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

[wyl1219]

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: 3d-dna/run-asm-pipeline.sh -r 0 hap1234.fa merged_nodups.txt, then, I only got 55.72M final.hic file, in the final.fasta file, has some words: The length of fasta does not match that suggested by the cprops file. Exiting!
would you tell me what's wrong, thank you, wish you best.

[dudcha]

This is not sufficient description to offer any advice I am afraid. I would suggested providing a more thorough report. I would also suggest checking that your fasta does not have any hidden characters (return carriage e.g.). 3d-dna does not do well with those. -Olga

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On Apr 12, 2023, at 12:46 AM, wyl1219 ***@***.***> wrote: 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: 3d-dna/run-asm-pipeline.sh -r 0 hap1234.fa merged_nodups.txt, then, I only got 55.72M final.hic file, in the final.fasta file, has some words: The length of fasta does not match that suggested by the cprops file. Exiting! would you tell me what's wrong, thank you, wish you best. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[wyl1219]

ok ,I will try, thank you.

[wyl1219]

Hello, when I used run-assembly-visualizer.sh -q 0 kl.assembly kl_merged_nodups.txt, I got kl.hic, As shown below

Could you tell me what might be wrong? thanks.

[dudcha]

I suspect you have issues with your alignment. If you used Juicer I suggest you take a look at the logs, and check the part where you generated restriction enzyme file. -Olga