Open sgalkina opened 3 weeks ago
It is difficult to know what went wrong. Can you try to run the GTDB-snake "manually" to see if any og the clusters seems to not have completed successfully?
snakemake --use-conda --latency-wait 150 -s MAGinator/maginator/workflow/gtdbtk.Snakefile --rerun-triggers mtime --config wd=
Dear authors,
Thanks for the great tool. I'm currently running the following command on Computerome:
maginator -v <...> \ -r <...> \ -c <...> \ -o <...> \ -g "/home/databases/gtdbtk/release207_v2" \ --cluster qsub --cluster_info "-l nodes=1:ppn={cores},mem={mem_gb}gb,walltime={runtime}" \ --max_cores=10 --max_mem=150
The command itself was also run through qsub system. The GTDBtk step seem to be completed succesfully, but then nothing more hapens. The main job is still running, and all the gtdbtk spawned job are finished. The output folder now looks like that:
The latest update in the folder was yesterday, and now the main job is running for more than 24 hours. It looks like it is hanging, but I see no errors.
Is it something you could help with?