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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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java error while running juicer on cluster #285

Open BijalThakkar opened 2 years ago

BijalThakkar commented 2 years ago

Dear Juicer team,

I am running HiC data using CPU version on our server system at Ugent. Can you tell me am i doing anything wrong here or is it a memory issue.

[Experiment]$ less 118/log.txt 

    at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:84)
    at juicebox.tools.HiCTools.main(HiCTools.java:96)

real 0m1.973s user 0m0.899s sys 0m0.394s Tue Jul 5 23:12:44 CEST 2022 Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m Not including fragment map Error while reading graphs file: java.io.FileNotFoundException: /data/gent/Test_Bijal/Experiment/118/aligned/inter_30_hists.m (No such file or directory) Start preprocess Writing header Writing body /data/gent/Test_Bijal/scripts/common/juicer_tools: line 24: 3590737 Killed java -Djava.awt.headless=true -Djava.library.path=dirname $0/lib64 -Ddevelopment=false -jar dirname $0/juicer_tools.jar $*

real 0m30.377s user 0m23.094s sys 0m9.693s Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m Error reading datasetnull java.io.EOFException at htsjdk.tribble.util.LittleEndianInputStream.readString(LittleEndianInputStream.java:119) at juicebox.data.DatasetReaderV2.read(DatasetReaderV2.java:127) at juicebox.tools.utils.original.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:78) at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:84) at juicebox.tools.HiCTools.main(HiCTools.java:96)

real 0m2.084s user 0m0.909s sys 0m0.367s /data/Test_Bijal/scripts/common/juicer_tools is post-processing Hi-C for hg19 Data read from /data/Test_Bijal/Experiment/118/aligned/inter_30.hic. Motifs read from /data/Test_Bijal/references/motif

ARROWHEAD:

Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m Exception in thread "main" jargs.gnu.CmdLineParser$IllegalOptionValueException: Illegal value '/data/Test_Bijal/Experiment/118/aligned/inter_30.hic' for option -z/--threads at jargs.gnu.CmdLineParser$Option$IntegerOption.parseValue(CmdLineParser.java:202) at jargs.gnu.CmdLineParser$Option.getValue(CmdLineParser.java:157) at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:485) at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:426) at juicebox.tools.HiCTools.main(HiCTools.java:61) ! Problem while running Arrowhead ! Error! Either inter.hic or inter_30.hic were not created Either inter.hic or inter_30.hic were not created. Check for results

i would appreciate if you look into this matter.

Regards Bijal Thakkar

Theo-wang0007 commented 2 years ago

I also encountered this problem when running ARROWHEAD. There is no "merged_nodups.txt" in aligned.

GrassW commented 1 year ago

I also encountered this problem when running ARROWHEAD. There is no "merged_nodups.txt" in aligned.

Hi, I met the problem of "no merged_nodups.txt", too. That is because I didn't use "-assembly" to produce "old style merged_nodups", as they said in the "--help". I guess you can either,

  1. Add "-assembly" when you restart to run juicer.sh .
  2. Execute this command line under the working folder, samtools view -@ ${ThreadsNum} -O SAM -F 1024 aligned/merged_dedup.*am | awk -v mnd=1 -f ${juiceDir}/scripts/sam_to_pre.awk > aligned/merged_nodups.txt , modified from line #1929 of SLURM/scripts/juicer.sh .

I choose 2 to save my time.