3d-dna

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Finilizing :tail: +: invalid number of bytes

27

Hi, I used 3d-dna to assembly genome, there were some strange outputs. **1**. The *FINAL.fasta file contain a lot of empty contigs, such as NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >HiC_scaffold_7 >HiC_scaffold_8 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...

xinkwu

No final.hic file generated

5

Hi, Here is my command and it took almost 28 days to finish. run-asm-pipeline.sh -m diploid -i 5000 --splitter-coarse-resolution 100000 --splitter-fine-resolution 1000 Perrie_HiC.asm.hic.p_ctg.fa merged_nodups.txt From *.rawchrom.fasta to get FINAL.fasta, it...

ithacajing

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

6

When I deal with a huge merged_nodups.txt file about 800G. There is an issue like '.Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded'. It happened at the visualize stage...

Zahnhh

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

4

Hello ! I hope for some solutions for my questions. My Bash version is: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu), and my 3d-dna version is version 180114. When running run-asm-pipeline.sh in...

Neo-xbx-00

Assembly file does not match cprops file. Exiting!

4

Hi, I'm currently trying to use 3d-dna (version 180922) to assemble a bird genome. The run-asm-pipeline.sh pipeline ran and generate almost all the .hic files except split stage. And, I...

fwlei123

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

4

Hi all, I meet a problem when finalizing the output after re-order the chromosome by juicer. And every time when after filling gaps. (finalize-output.sh) The program died with the temp.fasta...

zjuzexian

Hi, Is there a way to extract Hi-C link counts (per bin) using coordinate intervals and the .hic file?

chklopp

Syntax error - awk

3

Hi I tried to run 3d-dna/visualize/run-assembly-visualizer.sh script in order to generate.hic file, input files like .assembly an .pairs were generated following Method II here specified, after it is running, appear...

ddelgadillod

.assembly

1

Hi, i want to know the detail information about `.assembly ` file. For example, could you tell me some details like `.hic` data format. in my view, the `.assemly` file...

Jwindler

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

4

Dear developers, when i run the "run-asm-pipline.sh" ,encountered these errors and i hope you can give me some suggestions. nohup.out: temp.scaffolds.0.asm_mnd.txt does not exist or does not contain any reads....

Zoey1001