aidenlab / 3d-dna

3D de novo assembly (3D DNA) pipeline

aidenlab/3d-dna Issues

No FINAL* files created.
Updated 18 days ago
No FINAL* files created.
Updated 18 days ago9
some question about parameters
Updated 2 months ago
Could not read hic file: null ,error with run-asm-pipeline.sh
Updated 3 months ago4
No result file is generated
Updated 3 months ago
error when run the run-asm-pipeline-post-review.sh, the final.fasta was too small
Updated 3 months ago3
:( Annotations span several contigs. Exiting!
Updated 4 months ago1
Enhancement Request: Handling Telomeric Segments During 3D-DNA Correction and Potential Strategies to Prevent Trimming
Updated 4 months ago
What is the difference between 0.hic, 0.assembly and rawchrom.hic, rawchrom.assembly?
Updated 4 months ago
ask forhelp ： error when run run-asm-pipeline.sh
Updated 5 months ago5
Not including fragment map and not geneated the final fasta file use the run-asm-pipeline-post-review
Updated 5 months ago3
syntax error with run-assembly-visualizer.sh
Updated 5 months ago
3d-dna pipeline to scaffolding a hifiasm heterozygous assembly
Updated 5 months ago3
Abnormal size of *.0.hic
Updated 7 months ago5
Failed at visualize stage to generate the .hic file. Out of memory issues.
Updated 7 months ago6
.Exception in thread "main" java.lang.OutOfMemoryError: Java heap space and GC overhead limit exceeded
Updated 7 months ago
chromosome contains which contigs after run run-asm-pipeline-post-review.sh.
Updated 8 months ago
Unknown error: ERROR [2023-11-15 12:16:26,414] [DatasetReaderV2.java:229] [main] Error reading dataset java.io.EOFException
Updated 9 months ago
error with run-asm-pipeline-post-review.sh
Closed 9 months ago
Hifi and ONT behave differently in 3D-DNA(same species)
Updated a year ago2
very fragmented draft genome
Updated a year ago
error: java not available
Updated a year ago5
How to obtain a temporary gene.final.fasta?
Closed a year ago6
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
Updated a year ago4
current 3D-DNA version
Closed a year ago2
.assembly
Closed a year ago1
HiC resolution issue: Unable to dump
Closed a year ago1
How to obtain input mnd file from juicer2 output file？
Closed a year ago1
temp. genome.0.asm _ mnd.txt does not exist or does not contain any reads
Closed a year ago1
No hic output
Updated 2 years ago
sort: write failed: /home/sdc/3ddna/HIC_tmp/sorty4gvbq: Input/output error
Closed 2 years ago1
link coverage file extraction
Closed 2 years ago1
the problem of "no left space on the disk" when running 3D-DNA
Closed 2 years ago
issues about finalizing with run-asm-pipeline-post-review.sh
Updated 2 years ago4
Fragmented scaffolds - large and repetitive genome
Closed 2 years ago1
lift-input-annotations-to-asm-annotations.awk 2D annotation file
Updated 2 years ago
lift-input-annotations-to-asm-annotations.awk: line 108: regular expression compile failed (syntax error ^* or ^+)
Updated 2 years ago
overlong scaffold
Updated 2 years ago
No final.hic file generated
Updated 2 years ago5
tail: +: invalid number of bytes with run-asm-pipeline.sh in haploid mode
Updated 2 years ago4
3d-dna/visualize/juicebox_tools.sh: line 3: 180724 be killed
Closed 2 years ago4
Extract contig to contig link counts from Hi-C file
Updated 2 years ago
Syntax error - awk
Updated 2 years ago3
how t speed running the run-asm-pipeline.sh
Closed 2 years ago3
MERGING step seems not using GNU parallel?
Closed 2 years ago2
.Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
Closed 2 years ago2
HiFi and Nanopore behave differently in 3D DNA (due to different draft assembly sizes)
Closed 2 years ago1
I have assembled three genomes at the same time, and they have stayed in one place for a long time
Closed 2 years ago1
Truncated fasta headers
Closed 3 years ago1
Use 3d-dna to assist in assembling pacbio hifi data
Closed 3 years ago1