Java error while running juicer_tools pre

[Moshe Olshansky]

Hello,

I got the below strange error while attempting creating hic files. Let me note that it happens for one file only (others are created all right) and it happens both with the most recent (juicer_tools.1.8.9_jcuda.0.8.jar) and older (juicer_tools_linux_0.8.jar) versions of juicer tools.

So below is what happens:

java -jar ../juicer_tools.1.8.9_jcuda.0.8.jar pre -r 5000,10000,20000,40000,100000,500000,1000000 DP_Satb1/Lib7/r3/aligned/merged_nodups.txt DP_Satb1/Lib7/r3/aligned/inter.hic chrom_mm10.sizes

Not including fragment map

Start preprocess

Writing header

Writing body

java.lang.NumberFormatException: For input string: "60TTACGTTTTGAAAAAAAAAAAAGT"

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:223)

at juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:270)

at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:505)

at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:383)

at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:293)

at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:105)

at juicebox.tools.HiCTools.main(HiCTools.java:96)

and

java -jar ../juicer_tools_linux_0.8.jar pre -r 5000,10000,20000,40000,100000,500000,1000000 DP_Satb1/Lib7/r3/aligned/merged_nodups.txt DP_Satb1/Lib7/r3/aligned/inter.hic chrom_mm10.sizes

Not including fragment map

Start preprocess

Writing header

Writing body

java.lang.NumberFormatException: For input string: "60TTACGTTTTGAAAAAAAAAAAAGT"

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)

Thank you,

Moshe.

[Neva Durand]

Looks like a corrupt merged_nodups file; one of the fields that it expects to be an integer (position, fragment, or mapq) is instead that string.  From the string itself I suspect it's mapq.  I would grep that string in your merged_nodups and eliminate that line.

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[Moshe Olshansky]

Hi Neva,

Thank you for your response.

You are right. I also thought about such possibility (but only after I sent the post...) and yes, the merded_nodups.dups file contains the below line:
74821257:0 chr18 67707520 159961 16 chr18 67707877 159962 60TTACGTTTTGAAAAAAAAAAAAGT 60 74M TTTAAAAATAGGTGACACAGAATCAAGTTAGACTAAAGATTAACGGGAATCTGAGGATAGCATGTCCTTAGGAT NB551334:34:HV7FHBGX5:1:11203:1856:1946/2 NB551334:34:HV7FHBGX5:1:11203:1856:1946/1
i.e. there is no space/tab between 60 and TTACGTTTTGAAAAAAAAAAAAGT.
But merged_sorted.txt does not have this. So this is either a bug in dups.awk or it is a disk failure on our server. I will run dups.awk again and see what happens.

Best regards,
Moshe.

[Moshe Olshansky]

Hi Neva,

I ran dups.awk again and everything was OK. So it looks like disk/memory fault on our server. Sorry for disturbance.

On Friday, May 25, 2018 at 7:08:43 PM UTC+10, Moshe Olshansky wrote: