Milot Mirdita

Could you upload a few contigs? I am confused where it's actually crashing in the log it's crashing in `summarizealis` and in the snippet in `addtaxonomy`. It would be great...

I cannot get it to crash :/ Can you rerun the `easy-taxonomy` call with `--remove-tmp-files 0` and then once it crashes please run only `addtaxonomy` inside a debugger: ``` gdb...

The most surprising part is that it's crashing in `addtaxonomy`, which is comparatively an extremely boring module. Could you just try executing only this one command a few times in...

Every time? But once you start it inside `gdb` it doesn't crash anymore? I would be very interested to find out what's actually wrong. Would it be possible to start...

You can also run GDB non-interactively (if thats the issue): ``` COMMAND='mmseqs addtaxonomy "data/databases/gtdb" "data/04_taxgenes/contigs_tax/latest/result_aln_swapped_sum" "data/04_taxgenes/contigs_tax/latest/result_aln_swapped_sum_tax" --tax-lineage 0 --lca-ranks species,genus,family,order,class,phylum,superkingdom --pick-id-from 1 --compressed 0 --threads 48 -v 3' gdb -batch...

This error is very unexpected and I can't imagine how/why it could happen. I don't think it is related to this old issue though. If you can arrange some interactive...

Can you check how much swap spaces is being used (`free -h`). I guess the automatic memory limit detection is going wrong somehow. Do you set memory limits in the...

No the issue is (probably) that it’s using too much memory and runtime is thus degrading heavily. Larger chunks would mean a faster runtime if enough RAM was available. But...

If you have `aria2c` installed, it will prefer that over `curl` or `wget` and use multiple download connections. This should speed up downloads quite a bit.

Your kernel/libc versions are very old. I am surprised that conda runs at all. These error messages are thrown by MMseqs2 dependencies that are provided by conda-forge (libgomp/libstdc++), they require...