; else $7=0} $2<=$4{print $6, $2, $3, 0, $7, $4, $5, 1, "1 - - 1 - - -" } $4<$2{print $7, $4, $5, 0, $6, $2, $3, 1, "1 - - 1 - - -" }' > out.links.txt `

Is the last procedure correct?

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