DavideGue
commented
11 months ago Hi, it required a couple of days but finally succeded! Thanks
Closed DavideGue closed 11 months ago
DavideGue
commented
11 months ago Hi, it required a couple of days but finally succeded! Thanks
Hi @akcorut, I’m trying to run kgwasflow using a Virtual Machine on our local server. Whean I run kgwasflow run -t 14 it get stuck in "Downloading and installing remote packages". The complete message is attacched below: --- Logging error ---
Traceback (most recent call last):
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/logging/init.p y", line 1113, in emit
stream.write(msg + self.terminator)
UnicodeEncodeError: 'latin-1' codec can't encode character '\u2013' in position 22: ordinal not in range(256)
Call stack:
File "/home/davide/miniconda3/envs/kgwasflow/bin/snakemake", line 10, in <modu le>
sys.exit(main())
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snak emake/init.py", line 2954, in main
success = snakemake(
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snak emake/init.py", line 643, in snakemake
workflow.include(
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snak emake/workflow.py", line 1238, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/work flow/Snakefile", line 32, in
include: "rules/generate_kmers_table.smk"
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snak emake/workflow.py", line 1238, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/work flow/rules/common.smk", line 123, in
logger.info(" * Corut, A. K. & Wallace, J. G. kGWASflow: a modular, flex ible, ")
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snak emake/logging.py", line 357, in info
self.handler(dict(level="info", msg=msg, indent=indent))
File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snak emake/logging.py", line 332, in handler handler(msg) File "/home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snak emake/logging.py", line 583, in text_handler self.logger.warning(msg["msg"]) Message: ' Nat Genet 52, 534\u2013540 (2020). https://doi.org/10.1038/s41588 -020-0612-7 ' Arguments: ()
Building DAG of jobs... Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to confi gure strict priorities by executing 'conda config --set channel_priority strict' . Creating conda environment /home/davide/miniconda3/envs/kgwasflow/lib/python3.11 /site-packages/workflow/rules/../envs/kmers_gwas.yaml... Downloading and installing remote packages. Environment for /home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packa ges/workflow/rules/../envs/kmersgwas.yaml created (location: .snakemake/conda/4 4b8f6d73871916e7584e2bf11ecde66) Creating conda environment https://github.com/snakemake/snakemake-wrappers/raw/v 1.12.2/bio/fastqc/environment.yaml... Downloading and installing remote packages. Environment for https://github.com/snakemake/snakemake-wrappers/raw/v1.12.2/bio/ fastqc/environment.yaml created (location: .snakemake/conda/c1ccbd17355a644d3688 e2ad2d1acdeb_) Creating conda environment /home/davide/miniconda3/envs/kgwasflow/lib/python3.11 /site-packages/workflow/rules/../envs/kmer_stats.yaml... Downloading and installing remote packages. Environment for /home/davide/miniconda3/envs/kgwasflow/lib/python3.11/site-packa ges/workflow/rules/../envs/kmerstats.yaml created (location: .snakemake/conda/5 ae9adf2b1c889a662f4c1c91f2b3498) Creating conda environment /home/davide/miniconda3/envs/kgwasflow/lib/python3.11 /site-packages/workflow/rules/../envs/kmers_gwas_py2.yaml... Downloading and installing remote packages. Thanks!