Benjamin Buchfink
Benjamin Buchfink
> I was following the lead of this article, which used DIAMOND for taxonomic assignments for metaproteomics data: https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00334 They used Diamond for this sort of data, but surely must...
These parameters seem to work ok for me for your data: `-c1 --ultra-sensitive -s1 --id2 1 --short-query-ungapped-bitscore 1 -e10000 --algo 0 --masking 0 --gapped-filter-evalue 0` To use all of them,...
Can you send me those 2 xml files?
I'll look into it but it's probably going to take until later tomorrow.
Possibly, you can get diamond to include the full title by using the option --salltitles.
I ran your files but I always get this error message and it takes very long: BLAST result added to sequence: Cluster-120617.169989 Problem connecting to database b2g_apr12 on 10.10.100.203 as...
Try to use the latest version of diamond, I did change the format in 0.9.7.
Ok I'll change that in the next version.
What is your query file (type of sequences, sequence length, total size)? How much memory does your computer have? What is your command line for calling eggnog mapper or diamond?
I have run a similarly sized dataset against the eggnog protein database using the command line that you provided, comparing versions 2.0.13 and 2.0.11. The runtime, CPU and memory usage...