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akcorut / kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
https://github.com/akcorut/kGWASflow/wiki
MIT License
28 stars 8 forks source link

Error at __rule_extract_kmersGWAS #28

Open SakaMax opened 8 months ago

SakaMax commented 8 months ago

Hello,

I tested the kgwasflow with the kgwasflow test command. Then I got the errors below:

Full Traceback (most recent call last):
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snakemake/executors/__init__.py", line 2576, in run_wrapper
    run(
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/build_kmers_gwas.smk", line 85, in __rule_extract_kmersGWAS
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snakemake/shell.py", line 300, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'source /home/kosuke/miniconda3/envs/kgwasflow/bin/activate '/home/kosuke/kmer-test/testrun/.snakemake/conda/e90c7431d77b0f7e2b65ebe43a6aa0bf_'; set -euo pipefail;  unzip scripts/external/kmers_gwas/v0.3-beta.zip -d scripts/external/kmers_gwas 2> logs/build_kmers_gwas/extract_kmersGWAS.unzip.log' returned non-zero exit status 10.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snakemake/executors/__init__.py", line 666, in _callback
    raise ex
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snakemake/executors/__init__.py", line 652, in cached_or_run
    run_func(*args)
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/snakemake/executors/__init__.py", line 2612, in run_wrapper
    raise RuleException(
snakemake.exceptions.RuleException: CalledProcessError in file /home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/build_kmers_gwas.smk, line 39:
Command 'source /home/kosuke/miniconda3/envs/kgwasflow/bin/activate '/home/kosuke/kmer-test/testrun/.snakemake/conda/e90c7431d77b0f7e2b65ebe43a6aa0bf_'; set -euo pipefail;  unzip scripts/external/kmers_gwas/v0.3-beta.zip -d scripts/external/kmers_gwas 2> logs/build_kmers_gwas/extract_kmersGWAS.unzip.log' returned non-zero exit status 10.
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/build_kmers_gwas.smk", line 39, in __rule_extract_kmersGWAS

RuleException:
CalledProcessError in file /home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/build_kmers_gwas.smk, line 39:
Command 'source /home/kosuke/miniconda3/envs/kgwasflow/bin/activate '/home/kosuke/kmer-test/testrun/.snakemake/conda/e90c7431d77b0f7e2b65ebe43a6aa0bf_'; set -euo pipefail;  unzip scripts/external/kmers_gwas/v0.3-beta.zip -d scripts/external/kmers_gwas 2> logs/build_kmers_gwas/extract_kmersGWAS.unzip.log' returned non-zero exit status 10.
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/build_kmers_gwas.smk", line 39, in __rule_extract_kmersGWAS
  File "/home/kosuke/miniconda3/envs/kgwasflow/lib/python3.11/concurrent/futures/thread.py", line 58, in run

The complete command line is: 

mamba create -c bioconda -n kgwasflow kgwasflow && \
mamba activate kgwasflow && \
kgwasflow init --work-dir testrun && \
kgwasflow test --verbose --work-dir testrun --conda-frontend mamba 2>&1 | tee testrun-conda.log.txt

and this is the output testrun-conda.log.txt

Any suggestions will be appreciated. Thanks,