IanDMedeiros

Bug in how antiSMASH results are handled?

5

funannotate v1.8.12 `Funannotate annotate` failed when I included the argument `--antismash /path/to/annotate_misc/antiSMASH.results.gbk` because the file did not exist. I dug into it and discovered that annotate was removing the file...

Predict log suggests that it ran ok, but there is only a single CDS repeated ad nauseum in .gbk

5

**Are you using the latest release?** `funannotate v1.8.12` **Describe the bug** The logfile for funannotate predict seemed to show that everything ran ok. But the outputs (.protein.fa and .gff) contain...

New feature request: Integrate NCBI FCS-adaptor into funannotate clean?

8

Now that NCBI had released their internal adapter contamination screening tool for public use (https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/28/fcs-beta-tool/), would it be possible to add an option for FCS-adaptor to be run as part...

funannotate predict fails with test and with real data: "Not enough gene models ... to train Augustus"

17

**Are you using the latest release?** `funannotate v1.8.11`. **Describe the bug** funannotate test is failing at the predict step with error "Not enough gene models 175 to train Augustus (200...

NTR for subclasses of organic material related to fungi

7

Hello, I am requesting two new terms for organic materials relating to fungi. These would be used for "env_medium" annotations of DNA sequence data submitted to NCBI. This is my...

Imperfect solution to antiSMASH cluster numbering

4

This is the solution I am currently using for the issue described in #736 where antiSMASH cluster numbering starts over from 1 on each contig. It isn't terribly elegant, but...

Updated downloads.json to the current versions of MIBiG and dbCAN. Note: Because of an error with the dbCAN readme file, funannotate database will still show dbCAN v11.0 even with the...

error while parsing GFA path record

8

### Description of bug binspreader threw an error while parsing assembly_graph_with_scaffolds.gfa. It looks like there are semicolons where the program was expecting tabs. I did not modify the assembly graph...