IanDMedeiros

> Gah! this made me realize there was a private group for the signalP module that I was not added to and was preventing me from using it/loading it properly!...

I think the huge database is only for FCS-GX; the FCS-adaptor tool is small and runs quickly.

Ok—don't use --antismash if I just ran antismash with remote, got it. With that I am almost to the end of the pipeline ("writing genome annotation table!"), but there is...

Took a look at the cds transcript file in annotate_results as you suggested, and... bizarrely, it's doing the thing from #763 again — printing the same sequence to the output...

This turned out to be an error in how I was providing the locus tag prefix to funannotate; because of a poorly constructed table file, there was a hidden newline...

I am seeing the same discrepancy. Just to make sure I understand the problem, the issue is only that multiple clusters are all getting called Cluster_1 (or Cluster_2 or Cluster_3),...

The issue from the original post and my response (not sure about @ernesfranco) seems to be that antiSMASH numbers clusters at the contig level, and parses those numbers intelligibly in...

Thanks for the quick reply—I think the piece I was missing was re-running funannotate setup with the new augustus. (/hpc/home/idm7/miniconda3/envs/annotate/config/ is actually the config directory associated with the new augustus.)...

No, still failing on real data... ------------------------------------------------------- [Jun 30 01:32 AM]: OS: CentOS Stream 8, 12 cores, ~ 33 GB RAM. Python: 3.8.12 [Jun 30 01:32 AM]: Running funannotate v1.8.11...

I tried upgrading as you suggested and got a new error: ######################################################### Running `funannotate clean` unit testing: minimap2 mediated assembly duplications Downloading: https://osf.io/8pjbe/download?version=1 Bytes: 252076 8192 [3.25%]16384 [6.50%]24576 [9.75%]32768 [13.00%]40960...