aidenlab/3d-dna

Issues

• To speed up post review you can use this script

  #190 opened a month ago by Isoris
  0

• error when run the run-asm-pipeline-post-review.sh, the final.fasta was too small

  #179 opened a year ago by Jiangjiangzhang6
  8

• Incorrect information about the option "--gap-size"

  #189 opened 2 months ago by shelkmike
  0

• temp. genome.0.asm _ mnd.txt does not exist or does not contain any reads

  #165 opened 2 years ago by cui-yutong
  2

• Error reading datasetnull

  #188 opened 3 months ago by fisisi
  0

• Unrecognized value for mode flag. Running with default parameters

  #187 opened 4 months ago by dupuquan
  0

• No FINAL* files created.

  #186 opened 5 months ago by Yang-xia13
  0

• No FINAL* files created.

  #159 opened 2 years ago by Jung19911124
  9

• some question about parameters

  #185 opened 7 months ago by oddguyeee
  0

• Could not read hic file: null ,error with run-asm-pipeline.sh

  #144 opened 3 years ago by Zoey1001
  4

• No result file is generated

  #184 opened 8 months ago by zhangyuxin1012
  0

• :( Annotations span several contigs. Exiting!

  #183 opened 8 months ago by ZKYthli
  1

• Enhancement Request: Handling Telomeric Segments During 3D-DNA Correction and Potential Strategies to Prevent Trimming

  #182 opened 8 months ago by Hanjiangna
  0

• What is the difference between 0.hic, 0.assembly and rawchrom.hic, rawchrom.assembly?

  #168 opened 2 years ago by XXH123a
  0

• ask forhelp ： error when run run-asm-pipeline.sh

  #180 opened 10 months ago by Jiangjiangzhang6
  5

• Not including fragment map and not geneated the final fasta file use the run-asm-pipeline-post-review

  #178 opened a year ago by Jiangjiangzhang6
  3

• syntax error with run-assembly-visualizer.sh

  #181 opened 9 months ago by MY0NEMA
  0

• 3d-dna pipeline to scaffolding a hifiasm heterozygous assembly

  #156 opened 2 years ago by ericgonzalezs
  3

• Abnormal size of *.0.hic

  #173 opened a year ago by linshengnan09
  5

• Failed at visualize stage to generate the .hic file. Out of memory issues.

  #152 opened 2 years ago by Zahnhh
  6

• .Exception in thread "main" java.lang.OutOfMemoryError: Java heap space and GC overhead limit exceeded

  #177 opened a year ago by zhangna123-ux
  0

• chromosome contains which contigs after run run-asm-pipeline-post-review.sh.

  #176 opened a year ago by sumoii
  0

• Unknown error: ERROR [2023-11-15 12:16:26,414] [DatasetReaderV2.java:229] [main] Error reading dataset java.io.EOFException

  #175 opened a year ago by SwenDiepstraten
  0

• error with run-asm-pipeline-post-review.sh

  #174 opened a year ago by yangyyhh
  0

• Hifi and ONT behave differently in 3D-DNA(same species)

  #172 opened a year ago by anxuan-web
  2

• very fragmented draft genome

  #171 opened 2 years ago by sqwwww
  0

• error: java not available

  #167 opened 2 years ago by dandanWang2019
  5

• How to obtain a temporary gene.final.fasta?

  #166 opened 2 years ago by XXH123a
  6

• I have a hap_ctg.fa file with 4.5G, used juicer I got 52.31G merged_nodups_txt,then I used 3D-DNA run-asm-pipeline.sh, I only got 55.72M final.hic file

  #169 opened 2 years ago by wyl1219
  4

• current 3D-DNA version

  #170 opened 2 years ago by dustin-cram
  2

• .assembly

  #146 opened 2 years ago by Jwindler
  1

• HiC resolution issue: Unable to dump

  #161 opened 2 years ago by AzumaSerenThePatriot
  1

• How to obtain input mnd file from juicer2 output file？

  #164 opened 2 years ago by XuanZhang-Black
  1

• No hic output

  #163 opened 2 years ago by Donbbit
  0

• sort: write failed: /home/sdc/3ddna/HIC_tmp/sorty4gvbq: Input/output error

  #162 opened 2 years ago by Biscuite-wzy
  1

• link coverage file extraction

  #160 opened 2 years ago by chklopp
  1

• the problem of "no left space on the disk" when running 3D-DNA

  #158 opened 2 years ago by yxhuu
  0

• issues about finalizing with run-asm-pipeline-post-review.sh

  #149 opened 3 years ago by zjuzexian
  4

• Fragmented scaffolds - large and repetitive genome

  #157 opened 2 years ago by sighe
  1

• lift-input-annotations-to-asm-annotations.awk 2D annotation file

  #155 opened 2 years ago by chun-he-316
  0

• lift-input-annotations-to-asm-annotations.awk: line 108: regular expression compile failed (syntax error ^* or ^+)

  #154 opened 2 years ago by chun-he-316
  0

• overlong scaffold

  #153 opened 2 years ago by wangyzh
  0

• No final.hic file generated

  #151 opened 3 years ago by ithacajing
  5

• tail: +: invalid number of bytes with run-asm-pipeline.sh in haploid mode

  #150 opened 3 years ago by Neo-xbx-00
  4

• 3d-dna/visualize/juicebox_tools.sh: line 3: 180724 be killed

  #143 opened 3 years ago by xiaobaiymq
  4

• Extract contig to contig link counts from Hi-C file

  #148 opened 3 years ago by chklopp
  0

• Syntax error - awk

  #147 opened 3 years ago by ddelgadillod
  3

• MERGING step seems not using GNU parallel?

  #145 opened 3 years ago by wangc1106
  2

• HiFi and Nanopore behave differently in 3D DNA (due to different draft assembly sizes)

  #141 opened 3 years ago by kuangzhuoran
  1

• I have assembled three genomes at the same time, and they have stayed in one place for a long time

  #142 opened 3 years ago by kuangzhuoran
  1