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12/19/25

Index 3 out of bounds for length 2 Error

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2025-12-18T18:30:08780] [Globals.java:138] [main] Development mode

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Index 3 out of bounds for length 2 Error

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2025-12-18T18:30:08780] [Globals.java:138] [main] Development mode

12/19/25

Zihao Zhu, Moshe Olshansky8

5/17/25

speeding up processing for a large input file

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>>>> will impact performance. >>>>> WARN [2025-04-30T01:14:38420

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speeding up processing for a large input file

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>>>> will impact performance. >>>>> WARN [2025-04-30T01:14:38420

5/17/25

Samuel Kean, Beisi Xu2

4/3/25

Empty .hic file using Juicer pre

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2025-02-19T14:23:13307] [Globals.java:138] [main] Development

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Empty .hic file using Juicer pre

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2025-02-19T14:23:13307] [Globals.java:138] [main] Development

4/3/25

10/11/24

Error: the chromosome combination 1_2 appears in multiple blocks

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2024-10-11T11:26:11814] [Globals.java:138] [main] Development

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Error: the chromosome combination 1_2 appears in multiple blocks

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2024-10-11T11:26:11814] [Globals.java:138] [main] Development

10/11/24

Saumya, … Aditya Shrivastava8

8/22/24

eigenvector output file is empty

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>>> will impact performance. >>>> WARN [2024-04-15T20:17:46201] [Globals

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eigenvector output file is empty

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>>> will impact performance. >>>> WARN [2024-04-15T20:17:46201] [Globals

8/22/24

Rahul Kumar, … Krithika B5

8/8/24

Error in running hiccupsdiff

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >> will impact performance. >> >> WARN [2023-05-09T09:13:21906] [Globals.java

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Error in running hiccupsdiff

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >> will impact performance. >> >> WARN [2023-05-09T09:13:21906] [Globals.java

8/8/24

Sara Oppenheim, Olga Dudchenko4

6/21/24

visualizer format issue "Unexpected column count"

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>> will impact performance. >>> WARN [2024-03-24T15:48:31491] [Globals.java

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visualizer format issue "Unexpected column count"

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>> will impact performance. >>> WARN [2024-03-24T15:48:31491] [Globals.java

6/21/24

4/17/24

problem generating hic file using pre command

: > sun.reflect.Reflection.getCallerClass is not supported. This will impact > performance. > WARN [2024-04-15T11:17:15400] [Globals.java:138] [main] Development

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problem generating hic file using pre command

: > sun.reflect.Reflection.getCallerClass is not supported. This will impact > performance. > WARN [2024-04-15T11:17:15400] [Globals.java:138] [main] Development

4/17/24

4/16/24

Issue with Juicer Tools Pre: "Unable to find All-All or All-All"

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This > will impact performance.Skipping >chr1Skipping > NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNSkipping

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Issue with Juicer Tools Pre: "Unable to find All-All or All-All"

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This > will impact performance.Skipping >chr1Skipping > NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNSkipping

4/16/24

1/19/24

Getting Chromosome Error - Eigenvector tool

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.WARN [2024-01-19T11:59:09921] [Globals.java:138] [main] Development mode

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Getting Chromosome Error - Eigenvector tool

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.WARN [2024-01-19T11:59:09921] [Globals.java:138] [main] Development mode

1/19/24

不息淑, … Nasreen Bano5

12/18/23

Error when generating hic file

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-12-18T11:04:30987] [Globals.java:138] [main] Development mode

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Error when generating hic file

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-12-18T11:04:30987] [Globals.java:138] [main] Development mode

12/18/23

12/7/23

juicer2 mega map mega.sh mega_from_bams.sh error

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. Using 24 CPU thread(s) for primary task Using 10 CPU thread(s) for secondary task

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juicer2 mega map mega.sh mega_from_bams.sh error

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. Using 24 CPU thread(s) for primary task Using 10 CPU thread(s) for secondary task

12/7/23

abdullah padana, Olga Dudchenko2

9/8/23

After manual correction of juicebox convert to fasta

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2023-09-07T20:51:58793] [Globals.java:138] [main] Development

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After manual correction of juicebox convert to fasta

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2023-09-07T20:51:58793] [Globals.java:138] [main] Development

9/8/23

5/8/23

juicer tools dump demo isn't workiing

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2023-05-08T10:01:38763] [Globals.java:138] [main] Development

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juicer tools dump demo isn't workiing

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2023-05-08T10:01:38763] [Globals.java:138] [main] Development

5/8/23

Marine Bergot, … Nastya Gridasova9

4/17/23

Error: the chromosome combination 1_3 appears in multiple blocks

. On Sun, Apr 16, 2023 at 10:52 AM 'AM' via 3D Genomics <3d-genomics@googlegroups.com> wrote: Hi Moshe, How can I deal with this problem if I have pairs.gz file (porec_test

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Error: the chromosome combination 1_3 appears in multiple blocks

. On Sun, Apr 16, 2023 at 10:52 AM 'AM' via 3D Genomics <3d-genomics@googlegroups.com> wrote: Hi Moshe, How can I deal with this problem if I have pairs.gz file (porec_test

4/17/23

3/5/23

addNorm Exception msg at higher resolution

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2023-03-05T10:24:57574] [Globals.java:138] [main] Development

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addNorm Exception msg at higher resolution

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2023-03-05T10:24:57574] [Globals.java:138] [main] Development

3/5/23

3/5/23

eigenvector terminating abruptly

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-03-05T20:17:46201] [Globals.java:138] [main] Development mode

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eigenvector terminating abruptly

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-03-05T20:17:46201] [Globals.java:138] [main] Development mode

3/5/23

Alexander Predeus, Olga Dudchenko5

2/10/23

Arima Hi-C experiment - check if restriction map was included?

