[BUG] java develpment mode error

[ABDULLAHGUJJAR]

hi Juicerbox team, i am trying to use juicer pre for juicerbox files. i am facing this error. please anybody can guide me. Thanks

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-05-23T06:00:01,593] [Globals.java:138] [main] Development mode is enabled.

[sa501428]

This is a warning but should not cause anything to fail/ exit. What are you trying to do?

On Tue, May 23, 2023, 7:22 AM Muhammad Abdullah @.***> wrote:

hi Juicerbox team, i am trying to use juicer pre for juicerbox files. i am facing this error. please anybody can guide me. Thanks

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-05-23T06:00:01,593] [Globals.java:138] [main] Development mode is enabled.

— Reply to this email directly, view it on GitHub https://github.com/aidenlab/Juicebox/issues/1010, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABRT23POLY7ATANYMQWCWRLXHSTZZANCNFSM6AAAAAAYLZ4QOQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[ABDULLAHGUJJAR]

Hi Dear Saad, I am getting this error, after that I am not getting output for juicebox [04/55f2c5] process > PRINT_VERSIONS [100%] 1 of 1, cached: 1 ✔ [a1/8933f7] process > SAMTOOLS_FAIDX (1) [100%] 1 of 1, cached: 1 ✔ [62/69386f] process > CHROMAP_INDEX (1) [100%] 1 of 1, cached: 1 ✔ [ef/d55389] process > CHROMAP_ALIGN (1) [100%] 1 of 1, cached: 1 ✔ [15/78602f] process > YAHS_SCAFFOLD (1) [100%] 1 of 1, cached: 1 ✔ [78/3fede9] process > JUICER_PRE (1) [100%] 1 of 1, failed: 1 ✘ [24/196ac9] process > ASSEMBLY_STATS (1) [100%] 1 of 1, cached: 1 ✔ Error executing process > 'JUICER_PRE (1)'

Caused by: Process JUICER_PRE (1) terminated with an error exit status (1)

Command executed:

juicer pre -a -o out_JBAT yahs.out.bin yahs.out_scaffolds_final.agp contigs.fa.fai

asm_size=$(awk '{s+=$2} END{print s}' contigs.fa.fai) java -Xmx36G -jar /scratch/project/qaafi-cnafs/abdullah.WRB.HASLR/check/juicer_tools_1.22.01.jar pre out_JBAT.txt out_JBAT.hic <(echo "assembly ${asm_size}")

Command exit status: 1

Command output: WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-05-24T20:17:23,608] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body .

Command error: [I::main_pre] make juicer pre input from BIN file yahs.out.bin [I::make_juicer_pre_file_from_bin] 195631424 read pairs processed [I::main_pre] genome size: 403126564 [I::main_pre] scale factor: 1 [I::main_pre] chromosome sizes for juicer_tools pre - PRE_C_SIZE: assembly 403126564 [I::main_pre] JUICER_PRE CMD: java -Xmx36G -jar ${juicer_tools} pre out_JBAT.txt out_JBAT.hic <(echo "assembly 403126564") [I::main_pre] Version: 1.1 [I::main_pre] CMD: juicer pre -a -o out_JBAT yahs.out.bin yahs.out_scaffolds_final.agp contigs.fa.fai [I::main_pre] Real time: 33.716 sec; CPU: 33.412 sec; Peak RSS: 0.002 GB WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-05-24T20:17:23,608] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body .Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.base/java.lang.StringLatin1.newString(StringLatin1.java:715) at java.base/java.lang.String.substring(String.java:1879) at java.base/java.lang.String.subSequence(String.java:1913) at java.base/java.util.regex.Pattern.split(Pattern.java:1271) at java.base/java.lang.String.split(String.java:2317) at java.base/java.lang.String.split(String.java:2364) at juicebox.tools.clt.JuiceboxCLT.splitToList(JuiceboxCLT.java:47) at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:125) rk dirat juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:287) /scratat juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:673) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:425) p: youat juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:139) at juicebox.tools.HiCTools.main(HiCTools.java:94)

Work dir: /scratch/project_mnt/S0030/abdullah.WRB.HASLR/check/work/78/3fede93453ae13cce8532ff29fe7a6

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

I am using this nextflow script

https://github.com/WarrenLab/hic-scaffolding-nf.https://github.com/WarrenLab/hic-scaffolding-nf

Please check it. Thank you so much Regards Abdullah

From: Muhammad Saad Shamim @.> Sent: Wednesday, May 24, 2023 9:28 AM To: aidenlab/Juicebox @.> Cc: Muhammad Abdullah @.>; Author @.> Subject: Re: [aidenlab/Juicebox] [BUG] java develpment mode error (Issue #1010)

This is a warning but should not cause anything to fail/ exit. What are you trying to do?

On Tue, May 23, 2023, 7:22 AM Muhammad Abdullah @.<mailto:@.>> wrote:

hi Juicerbox team, i am trying to use juicer pre for juicerbox files. i am facing this error. please anybody can guide me. Thanks

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-05-23T06:00:01,593] [Globals.java:138] [main] Development mode is enabled.

— Reply to this email directly, view it on GitHub https://github.com/aidenlab/Juicebox/issues/1010, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABRT23POLY7ATANYMQWCWRLXHSTZZANCNFSM6AAAAAAYLZ4QOQ . You are receiving this because you are subscribed to this thread.Message ID: @.<mailto:@.>>

— Reply to this email directly, view it on GitHubhttps://github.com/aidenlab/Juicebox/issues/1010#issuecomment-1560253345, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHNHFM47DDSA5E4AYK2QYC3XHVBY3ANCNFSM6AAAAAAYLZ4QOQ. You are receiving this because you authored the thread.Message ID: @.**@.>>