Assembly file contains multiple entries of the same contig. Exiting!

[Zhaoxi Liu]

Hello everyone,

When I run <run-asm-pipeline.sh> using this  command "run-asm-pipeline.sh -r 5 -m diploid --editor-coarse-norm "NONE" ../references/mel_contigs_pilon.fasta ../aligned/merged_nodups.txt  "

 I got this errer "  :( Assembly file contains multiple entries of the same contig. Exiting! "

and also " tail: +: invalid number of bytes

tail: +: invalid number of bytes

tail: +: invalid number of bytes

…… "

the vesion is 3d-dna/190716

Although it seems that I got all the files including rawchrom.hic and final .assembly and so on, when I use JBAT to open them, there are not large scaffolds but small fragments.  The scaffolds are even smaller than the contigs before the assembly. Could you tell me what the problems are? thanks a lot !!!

Best wishes, 

Zhaoxi

[Zhaoxi Liu]

[Olga Dudchenko]

Hi Liu,

Please note that we no longer offer support to the diploid workflow. You'd have to use legacy versions if you want to run in diploid mode, and I would not certainly assume it from the getgo.

Before moving on to reviewing rawchrom files our recommendation is always to examine .0.hic files and tracks.

Apologies for the delayed response.

Thanks,

Olga

On Friday, July 30, 2021 at 3:18:56 AM UTC-5 liuzha...@gmail.com wrote:

[Zhaoxi Liu]

Hi  Dudchenko，

Thank you for your advice!

We realized the serious undercollapsed heterozygocity and changed the assembly software HiCanu to wtdbg2 to reassemble the contigs. And then we used the haploid mode of 3D-DNA to scaffold. Now the problems have been solved.

Thanks again and best wishes.

Zhaoxi