Snakemake cannot succesfully load a conda environment

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I created a minimal example with this structure

./Snakefile
./simple_file.py
./envs/binvestigate_3_6_fresh.yml

Snakefile contains

rule step_1:
    input:

    output:
        "step_1_dummy.txt"
    conda:
        "envs/binvestigate_3_6_fresh.yml"
    script:
        "simple_file.py"

simple_file.py contains

import pandas
import os

if __name__=="__main__":

    
    os.system('touch /home/rictuar/coding_projects/delete_crap/step_1_dummy.txt')

binvestigate_3_6_fresh.yml contains

    name: binvestigate_3_6_fresh
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - aioeasywebdav=2.4.0=py36h5fab9bb_1001
  - aiohttp=3.7.4.post0=py36h8f6f2f9_0
  - alsa-lib=1.2.3=h516909a_0
  - appdirs=1.4.4=pyh9f0ad1d_0
  - async-timeout=3.0.0=py36_0
  - attrs=21.2.0=pyhd8ed1ab_0
  - ca-certificates=2021.10.8=ha878542_0
  - certifi=2016.9.26=py36_0
  - chardet=4.0.0=py36h5fab9bb_1
  - configargparse=1.5.3=pyhd8ed1ab_0
  - dbus=1.13.6=h48d8840_2
  - docutils=0.16=py36h5fab9bb_3
  - dropbox=7.3.1=py36_0
  - ecdsa=0.17.0=pyhd8ed1ab_0
  - ete3=3.1.2=pyh9f0ad1d_0
  - expat=2.4.1=h9c3ff4c_0
  - filechunkio=1.8=py_2
  - fontconfig=2.13.1=hba837de_1005
  - freetype=2.10.4=h0708190_1
  - ftputil=5.0.1=pyhd8ed1ab_0
  - gettext=0.19.8.1=h73d1719_1008
  - glib=2.70.0=h780b84a_1
  - glib-tools=2.70.0=h780b84a_1
  - gst-plugins-base=1.18.5=hf529b03_2
  - gstreamer=1.18.5=h9f60fe5_2
  - icu=68.2=h9c3ff4c_0
  - idna=3.1=pyhd3deb0d_0
  - idna_ssl=1.1.0=pyhd8ed1ab_1002
  - jpeg=9d=h36c2ea0_0
  - krb5=1.19.2=hcc1bbae_3
  - ld_impl_linux-64=2.36.1=hea4e1c9_2
  - libblas=3.9.0=12_linux64_openblas
  - libcblas=3.9.0=12_linux64_openblas
  - libclang=11.1.0=default_ha53f305_1
  - libedit=3.1.20191231=he28a2e2_2
  - libevent=2.1.10=h9b69904_4
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=11.2.0=h1d223b6_11
  - libgfortran-ng=11.2.0=h69a702a_11
  - libgfortran5=11.2.0=h5c6108e_11
  - libglib=2.70.0=h174f98d_1
  - libgomp=11.2.0=h1d223b6_11
  - libiconv=1.16=h516909a_0
  - liblapack=3.9.0=12_linux64_openblas
  - libllvm11=11.1.0=hf817b99_2
