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EMBL-PKU / BASALT

MIT License
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FileNotFoundError: [Errno 2] No such file or directory: '/work/home/songbing/.cache/BASALT' or ModuleNotFoundError: No module named 'Bio' #28

Open B1991ing opened 2 months ago

B1991ing commented 2 months ago

Dear BASALT team

I am using BASALT to generate bins through directly running on the HPC node and submit slurm job script, both have errors.

Error screenshot - directly running on the HPC node

截屏2024-04-27 09 28 26

Command line mamba activate BASALT spades_output=/work/home/songbing/assembly/individual_assemble/metaspades/diarrhea/cecum/ contigs=/contigs.fasta fq_dir=/work/home/songbing/clean_reads/diarrhea/cecum/paired/ cd ${fq_dir} /work/home/songbing/miniforge3/envs/BASALT/bin/BASALT \ -a ${spades_output}3${contigs},${spades_output}4${contigs},${spades_output}5${contigs},${spades_output}7${contigs},${spades_output}9${contigs},${spades_output}15${contigs} \ -s 3CA_1.TM_paired.fq.gz,3CA_2.TM_paired.fq.gz/4CA_1.TM_paired.fq.gz,4CA_2.TM_paired.fq.gz/5CA_1.TM_paired.fq.gz,5CA_2.TM_paired.fq.gz/7CA_1.TM_paired.fq.gz,7CA_2.TM_paired.fq.gz/9CA_1.TM_paired.fq.gz,9CA_2.TM_paired.fq.gz/15CA_1.TM_paired.fq.gz,15CA_2.TM_paired.fq.gz \ -t 60 -m 256 --min-cpn 50 --max-ctn 5

Error screenshot - sbatch submit job script to the HPC node

截屏2024-04-27 09 29 44

Error screenshot - directly running on the HPC node sbatch -J diarrhea_cecum_BASALT -p xahcnormal -N 1 --ntasks-per-node=1 --cpus-per-task=60 --mem=256 -t 720:00:00 /work/home/songbing/scripts/diarrhea_cecum_BASALT.sh

Job script diarrhea_cecum_BASALT.sh.txt

Installation git clone https://github.com/EMBL-PKU/BASALT.git cd BASALT mamba env create -n BASALT --file basalt_env.yml To activate this environment, use $ mamba activate BASALT To deactivate an active environment, use $ mamba deactivate chmod -R 777 /work/home/songbing/miniforge3/envs/BASALT/bin/*

Hope to get your reply as soon as possible.

Thank you very much.

Best，

Bing