Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
https://ecogenomics.github.io/GTDBTk/
GNU General Public License v3.0
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Inquiry on the error "libgsl.so.25" #586

Closed songmj86 closed 5 months ago

songmj86 commented 5 months ago

Hi !

I installed a new version of gtdbtk.

I had a initial run to test and prepare mash DB with the following prompt.

conda activate gtdbtk-2.4.0 ; DB="/home/sandia/databases/gtdbtk/release220/mash" ; In="/home/sandia/Downloads/gtdbtk/0_Raw" ; Out="/home/sandia/Downloads/gtdbtk/1_Out" ; gtdbtk classify_wf --write_single_copy_genes --keep_intermediates --mash_db $DB --cpus 100 --pplacer_cpus 100 --force -x fna --genome_dir $In --out_dir $Out ; conda deactivate ;

And I got this error. Do you have any idea how to resolve this issue?

[2024-05-03 10:43:53] INFO: GTDB-Tk v2.4.0 [2024-05-03 10:43:53] INFO: gtdbtk classify_wf --write_single_copy_genes --keep_intermediates --mash_db /home/sandia/databases/gtdbtk/release220/mash --cpus 100 --pplacer_cpus 100 --force -x fna --genome_dir /home/sandia/Downloads/gtdbtk/0_Raw --out_dir /home/sandia/Downloads/gtdbtk/1_Out [2024-05-03 10:43:53] INFO: Using GTDB-Tk reference data version r220: /home/sandia/databases/gtdbtk/release220 [2024-05-03 10:43:53] INFO: Loading reference genomes. [2024-05-03 10:43:54] INFO: Using Mash version unknown [2024-05-03 10:43:54] INFO: Creating Mash sketch file: /home/sandia/Downloads/gtdbtk/1_Out/classify/ani_screen/intermediate_results/mash/gtdbtk.user_query_sketch.msh [2024-05-03 10:43:54] ERROR: Error generating Mash sketch:
mash: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory [2024-05-03 10:43:54] ERROR: Controlled exit resulting from an unrecoverable error or warning.

Thanks !

Environment

Server information

Debugging information

songmj86 commented 5 months ago

I resolved the issue. That was associated with gsl package

Thanks