createdb dies when setting up GTDB taxonomy database

rikander commented 8 months ago

Hi folks! Thanks for maintaining this software. I've been trying to set up the GTDB database for taxonomy analysis, but can't seem to get the database set up regardless of the computer used (I've tried both my Linux server as well as my own Mac laptop; mmseqs was installed using conda on the server and using the MacOSX binary available on the mmseqs installation page on the laptop). Details are below. Thanks in advance for any light you can shed on the issue!

Expected Behavior

Creation of a taxonomy database using GTDB as the database.

Current Behavior

the createdb step dies after downloading the GTDB database.

Steps to Reproduce (for bugs)

command: mmseqs databases GTDB outpath/GTDB tmp

MMseqs Output (for bugs)

bash-3.2$ bin/mmseqs databases GTDB outpath/GTDB tmp databases GTDB outpath/GTDB tmp

MMseqs Version: 2fad714b525f1975b62c2d2b5aff28274ad57466 Tsv false Force restart with latest tmp false Remove temporary files false Compressed 0 Threads 8 Verbosity 3

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 31 100 31 0 0 41 0 --:--:-- --:--:-- --:--:-- 41 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 51.3G 100 51.3G 0 0 1565k 0 9:33:26 9:33:26 --:--:-- 2662k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 54.4M 100 54.4M 0 0 1374k 0 0:00:40 0:00:40 --:--:-- 939k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1080k 100 1080k 0 0 489k 0 0:00:02 0:00:02 --:--:-- 491k tar2db tmp/14668141768776664068/gtdb.tar.gz tmp/14668141768776664068/tardb --tar-include faa.gz$ --threads 8 -v 3

Time for merging to tardb: 0h 0m 0s 28ms Time for merging to tardb.lookup: 0h 0m 0s 13ms Time for processing: 0h 7m 32s 203ms createdb tmp/14668141768776664068/tardb outpath/GTDB --compressed 0 -v 3

Converting sequences Cannot open outpath/GTDB.source for writing Error: createdb died

Context

Please note that I get this error on both my local computer and on my server; using different methods of installation.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters): MMseqs2 Version: 2fad714b525f1975b62c2d2b5aff28274ad57466 (local MacOSX computer) as well as MMseqs2 Version: 15.6f452 (on Linux server)
Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): Installed with both conda (linux server) and using the MacOSX binary available on the mmseqs download page (local computer)
For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
Server specifications (especially CPU support for AVX2/SSE and amount of system memory): for Linux server: supports AVX2, 1TB RAM. for local MacOSX computer: supports AVX2 (I think?), 16 GB RAM
Operating system and version: Linux server: Rocky Linux 8.9 local computer: macOS Monterey 12.7.2

hariszaf commented 8 months ago

Had the exact same behaviour on linux.

Amanda-Pinski commented 1 month ago

I have this same issue on linux. I can't figure out what it is.

soedinglab / MMseqs2