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2023-01-20T01:47:19086] [Globals.java:138] [main] Development

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Arima Hi-C experiment - check if restriction map was included?

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2023-01-20T01:47:19086] [Globals.java:138] [main] Development

2/10/23

1/13/23

juicer APA problem：APA diagram is blank

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.* *WARN [2023-01-13T17:14:31988] [Globals.java:138] [main] Development

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juicer APA problem：APA diagram is blank

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.* *WARN [2023-01-13T17:14:31988] [Globals.java:138] [main] Development

1/13/23

Alex van Rensburg, Olga Dudchenko2

10/27/22

Error converting out_JBAT.txt to out_JBAT.hic

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2022-10-26T13:44:02788] [Globals.java:138] [main] Development

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Error converting out_JBAT.txt to out_JBAT.hic

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2022-10-26T13:44:02788] [Globals.java:138] [main] Development

10/27/22

zhengdafangyuan zhong, … Shawn Bai5

10/19/22

APA problem: Loop list is empty or incorrect path provided.

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>>> will impact performance. >>>> WARN [2022-01-11T21:02:43339] [Globals

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APA problem: Loop list is empty or incorrect path provided.

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>>> will impact performance. >>>> WARN [2022-01-11T21:02:43339] [Globals

10/19/22

HT Chung, Moshe Olshansky2

8/14/22

Create_hic error "sun.reflect.Reflection.getCallerClass"

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2022-08-08T00:30:19474] [Globals.java:138] [main] Development

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Create_hic error "sun.reflect.Reflection.getCallerClass"

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2022-08-08T00:30:19474] [Globals.java:138] [main] Development

8/14/22

8/10/22

create_hic error WARNING: sun.reflect.Reflection.getCallerClass

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2022-08-08T00:30:19474] [Globals.java:138] [main] Development mode

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create_hic error WARNING: sun.reflect.Reflection.getCallerClass

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2022-08-08T00:30:19474] [Globals.java:138] [main] Development mode

8/10/22

Muhammad Shamim, … Moshe Olshansky15

6/19/22

Re: JUICER issues at the end of the pipeline

Hi Levi, Thank you for your help and explanations. On Thursday, June 16, 2022 at 5:49:39 AM UTC+10 Levi Bauer wrote: > Hi Lia, > I may be

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Re: JUICER issues at the end of the pipeline

Hi Levi, Thank you for your help and explanations. On Thursday, June 16, 2022 at 5:49:39 AM UTC+10 Levi Bauer wrote: > Hi Lia, > I may be

6/19/22

Moshe Olshansky

4/3/22

Re: Either inter.hic or inter_30.hic were not created

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > Using 1 CPU thread(s) for primary task > Picked up _JAVA_OPTIONS

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Re: Either inter.hic or inter_30.hic were not created

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > Using 1 CPU thread(s) for primary task > Picked up _JAVA_OPTIONS

4/3/22

Kristy Mualim, Moshe Olshansky2

4/3/22

Trouble processing new ENCODE Hi-C files using juicer_tools

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2022-03-14T11:50:10708] [Globals.java:138] [main] Development

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Trouble processing new ENCODE Hi-C files using juicer_tools

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > > WARN [2022-03-14T11:50:10708] [Globals.java:138] [main] Development

4/3/22

Nolan Ruffenach2

3/29/22

inter.hic and inter_30.hic issues & inter_30_loops could not be parsed

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > Using 1 CPU thread(s) for primary task > Picked up _JAVA_OPTIONS

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inter.hic and inter_30.hic issues & inter_30_loops could not be parsed

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > Using 1 CPU thread(s) for primary task > Picked up _JAVA_OPTIONS

3/29/22

Sang-ah Park, Muhammad Shamim3

12/21/21

Juicer tools version 1 and 2? : java.lang.NullPointerException

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >> will impact performance. >> WARN [2021-11-19T15:35:12108] [Globals.java:138] [main

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Juicer tools version 1 and 2? : java.lang.NullPointerException

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >> will impact performance. >> WARN [2021-11-19T15:35:12108] [Globals.java:138] [main

12/21/21

picas...@gmail.com, Olga Dudchenko2

9/14/21

Bad scaffolding. What others parameters can I tweak ?

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2021-09-03T17:22:07489] [Globals.java:138] [main] Development

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Bad scaffolding. What others parameters can I tweak ?

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will > impact performance. > WARN [2021-09-03T17:22:07489] [Globals.java:138] [main] Development

9/14/21

Zhang Cheng, … Tom5

8/4/21

generating ,hic for big files: java heap space error

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>> will impact performance. >>> WARN [2020-08-31T13:58:39546] [Globals.java

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generating ,hic for big files: java heap space error

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This >>> will impact performance. >>> WARN [2020-08-31T13:58:39546] [Globals.java

8/4/21

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