Visualization issue

[OwenNaicker]

Hi, I am having trouble visualizing the output from GECCO on antiSMASH. I followed the instructions in the GECCO documentation and uploaded the JSON file generated by GECCO into the "extra annotations" tab on antiSMASH but I do not see any of the information from GECCO after running antiSMASH. I get the same results as if I never uploaded the JSON file. Any idea how to solve this issue?

[althonos]

Hi Owen,

Does this happen with a particular sequence or with all sequences you've tried? Are you running the latest GECCO, and the latest antiSMASH?

[OwenNaicker]

Hi Althonos,
GECCO-visualization_issue.zip

I tried the visualization with the s.cerevisiae genome and it works fine. The issue seems to occur with the particular sequence I am trying to use. please see attached. I am using the antiSMASH web page and GECCO 0.9.4.

[althonos]

Hi Owen,

it looks like the antiSMASH website decided to rename the contigs you upload to get rid of the record version when rendering the results (e.g. JAHXDO010000001.1 becomes JAHXDO010000001). After manually fixing the identifiers the antiSMASH website was able to recognize the metadata in the sideload file: JAHXDO01000000-genome-sideload-fixed.json.zip

I'm wondering how to fix this, as it seems to be caused by antiSMASH aggressively tweaking the record accession, which is not something we want to do in GECCO, and I'm not sure how to emulate that for the JSON file only. I'll have a look if this was changed from antiSMASH v5 to v6.

[OwenNaicker]

Thank you.