aidenlab 3d-dna issues - Githubissues

aidenlab / 3d-dna

3D de novo assembly (3D DNA) pipeline

MIT License

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issues

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

#189 shelkmike opened 2 weeks ago
0
Error reading datasetnull

#188 fisisi opened 2 months ago
0
Unrecognized value for mode flag. Running with default parameters

#187 dupuquan opened 2 months ago
0
No FINAL* files created.

#186 Yang-xia13 opened 4 months ago
0
some question about parameters

#185 oddguyeee opened 5 months ago
0
No result file is generated

#184 zhangyuxin1012 opened 6 months ago
0
:( Annotations span several contigs. Exiting!

#183 ZKYthli opened 7 months ago
1
Enhancement Request: Handling Telomeric Segments During 3D-DNA Correction and Potential Strategies to Prevent Trimming

#182 Hanjiangna opened 7 months ago
0
syntax error with run-assembly-visualizer.sh

#181 MY0NEMA opened 8 months ago
0
ask forhelp ： error when run run-asm-pipeline.sh

#180 Jiangjiangzhang6 opened 9 months ago
5
error when run the run-asm-pipeline-post-review.sh, the final.fasta was too small

#179 Jiangjiangzhang6 opened 10 months ago
7
Not including fragment map and not geneated the final fasta file use the run-asm-pipeline-post-review

#178 Jiangjiangzhang6 opened 10 months ago
3
.Exception in thread "main" java.lang.OutOfMemoryError: Java heap space and GC overhead limit exceeded

#177 zhangna123-ux opened 10 months ago
0
chromosome contains which contigs after run run-asm-pipeline-post-review.sh.

#176 sumoii opened 11 months ago
0
Unknown error: ERROR [2023-11-15 12:16:26,414] [DatasetReaderV2.java:229] [main] Error reading dataset java.io.EOFException

#175 SwenDiepstraten opened 1 year ago
0
error with run-asm-pipeline-post-review.sh

#174 yangyyhh closed 1 year ago
0
Abnormal size of *.0.hic

#173 linshengnan09 opened 1 year ago
5
Hifi and ONT behave differently in 3D-DNA(same species)

#172 anxuan-web opened 1 year ago
2
very fragmented draft genome

#171 sqwwww opened 1 year ago
0
current 3D-DNA version

#170 dustin-cram closed 1 year ago
2
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 wyl1219 opened 1 year ago
4
What is the difference between 0.hic, 0.assembly and rawchrom.hic, rawchrom.assembly?

#168 XXH123a opened 1 year ago
0
error: java not available

#167 dandanWang2019 opened 1 year ago
5
How to obtain a temporary gene.final.fasta?

#166 XXH123a closed 1 year ago
6
temp. genome.0.asm _ mnd.txt does not exist or does not contain any reads

#165 cui-yutong closed 1 year ago
2
How to obtain input mnd file from juicer2 output file？

#164 XuanZhang-Black closed 1 year ago
1
No hic output

#163 Donbbit opened 1 year ago
0
sort: write failed: /home/sdc/3ddna/HIC_tmp/sorty4gvbq: Input/output error

#162 Biscuite-wzy closed 1 year ago
1
HiC resolution issue: Unable to dump

#161 AzumaSerenThePatriot closed 1 year ago
1
link coverage file extraction

#160 chklopp closed 1 year ago
1
No FINAL* files created.

#159 Jung19911124 opened 2 years ago
9
the problem of "no left space on the disk" when running 3D-DNA

#158 yxhuu closed 2 years ago
0
Fragmented scaffolds - large and repetitive genome

#157 sighe closed 2 years ago
1
3d-dna pipeline to scaffolding a hifiasm heterozygous assembly

#156 ericgonzalezs opened 2 years ago
3
lift-input-annotations-to-asm-annotations.awk 2D annotation file

#155 chun-he-316 opened 2 years ago
0
lift-input-annotations-to-asm-annotations.awk: line 108: regular expression compile failed (syntax error ^* or ^+)

#154 chun-he-316 opened 2 years ago
0
overlong scaffold

#153 wangyzh opened 2 years ago
0
Failed at visualize stage to generate the .hic file. Out of memory issues.

#152 Zahnhh opened 2 years ago
6
No final.hic file generated

#151 ithacajing opened 2 years ago
5
tail: +: invalid number of bytes with run-asm-pipeline.sh in haploid mode

#150 Neo-xbx-00 opened 2 years ago
4
issues about finalizing with run-asm-pipeline-post-review.sh

#149 zjuzexian opened 2 years ago
4
Extract contig to contig link counts from Hi-C file

#148 chklopp opened 2 years ago
0
Syntax error - awk

#147 ddelgadillod opened 2 years ago
3
.assembly

#146 Jwindler closed 1 year ago
1
MERGING step seems not using GNU parallel?

#145 wangc1106 closed 2 years ago
2
Could not read hic file: null ,error with run-asm-pipeline.sh

#144 Zoey1001 opened 2 years ago
4
3d-dna/visualize/juicebox_tools.sh: line 3: 180724 be killed

#143 xiaobaiymq closed 2 years ago
4
I have assembled three genomes at the same time, and they have stayed in one place for a long time

#142 kuangzhuoran closed 2 years ago
1
HiFi and Nanopore behave differently in 3D DNA (due to different draft assembly sizes)

#141 kuangzhuoran closed 2 years ago
1
how t speed running the run-asm-pipeline.sh

#140 Aannaw closed 2 years ago
3