Open johnlees opened 1 month ago
@sydelstan opening new issue to track this
I'd require more information to diagnose this: command and ideally a minimal reproducible example (e.g. a genome that causes this issue)
Hello,
I used the code
poppunk_assign --db GPS_v8_ref --external-clustering GPS_v8_external_clusters.csv --query qfile.txt --output
based on these instructions:
https://www.pneumogen.net/gps/#/training
These are some of the accession numbers I used:
ERR884352 ERR884330 ERR1788221 ERR025290 SRR3661255 ERR884389
I have checked with my colleague @HarryHung in the GPS project who says the following:
Checking ERR884352 It is one of the GPS samples with: Public Name: GPS_PL_1533_10 This sample has been re-analysed by the GPS Pipeline just few days ago, and its GPSC is correctly assigned to GPSC 12 with v8_ref database and PopPUNK v2.6.3 (via Docker image staphb/poppunk:2.6.3)
I am not sure what is going on their side. I wonder if they are using raw reads as input (in my pipeline, pre-processing and de novo assembly were done before passing the assemblies to PopPUNK)? Or it could be some installation issues (might try out the Docker image)?
Are you using reads or an assembly as input?
Using assemblies and not reads fixed the issue, thanks
Originally posted by @sydelstan in https://github.com/bacpop/PopPUNK/issues/309#issuecomment-2111339654