installation problem

[l-gallucci]

Hi @ohickl,

I have a problem with the installation.

I tried both cloning or conda install.

In the case of conda install, once I installed it successfully, then I run binny -s setup --db_path /path/to/db/folders and this produce metadata.tsv missing files from database folder (checkM) and other failures. Now I'm not able to replicate that because after few trials also the installation of binny started to not work giving error for a missing binny.binning in binny.py.

For cloning install:

 ./binny -i config/config.init.yaml
Using existing Prokka env: /bioinf/home/lgallucc/software/miniconda3/envs/prokka
Using existing Mantis env: /bioinf/home/lgallucc/software/miniconda3/envs/mantis
Will use conda source path: /bioinf/home/lgallucc/software/binny/workflow/envs
Using existing Snakemake env: /bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env
Config file /bioinf/home/lgallucc/software/binny/config/config.default.yaml is extended by additional config specified via the command line.
named /bioinf/home/lgallucc/software/miniconda3/envs/prokka
named /bioinf/home/lgallucc/software/miniconda3/envs/mantis
Setting up marker database
Initializing conda environments.
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 configure strict priorities by executing 'conda config --set channel_priority strict'.
Creating conda environment ../workflow/envs/fasta_processing.yaml...
Downloading and installing remote packages.
Full Traceback (most recent call last):
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 590, in create
    out = create_env(env_file, filetype="yaml")
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 552, in create_env
    out = shell.check_output(
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/site-packages/snakemake/shell.py", line 63, in check_output
    return sp.check_output(cmd, shell=True, executable=executable, **kwargs)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/subprocess.py", line 415, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'mamba env create --quiet --file "/bioinf/home/lgallucc/software/binny/workflow/envs/8ba969ed76161d97b3f888347524ef05_.yaml" --prefix "/bioinf/home/lgallucc/software/binny/workflow/envs/8ba969ed76161d97b3f888347524ef05_"' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/site-packages/snakemake/__init__.py", line 736, in snakemake
    success = workflow.execute(
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/site-packages/snakemake/workflow.py", line 924, in execute
    dag.create_conda_envs(
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/site-packages/snakemake/dag.py", line 319, in create_conda_envs
    env.create(dryrun)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/snakemake_env/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 609, in create
    raise CreateCondaEnvironmentException(
snakemake.exceptions.CreateCondaEnvironmentException: Could not create conda environment from /bioinf/home/lgallucc/software/binny/workflow/envs/fasta_processing.yaml:
Command:
mamba env create --quiet --file "/bioinf/home/lgallucc/software/binny/workflow/envs/8ba969ed76161d97b3f888347524ef05_.yaml" --prefix "/bioinf/home/lgallucc/software/binny/workflow/envs/8ba969ed76161d97b3f888347524ef05_"
Output:
error    libmamba Non-conda folder exists at prefix - aborting.
critical libmamba Non-conda folder exists at prefix - aborting.


CreateCondaEnvironmentException:
Could not create conda environment from /bioinf/home/lgallucc/software/binny/workflow/envs/fasta_processing.yaml:
Command:
mamba env create --quiet --file "/bioinf/home/lgallucc/software/binny/workflow/envs/8ba969ed76161d97b3f888347524ef05_.yaml" --prefix "/bioinf/home/lgallucc/software/binny/workflow/envs/8ba969ed76161d97b3f888347524ef05_"
Output:
error    libmamba Non-conda folder exists at prefix - aborting.
critical libmamba Non-conda folder exists at prefix - aborting.

unlocking
removing lock
removing lock
removed all locks
Setting up Mantis with the CheckM databases
Loading mantis env from: /bioinf/home/lgallucc/software/binny/workflow/envs/mantis

EnvironmentLocationNotFound: Not a conda environment: /bioinf/home/lgallucc/software/binny/workflow/envs/mantis

Command 'hmmpress' not found, but can be installed with:
apt install hmmer
Please ask your administrator.

Do you have any sugggestions?

[ohickl]

Hi Luigi,

could you give the conda version a try like e.g. this:

mamba create -n binny bioconda::binny

binny \
  --assembly /absolute/path/to/assembly.fa  \
  --contig_depth /absolute/path/to/contig_depth.txt \
  --outputdir /absolute/path/to/binny_out \
  --tmp_dir /absolute/path/to/binny_tmp \
  --threads 16

you can run this on a small test sample, it should automatically set up everything.
Id then go with the simple command line use (see binny --help), as common with other tools, instead of the config.

If you need the db at a path different from the default (in the env binny package dir) you can of course use setup with a custom path.

I just did a quick test with a fresh environment like above and it worked. Let me know if there are still problems!

Best

Oskar

[l-gallucci]

@ohickl thank you for the reply, I'm really curious to test the tool on my assembly!

