Can not initializing conda environment
Hi, thank you for developing this tool!
when I run this command according to "How to install IMP3", this error happens:
$ ./runIMP3 -i config/config.imp_init.yaml
Initializing conda environments.
adjusted memory settings because there is only one kind of core in this run. CAUTION: we're using the bigger number of normal_mem_per_core_gb and big_mem_per_core_gb and the number of threads granted to IMP3.
Final resource settings:
maximal number of cores: 1
normal mem: 36G
big mem: 36G
big mem cores: 1
big mem total: 36G
/home/IMP3/.
Traceback (most recent call last):
File "/home/IMP3/conda/snakemake_env/lib/python3.9/site-packages/snakemake/__init__.py", line 593, in snakemake
workflow.include(
File "/home/IMP3/conda/snakemake_env/lib/python3.9/site-packages/snakemake/workflow.py", line 1182, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/home/IMP3/Snakefile", line 91, in <module>
File "/home/IMP3/conda/snakemake_env/lib/python3.9/site-packages/snakemake/workflow.py", line 1182, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/home/IMP3/workflow/rules/modules/single_omics/mg/Taxonomy.smk", line 14, in <module>
"../../../Taxonomy/kraken_contigs.smk"
File "/home/IMP3/conda/snakemake_env/lib/python3.9/site-packages/snakemake/workflow.py", line 1182, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/home/IMP3/workflow/rules/modules/single_omics/mg/../../../Taxonomy/kraken_reads.smk", line 2, in <module>
KRAKSIZE = float(os.path.getsize(DBPATH + "/" + config['krakendb'] + "/hash.k2d" )) / 1000000000
File "/home/IMP3/conda/snakemake_env/lib/python3.9/genericpath.py", line 50, in getsize
return os.stat(filename).st_size
FileNotFoundError: [Errno 2] No such file or directory: '/home/IMP3/./../DBs/minikraken2/hash.k2d'
ls: cannot access '/home/IMP3/conda/*/etc/conda/activate.d/activate-r-base.sh': No such file or directory
I couldn't find "activate-r-base.sh" as follows.
$pwd
/home/IMP3/conda/snakemake_env/etc
$ls
ImageMagick-7 fish fonts gtk-2.0 profile.d request-key.conf
conda version is 4.12.0 and Python version is 3.7.1. Help? Thank you.