Closed ohan-Bioinfo closed 1 year ago
Hello @ohan-Bioinfo,
Apologies for the delay in getting back to you - I was on vacation last week.
A couple initial questions to help with troubleshooting:
ntJoin
command? (I just see the ntjoin_assemble.py
command there)Thank you for your interest in ntJoin! Lauren
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in ntJoin!
Hello, @lcoombe,
thank's for this great tool, it's awsome. I have the same error when trying to scaffold an assembly using a bacterial ncbi reference genome containing a chromosome and a plasmid sequence.
Heres is the command I used:
$ for assembly in *fasta; do ../ntJoin-1.1.1/ntJoin assemble target=${assembly} target_weight=1 reference_config=config_file.csv k=32 w=500; done
Thanks in advance.
Cheers,
Jaime
EDIT:
I was able to run ntJoin previously with other reference without trouble.
EDIT2:
I got the solution, based on the parameter considerations that you recommend setting the reference weight(s) to be higher than the target weight, unless you trust each of the input references and target equally, it has to be this way, at least for me. I modified the config file, setting the weight of the reference from 2 to 1 and the command I used was:
$ for assembly in *fasta; do ../ntJoin-1.1.1/ntJoin assemble target=${assembly} target_weight=2 reference_config=config_file.csv k=32 w=500; done
Setting the target_weight to 2 instead of 1.
Now it works. Thank's a lot!
Hi @Jimaz,
Thanks for your interest in ntJoin and documenting your solution here! I'm glad to hear you got it working.
Thanks! Lauren
Dear Developer
Thank you for the great tool
kindly I'm trying to scaffold a viral genome containing only three contigs, and the error below occurred.
Can you please advice