fixstart with user supplied gene sequences does not work

[yjx1217]

Hello,

I tried the following command to let circlator (v.1.5.1) only reset the start point of the contig using a pre-defined gene sequence but it seems that circlator just ignore the sequence that I provided and went ahead to reset start point based on Prodigal's output.

my command:
circlator fixstart --genes_fa start_gene.cds.fa --min_id 90 test.mt_contig.fa test.mt_contig.circlator

The detailed log file goes like this:
No suitable promer matches found
Using the following prodigal predictions to circularize contigs:
chr_chrMT Prodigal_v2.6.2 CDS 25812 25955 23.6 - 0 ;gc_cont=0.417;tscore=2.15;

I didn't encounter this problem with earlier versions of circlator though.

Best,
Jia-Xing

[yjx1217]

hmm, I think the problem is due to the assembly rather than circlator. The gene for fixstart seems missing in the assembly, which should not usually happen. Sorry~