  - libogg=1.3.4=h7f98852_1
  - libopenblas=0.3.18=pthreads_h8fe5266_0
  - libopus=1.3.1=h7f98852_1
  - libpng=1.6.37=h21135ba_2
  - libpq=13.3=hd57d9b9_3
  - libstdcxx-ng=11.2.0=he4da1e4_11
  - libuuid=2.32.1=h7f98852_1000
  - libvorbis=1.3.7=h9c3ff4c_0
  - libxcb=1.13=h7f98852_1004
  - libxkbcommon=1.0.3=he3ba5ed_0
  - libxml2=2.9.12=h72842e0_0
  - libxslt=1.1.33=h15afd5d_2
  - libzlib=1.2.11=h36c2ea0_1013
  - lxml=3.8.0=py36_0
  - lz4-c=1.9.3=h9c3ff4c_1
  - multidict=5.2.0=py36h8f6f2f9_0
  - mysql-common=8.0.27=ha770c72_1
  - mysql-libs=8.0.27=hfa10184_1
  - ncurses=6.2=h58526e2_4
  - nspr=4.32=h9c3ff4c_1
  - nss=3.72=hb5efdd6_0
  - numpy=1.19.5=py36hfc0c790_2
  - openssl=1.1.1l=h7f98852_0
  - pandas=1.1.5=py36h284efc9_0
  - paramiko=1.18.2=py36_0
  - pcre=8.45=h9c3ff4c_0
  - pip=21.3.1=pyhd8ed1ab_0
  - psutil=5.8.0=py36h8f6f2f9_1
  - pthread-stubs=0.4=h36c2ea0_1001
  - pycrypto=2.6.1=py36he6145b8_1005
  - pyqt=5.12.3=py36h5fab9bb_7
  - pyqt-impl=5.12.3=py36h7ec31b9_7
  - pyqt5-sip=4.19.18=py36hc4f0c31_7
  - pyqtchart=5.12=py36h7ec31b9_7
  - pyqtwebengine=5.12.1=py36h7ec31b9_7
  - pysftp=0.2.9=py_1
  - python=3.6.13=hb7a2778_2_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python_abi=3.6=2_cp36m
  - pytz=2021.3=pyhd8ed1ab_0
  - pyyaml=5.4.1=py36h8f6f2f9_1
  - qt=5.12.9=hda022c4_4
  - ratelimiter=1.2.0=py_1002
  - readline=8.1=h46c0cb4_0
  - requests=2.12.5=py36_0
  - scipy=1.5.3=py36h81d768a_1
  - setuptools=49.6.0=py36h5fab9bb_3
  - six=1.16.0=pyh6c4a22f_0
  - snakemake=4.3.0=py36_0
  - sqlite=3.36.0=h9cd32fc_2
  - tk=8.6.11=h27826a3_1
  - typing-extensions=3.10.0.2=hd8ed1ab_0
  - typing_extensions=3.10.0.2=pyha770c72_0
  - urllib3=1.12=py36_0
  - wheel=0.37.0=pyhd8ed1ab_1
  - wrapt=1.12.1=py36h8f6f2f9_3
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.7.2=h7f98852_0
  - xorg-libxau=1.0.9=h7f98852_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h7f98852_1
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.5=h516909a_1
  - yaml=0.2.5=h516909a_0
  - yarl=1.6.3=py36h8f6f2f9_2
  - zlib=1.2.11=h36c2ea0_1013
  - zstd=1.5.0=ha95c52a_0
prefix: /home/rictuar/anaconda3/envs/binvestigate_3_6_fresh

