bheimbu

Hi @jdblischak, I was using your `config.yaml` for a while and everything was running smoothly, but now I've updated my `snakemake` installation (to `8.8.0`) and it gives me several errors....

Hi and a happy new year, I'm experiencing the same issue, any help would be highly appreciated?! It would also be nice if the website (https://fephyfofum.github.io/PyPHLAWD/) could be updated as...

Hi @YingyingYang2019, you make my day, it's working with the old version (downloaded as source code from [here](https://github.com/FePhyFoFum/PyPHLAWD/archive/refs/tags/v1.0.tar.gz)). Cheers Bastian

After updating `gtdb_to_diamond.py` I get following error: ``` gtdb_to_diamond.py -o gtdb_vers207 gtdb_proteins_aa_reps_r207.tar.gz taxdump/names.dmp taxdump/nodes.dmp 2023-08-24 09:28:58,061 - Read nodes.dmp file: taxdump/nodes.dmp 2023-08-24 09:28:58,616 - File written: gtdb_vers207/nodes.dmp 2023-08-24 09:28:58,616 -...

I've changed your code (here is the adjusted [python script](https://github.com/nick-youngblut/gtdb_to_taxdump/files/12429016/gtdb_to_diamond.py.txt)) and it now runs. However, all accession numbers in `accession2taxid.tsv` are assigned to `Not found`, that is `gtdb_to_diamond.py` gives me...

Thanks, for your reply. I'll try to use `--packed` and see how it goes. Cheers Bastian

Hi @aaronmussig, any news on this? The download speed from Germany is super slow, like 200 kb/s. Cheers Bastian

Hi there, I got the same error. I've downloaded the nt database from here https://benlangmead.github.io/aws-indexes/k2, but the file k2_nt_20230502.tar.gz does not include database150mers.kmer_distrib. Do I have to generate this file...

Hi @queirozhanna, did you > Download KOfam database from ftp://ftp.genome.jp/pub/db/kofam/ and decompress it. You will get profile HMMs in profiles/ directory and ko_list. If so specify the path with ```...

Hi, I got also stuck at the downloading stage (Taxid: 48704). Any thoughts on implementing a NCBI API key? Cheers Bastian