palmscan False Negative of Orthomyxoviridae

[batson]

Describe the bug
Timeout

Hash: 7603a13b7fcfe7768ded959684192115c6f8947c
Submission time (ISO): 2022-09-14T05:43:31.734Z

Submission was genome of Wuhan Mosquito Virus 6 from NCBI: https://www.ncbi.nlm.nih.gov/nuccore/MW434423.1?report=fasta

[ababaian]

Yes this is a known bug :) I'd have sent you this link for palmID for WMV6 otherwise. palmscan PSSM are not hitting Orthomyxoviridae very efficiently, it's a false-negative. You'll need to perform the SRA-list parsing manually against the micro-assembly rdrp1.mu.fa contigs. Once you have that you can walk through the remaining palmID R script to generate the report locally.

Sorry about that. I'll leave this open as a ticket to swing back to it.

[batson]

Thanks, @ababaian. I ended up going through all the WMV6 microassembly contigs more or less manually, and finding sequence from Tunesia, the Philippines, and CT (USA) which hadn't made it to GenBank. We're updating the paper accordingly (going from five continents to six!) and citing Serratus!