When I run

snakemake "/home/rictuar/coding_projects/delete_crap/step_1_dummy.txt" --core 5 --use-conda

I get

    Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 5
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   step_1
    1
Select jobs to execute...

[Mon Nov 15 15:01:20 2021]
rule step_1:
    output: /home/rictuar/coding_projects/delete_crap/step_1_dummy.txt
    jobid: 0

Activating conda environment: /home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e
Activating conda environment: /home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e
Traceback (most recent call last):
  File "/home/rictuar/coding_projects/delete_crap/.snakemake/scripts/tmpicplrg37.simple_file.py", line 3, in <module>
    import sys; sys.path.extend(['/home/rictuar/anaconda3/lib/python3.8/site-packages', '/home/rictuar/coding_projects/delete_crap']); import pickle; snakemake = pickle.loads(b'\x80\x04\x95\xb4\x03\x00\x00\x00\x00\x00\x00\x8c\x10snakemake.script\x94\x8c\tSnakemake\x94\x93\x94)\x81\x94}\x94(\x8c\x05input\x94\x8c\x0csnakemake.io\x94\x8c\nInputFiles\x94\x93\x94)\x81\x94}\x94(\x8c\x06_names\x94}\x94\x8c\x12_allowed_overrides\x94]\x94(\x8c\x05index\x94\x8c\x04sort\x94eh\x0f\x8c\tfunctools\x94\x8c\x07partial\x94\x93\x94h\x06\x8c\x19Namedlist._used_attribute\x94\x93\x94\x85\x94R\x94(h\x15)}\x94\x8c\x05_name\x94h\x0fsNt\x94bh\x10h\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x10sNt\x94bub\x8c\x06output\x94h\x06\x8c\x0bOutputFiles\x94\x93\x94)\x81\x94\x8c:/home/rictuar/coding_projects/delete_crap/step_1_dummy.txt\x94a}\x94(h\x0b}\x94h\r]\x94(h\x0fh\x10eh\x0fh\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x0fsNt\x94bh\x10h\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x10sNt\x94bub\x8c\x06params\x94h\x06\x8c\x06Params\x94\x93\x94)\x81\x94}\x94(h\x0b}\x94h\r]\x94(h\x0fh\x10eh\x0fh\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x0fsNt\x94bh\x10h\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x10sNt\x94bub\x8c\twildcards\x94h\x06\x8c\tWildcards\x94\x93\x94)\x81\x94}\x94(h\x0b}\x94h\r]\x94(h\x0fh\x10eh\x0fh\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x0fsNt\x94bh\x10h\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x10sNt\x94bub\x8c\x07threads\x94K\x01\x8c\tresources\x94h\x06\x8c\tResources\x94\x93\x94)\x81\x94(K\x01K\x01e}\x94(h\x0b}\x94(\x8c\x06_cores\x94K\x00N\x86\x94\x8c\x06_nodes\x94K\x01N\x86\x94uh\r]\x94(h\x0fh\x10eh\x0fh\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x0fsNt\x94bh\x10h\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x10sNt\x94bhTK\x01hVK\x01ub\x8c\x03log\x94h\x06\x8c\x03Log\x94\x93\x94)\x81\x94}\x94(h\x0b}\x94h\r]\x94(h\x0fh\x10eh\x0fh\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x0fsNt\x94bh\x10h\x13h\x15\x85\x94R\x94(h\x15)}\x94h\x19h\x10sNt\x94bub\x8c\x06config\x94}\x94\x8c\x04rule\x94\x8c\x06step_1\x94\x8c\x0fbench_iteration\x94N\x8c\tscriptdir\x94\x8c)/home/rictuar/coding_projects/delete_crap\x94ub.'); from snakemake.logging import logger; logger.printshellcmds = False; __real_file__ = __file__; __file__ = '/home/rictuar/coding_projects/delete_crap/simple_file.py';
AttributeError: Can't get attribute 'Namedlist._used_attribute' on <module 'snakemake.io' from '/home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e/lib/python3.6/site-packages/snakemake/io.py'>
[Mon Nov 15 15:01:23 2021]
Error in rule step_1:
    jobid: 0
    output: /home/rictuar/coding_projects/delete_crap/step_1_dummy.txt
    conda-env: /home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e

RuleException:
CalledProcessError in line 11 of /home/rictuar/coding_projects/delete_crap/Snakefile:
Command 'source /home/rictuar/anaconda3/bin/activate '/home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e'; set -euo pipefail;  python /home/rictuar/coding_projects/delete_crap/.snakemake/scripts/tmpicplrg37.simple_file.py' returned non-zero exit status 1.
  File "/home/rictuar/anaconda3/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2326, in run_wrapper
  File "/home/rictuar/coding_projects/delete_crap/Snakefile", line 11, in __rule_step_1
  File "/home/rictuar/anaconda3/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 568, in _callback
  File "/home/rictuar/anaconda3/lib/python3.8/concurrent/futures/thread.py", line 57, in run
  File "/home/rictuar/anaconda3/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 554, in cached_or_run
  File "/home/rictuar/anaconda3/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2357, in run_wrapper
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/rictuar/coding_projects/delete_crap/.snakemake/log/2021-11-15T150120.368767.snakemake.log

Expected behavior is that this would simply work. When I

conda activate binvestigate_fresh_3_6

This code runs without issue. But, snakemake should be able to make conda environments on the fly. Intrestingly, it seems like snakemake is trying to use whatever environment I am in when i run Snakemake. Notice that it searches for python 3.8 when I run it from (base)

The logfile

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 5
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   step_1
    1
Select jobs to execute...

