Closed songmj86 closed 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 !
conda list && conda list --revisions
gtdbtk.log
I resolved the issue. That was associated with gsl package
Thanks
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
conda list && conda list --revisions
Environment.txtServer information
Debugging information
gtdbtk.log
has been included (drag and drop the file to upload).