Hybrid_scaffolds assembly issue

[Sparkle-27]

Hi

I recently ran into a problem when running hybridScaffold.pl script, job stopped in align0 step without any error information, scripts as following:

Do you have any suggestion for these? Thanks in advance.

[yuxuanyuan]

Hi,

Have you tried 'runBNG hybrid'?

Cheers, Andy

[Sparkle-27]

Hi Thanks for the software, I have successfully run denovo pipeline,but no CMAP result have been generated. Where could I find the denovo result? Thx

[yyx8671]

You may find the 'EXP_REFINEFINAL1.cmap' file at ./contigs/exp_refineFinal1

[Sparkle-27]

@yyx8671 Hi I could only find ./contigs/exp_unrefined/, multiple cmap file exist in the folder, Should I merge all the exp_unrefined_contig***.cmap files and how could i do that. Thx

[yyx8671]

@huanfa If you run 'runBNG denovo' successfully, the contigs folder will contain some folders like:

May I please ask if you use the runBNG required Bionano tools and scripts?

Cheers, Andy

[Sparkle-27]

Hi @yyx8671 Thanks for your help, I have run the de novo pipeline successfully, but new error appears in hybrid step. Do you have any suggestions? Thx.

[yyx8671]

@huanfa May I please know your settings in 'runBNG hybrid'?

[yyx8671]

@ Can you try ‘-B 1 -N 2’ ? or you may want to tune '-c -u -g -d and -p'

[Sparkle-27]

@yyx8671 Hi, thanks for the suggestions, I have tried '-B 1 N 2' and '-B 1 -N 1', but same error appeared. I guess parameters is not the reason why error appears. Is my input file format wrong? I have no idea, thanks a lot.

[yyx8671]

@huanfa Can you try to align your assembled cmap file to your NGS assembly using Irysview and to see if the quality of the BNG denovo assembly is good?

[Sparkle-27]

Hi @yyx8671 I have successfully run the pipeline, Thanks for your patient reply, I found the script download from the website you provided /scripts/HybridScaffold/scripts/perl5/BNG/Utility.pm is different from Solve software