[Mon Nov 15 15:01:20 2021]
rule step_1:
    output: /home/rictuar/coding_projects/delete_crap/step_1_dummy.txt
    jobid: 0

Activating conda environment: /home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e
Activating conda environment: /home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e
[Mon Nov 15 15:01:23 2021]
Error in rule step_1:
    jobid: 0
    output: /home/rictuar/coding_projects/delete_crap/step_1_dummy.txt
    conda-env: /home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e

RuleException:
CalledProcessError in line 11 of /home/rictuar/coding_projects/delete_crap/Snakefile:
Command 'source /home/rictuar/anaconda3/bin/activate '/home/rictuar/coding_projects/delete_crap/.snakemake/conda/b84153cbaa4647564a32063b6a2b831e'; set -euo pipefail;  python /home/rictuar/coding_projects/delete_crap/.snakemake/scripts/tmpicplrg37.simple_file.py' returned non-zero exit status 1.
  File "/home/rictuar/anaconda3/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2326, in run_wrapper
  File "/home/rictuar/coding_projects/delete_crap/Snakefile", line 11, in __rule_step_1
  File "/home/rictuar/anaconda3/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 568, in _callback
  File "/home/rictuar/anaconda3/lib/python3.8/concurrent/futures/thread.py", line 57, in run
  File "/home/rictuar/anaconda3/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 554, in cached_or_run
  File "/home/rictuar/anaconda3/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2357, in run_wrapper
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/rictuar/coding_projects/delete_crap/.snakemake/log/2021-11-15T150120.368767.snakemake.log
e
snakemake conda package python
1 Answers

I think you found a bug in Snakemake 6.10.0 (the one I tried, I don't know other versions). It seems directive conda doesn't play well with script, at least when the script is python. For the time being, I would work around it by turning simple_file.py in a standalone script and running it with the shell directive (it may not be a bad thing anyway). E.g:

rule step_1:
    output:
        "step_1_dummy.txt"
    conda:
        "envs/binvestigate_3_6_fresh.yml"
    shell:
        r"""
        python /path/to/simple_file.py {input} > {output}
        """

I can reproduce the issue with:

Snakefile

rule step_1:
    output:
        "step_1_dummy.txt"
    conda:
        "envs/binvestigate_3_6_fresh.yml"
    script:
        "simple_file.py"

simple_file.py:

print('DONE')

binvestigate_3_6_fresh.yml

name: binvestigate_3_6_fresh
dependencies:
  - python

Execute:

snakemake --core 1 --use-conda

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job       count    min threads    max threads
------  -------  -------------  -------------
step_1        1              1              1
total         1              1              1

Select jobs to execute...

[Tue Nov 16 10:32:54 2021]
rule step_1:
    output: step_1_dummy.txt
    jobid: 0
    resources: tmpdir=/tmp

