"No viral RdRP identified in input sequence (or a server error occured)"

[murrellb]

Might be a bug - not 100% sure. I downloaded the Paramyxoviridae RdRp MSA file (from here: https://serratus.io/trees), and took one of the sequences (u5506):

>test_u5506
LTTDLQKYCLNWRYPTIKLFAMKLNQILGIPHGFEWIHLRLRDTTMFVGDPYNPPNDINFINLDDQKNDSIFIVSPRGGIEGLCQKMWTMISISAIHLSATKTGCRVASMVQGDNQAI

and uploaded it to https://serratus.io/palmid

Which gives me the following error:

I've previously done this for other RdRp sequences, and it worked fine, but it doesn't seem to work for any Paramyxoviridae sequences I've tried.

[ababaian]

Much apologies @murrellb about the delay. I've been on a bit of a snooze over summer.

Anyways, the problem was localized to the palmid.Rmd script

Quitting from lines 65-148 (palmid.Rmd)
Error in if (!all(palm.geo.tmp$biosample_id == palm.sra$biosample_id)) { :

It appears there were some SRA accessions which did not contain a valid biosample ID. This shouldn't be the case. For some reason a handful of datasets which contain measles did not contain a BioSample identifier, I went in and fixed this manually in the database and everything is working. Anytime these measles datasets were being retrieved it would end up stalling, thus a bunch of Paramyxoviridae were not accessible. Strange bug, but easy fix.

Here is your virus report for taxpayingPension virus (u5506). Please let me know if I can help (and it should be quicker this time).