FileNotFoundError: [Errno 2] No such file or directory: '/work/home/songbing/.cache/BASALT'

[B1991ing]

Dear BASALT team,

Do you have any idea how to solve the issue mentioned before - command not found #18 (https://github.com/EMBL-PKU/BASALT/issues/18)?

Error screenshot

Command line mamba init 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 -qc checkm2

mamba deactivate

Installation BASALT_installation.txt

Looking forward your reply as soon as possible.

Thank you very much.

Best,

Bing

[noddevil4949]

Hi,

Unfortunately, BASALT does not support absolute path as input. You can create soft links to your working directory and try again, it should run successfully.

Thanks for using BASALT.

Regards

[noddevil4949]

Please also check if neural network models are in the correct path.