Activating conda environment: /home/dario/Downloads/.snakemake/conda/91f722014e097418892b581ac3a944f0
Activating conda environment: /home/dario/Downloads/.snakemake/conda/91f722014e097418892b581ac3a944f0
Traceback (most recent call last):
  File "/home/dario/Downloads/.snakemake/scripts/tmp9i0qygfm.simple_file.py", line 3, in <module>
    import sys; sys.path.extend(['/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages', '/home/dario/Downloads']); import pickle; snakemake = pickle.loads(b'\x80\x03csnakemake.script\nSnakemake\nq\x00)\x81q\x01}q\x02(X\x05\x00\x00\x00inputq\x03csnakemake.io\nInputFiles\nq\x04)\x81q\x05}q\x06(X\x06\x00\x00\x00_namesq\x07}q\x08X\x12\x00\x00\x00_allowed_overridesq\t]q\n(X\x05\x00\x00\x00indexq\x0bX\x04\x00\x00\x00sortq\x0ceh\x0bcfunctools\npartial\nq\rcbuiltins\ngetattr\nq\x0ecsnakemake.io\nNamedlist\nq\x0fX\x0f\x00\x00\x00_used_attributeq\x10\x86q\x11Rq\x12\x85q\x13Rq\x14(h\x12)}q\x15X\x05\x00\x00\x00_nameq\x16h\x0bsNtq\x17bh\x0ch\rh\x12\x85q\x18Rq\x19(h\x12)}q\x1ah\x16h\x0csNtq\x1bbubX\x06\x00\x00\x00outputq\x1ccsnakemake.io\nOutputFiles\nq\x1d)\x81q\x1eX\x10\x00\x00\x00step_1_dummy.txtq\x1fa}q (h\x07}q!h\t]q"(h\x0bh\x0ceh\x0bh\rh\x12\x85q#Rq$(h\x12)}q%h\x16h\x0bsNtq&bh\x0ch\rh\x12\x85q\'Rq((h\x12)}q)h\x16h\x0csNtq*bubX\x06\x00\x00\x00paramsq+csnakemake.io\nParams\nq,)\x81q-}q.(h\x07}q/h\t]q0(h\x0bh\x0ceh\x0bh\rh\x12\x85q1Rq2(h\x12)}q3h\x16h\x0bsNtq4bh\x0ch\rh\x12\x85q5Rq6(h\x12)}q7h\x16h\x0csNtq8bubX\t\x00\x00\x00wildcardsq9csnakemake.io\nWildcards\nq:)\x81q;}q<(h\x07}q=h\t]q>(h\x0bh\x0ceh\x0bh\rh\x12\x85q?Rq@(h\x12)}qAh\x16h\x0bsNtqBbh\x0ch\rh\x12\x85qCRqD(h\x12)}qEh\x16h\x0csNtqFbubX\x07\x00\x00\x00threadsqGK\x01X\t\x00\x00\x00resourcesqHcsnakemake.io\nResources\nqI)\x81qJ(K\x01K\x01X\x04\x00\x00\x00/tmpqKe}qL(h\x07}qM(X\x06\x00\x00\x00_coresqNK\x00N\x86qOX\x06\x00\x00\x00_nodesqPK\x01N\x86qQX\x06\x00\x00\x00tmpdirqRK\x02N\x86qSuh\t]qT(h\x0bh\x0ceh\x0bh\rh\x12\x85qURqV(h\x12)}qWh\x16h\x0bsNtqXbh\x0ch\rh\x12\x85qYRqZ(h\x12)}q[h\x16h\x0csNtq\\bhNK\x01hPK\x01hRhKubX\x03\x00\x00\x00logq]csnakemake.io\nLog\nq^)\x81q_}q`(h\x07}qah\t]qb(h\x0bh\x0ceh\x0bh\rh\x12\x85qcRqd(h\x12)}qeh\x16h\x0bsNtqfbh\x0ch\rh\x12\x85qgRqh(h\x12)}qih\x16h\x0csNtqjbubX\x06\x00\x00\x00configqk}qlX\x04\x00\x00\x00ruleqmX\x06\x00\x00\x00step_1qnX\x0f\x00\x00\x00bench_iterationqoNX\t\x00\x00\x00scriptdirqpX\x15\x00\x00\x00/home/dario/Downloadsqqub.'); from snakemake.logging import logger; logger.printshellcmds = False; __real_file__ = __file__; __file__ = '/home/dario/Downloads/simple_file.py';
AttributeError: type object 'Namedlist' has no attribute '_used_attribute'
[Tue Nov 16 10:32:55 2021]
Error in rule step_1:
    jobid: 0
    output: step_1_dummy.txt
    conda-env: /home/dario/Downloads/.snakemake/conda/91f722014e097418892b581ac3a944f0

Traceback (most recent call last):
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 593, in _callback
    raise ex
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/concurrent/futures/thread.py", line 56, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 579, in cached_or_run
    run_func(*args)
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 2461, in run_wrapper
    raise ex
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/executors/__init__.py", line 2442, in run_wrapper
    runtime_sourcecache_path,
  File "/home/dario/Downloads/Snakefile", line 17, in __rule_step_1
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/script.py", line 1371, in script
    executor.evaluate()
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/script.py", line 381, in evaluate
    self.execute_script(fd.name, edit=edit)
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/script.py", line 583, in execute_script
    "{py_exec} {fname:q}", py_exec=py_exec, fname=fname, is_python_script=True
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/script.py", line 425, in _execute_cmd
    **kwargs
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakemake/shell.py", line 266, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'source /home/dario/miniconda3/bin/activate '/home/dario/Downloads/.snakemake/conda/91f722014e097418892b581ac3a944f0'; set -euo pipefail;  python /home/dario/Downloads/.snakemake/scripts/tmp9i0qygfm.simple_file.py' returned non-zero exit status 1.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/dario/Downloads/.snakemake/log/2021-11-16T103252.987957.snakemake.log
user_11144530
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