search

ababaian / serratus

Ultra-deep search for novel viruses
http://serratus.io
GNU General Public License v3.0
250 stars 32 forks source link

palmID viral RdRp analysis crash #265

Closed FBeguier closed 1 year ago

ababaian commented 1 year ago

is this resolved now?

FBeguier commented 1 year ago

Hi,

I tought it was resolved (it worked for one analysis), that's why I deleted my post. But I try antoher one and I just received the same error message.

This is the end of the error message: image

ababaian commented 1 year ago

welcome to github :) it helps to not delete information and simply close the issue when it's done.

Can you please post the hash link so I can take a look at the full error logs and see what's going on.

FBeguier commented 1 year ago

Oops yes, sorry for that !

I'm not a bioinformaticien.. what is the hash link ?

Here is the link of the message I just obtained : (https://serratus.io/palmid?hash=3438969b1ac28e9d40bcd82a923b1771a0f43fb3)

FBeguier commented 1 year ago

I think I just found it...

I found this Hash code on the page: 669b2f1b0c79db4a97a29147a03d68e0

ababaian commented 1 year ago

Are you certain the input sequence is an RdRp? palmscan does not seem to be retrieving a palmprint domain and MUSCLE is not finding any alignments.

ababaian commented 1 year ago

I'm mostly certain it's not an RdRp sequence input, in the closest virus "Mute Swan Tombu", ORF2 is the RdRp (see: https://serratus.io/palmid?hash=b6a0e63f3e1a559c18823852f9e97000284c207b) but the sequence you are inputting matches ORF1, which is another protein.

palmID works strictly for virus RdRp sequences, you will not get any output if you do not enter an RdRp.

FBeguier commented 1 year ago

Actually, I don't know, I check different viral sequences for RdRp presence by using Serratus.

So if I receive this message, it means that there is no RdRp in my sequence ?

ababaian commented 1 year ago

That's mostly correct yes, if you REALLY think there should be an RdRp, you can check InterPro which has higher sensitivity: https://www.ebi.ac.uk/interpro/result/InterProScan/

FBeguier commented 1 year ago

Ok perfect, thanks a lot for your help !