bheimbu

Hi, I cannot download any of the prebuilt databases, is the server down? Now I'm about to build a database for invertebrates but it take ages, as you can imagine....

KeyError: 'Cannot find GCA003697015.1 accession in names.dmp'

3

Hi @nick-youngblut, when I try to build the gtdb database using r207, I get: ``` gtdb_to_diamond.py -o gtdb gtdb_proteins_aa_reps_r207.tar.gz taxdump/names.dmp taxdump/nodes.dmp 2023-08-23 13:53:35,547 - Read nodes.dmp file: taxdump/nodes.dmp 2023-08-23 13:53:35,813...

Building index of NCBI's Refseq bacterial genomes

4

Hi there, I'm trying a build a huge index of NCBI's Refseq bacterial genomes, which is about 97 GB (in fna.gz format). I'm working on a HPC with 512 GB...

Hello, I've installed MetaCoAG 1.1.4 with mamba but it cannot find run_FragGeneScan.pl, while it is present. I've not experienced something like this before. ``` $ mamba activate mags (mags)$ which...

Hi, it's just an idea but it would be great if some databases like UniRef90 or NCBI's nr could be downloaded in a pre-built manner. There is https://benlangmead.github.io/aws-indexes/ for Kraken2,...

Hi there, I know this might be not the right place, but the download speed of databases from https://benlangmead.github.io/aws-indexes/ is quite slow from Germany. I'm downloading the whole nt Database,...

Question about avp prepare output

23

Hi @GDKO, it's me again @bheimbu. I have a question concerning the output of `avp prepare`… ``` query name donor ingroup AI HGTindex query hits number AHS outg_pct 229769_8676 Uniref90|UniRef90_A0A4R7CTD7:14:38.4:8.48e-75:250...