I did as you suggested and also giving a trial to binny --setup and the following error appears:

Preparing NLP Resources!
Traceback (most recent call last):
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/__main__.py", line 224, in binny_setup
    check_installation(mantis_config=mantis_cfg, no_taxonomy=True)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/assembler.py", line 27, in check_installation
    mantis.check_installation(check_sql=check_sql)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/assembler.py", line 628, in check_installation
    raise InstallationCheckNotPassed
mantis.exceptions.InstallationCheckNotPassed: Installation check not passed! Make sure you've setup the databases

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/bin/binny", line 10, in <module>
    sys.exit(main())
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/__main__.py", line 293, in main
    binny_setup(arguments)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/__main__.py", line 227, in binny_setup
    setup_databases(mantis_config=mantis_cfg, no_taxonomy=True, chunk_size=1200, cores=args.threads)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/assembler.py", line 21, in setup_databases
    mantis.setup_databases()
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/utils.py", line 610, in wrapper
    res = f(self, *args, **kwargs)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/database_generator.py", line 109, in setup_databases
    UniFunc_wrapper.__init__(self)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/unifunc_wrapper.py", line 25, in __init__
    UniFunc.__init__(self)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/UniFunc/unifunc/source.py", line 1082, in __init__
    self.tagger = PerceptronTagger()
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/nltk/tag/perceptron.py", line 183, in __init__
    self.load_from_json(lang)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/nltk/tag/perceptron.py", line 273, in load_from_json
    loc = find(f"taggers/averaged_perceptron_tagger_{lang}/")
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/nltk/data.py", line 579, in find
    raise LookupError(resource_not_found)
LookupError:
**********************************************************************
  Resource averaged_perceptron_tagger_eng not found.
  Please use the NLTK Downloader to obtain the resource:

  >>> import nltk
  >>> nltk.download('averaged_perceptron_tagger_eng')

  For more information see: https://www.nltk.org/data.html

  Attempted to load taggers/averaged_perceptron_tagger_eng/

  Searched in:
    - '/home/lgallucc/nltk_data'
    - '/bioinf/home/lgallucc/software/miniconda3/envs/binny/nltk_data'
    - '/bioinf/home/lgallucc/software/miniconda3/envs/binny/share/nltk_data'
    - '/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/nltk_data'
    - '/usr/share/nltk_data'
    - '/usr/local/share/nltk_data'
    - '/usr/lib/nltk_data'
    - '/usr/local/lib/nltk_data'
**********************************************************************

If I have already installed a conda env for Mantis and Prokka and I have a database ofr CheckM, how I can address this with the conda installation? I will use this on a Slurm server, so in principle I can setup the cluster setting but I prefer to have a control on it and just running interactively.

I also have a co-assembly, so I can give to it multiple depth files and my contigs, to use it automatically in coassembly mode, right?

[ohickl]

I couldn't reproduce with another fresh install unfortunately. Can you try this:

# Choose env manager
env_manager="micromamba" # micromamba mamba conda  # USER INPUT

# Optionally, clean cache etc.
${env_manager} clean --all --yes  # USER INPUT
# Check carefully if this is ok!!!
# rm -rf ~/${env_manager}/pkgs/*  # USER INPUT

# Create binny env
${env_manager} create -n binny bioconda::binny

# Set custom db path
binny_db="$SCRATCH/databases/binny"  # USER INPUT

# Setup binny
binny \
  --setup  \
  --db_path ${binny_db}

# Run binny test
cd /dev/shm  # USER INPUT
tmp_dir=$(mktemp -d binny_test_XXXXXX)
cd ${tmp_dir}

# Get test data
wget https://raw.githubusercontent.com/a-h-b/binny/refs/heads/main/test/contigs_4bins.fa
wget https://raw.githubusercontent.com/a-h-b/binny/refs/heads/main/test/reads_4bins.bam
wget https://raw.githubusercontent.com/a-h-b/binny/refs/heads/main/test/reads_4bins2.bam

# Run binny
binny_threads=16  # USER INPUT
binny_tmp_dir="/dev/shm/binny_tmp"  # USER INPUT

binny \
  --assembly "${PWD}"/contigs_4bins.fa \
  --bam "${PWD}"/reads_4bins*.bam \
  --outputdir "${PWD}"/binny_out \
  --tmp_dir ${binny_tmp_dir} \
  --db_path ${binny_db} \
  --threads ${binny_threads}

, adjusting the necessary vars to your liking?
Regarding the co-assembly mode, if you keep the default (auto) it will detect if there are >1 input bam or contig depth tables and use co-assembly mode. Or you can set --coassembly_mode on.
You could try the manual install with your existing mantis and prokka envs etc. but i think it is more robust and easier doing it like the above. It also ensure version compatibility.

Let me know if that works for you!

[l-gallucci]

I tried to replicate this but unfortunately I cannot delete the entire pkgs folder. Maybe, something there is creating the conflict. I cleaned everything related to binny, but this is not changing the installation...and the setup flag output.

This is the complete log:

binny \
  --setup  \
  --db_path ${binny_db}
Cloning into '/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/UniFunc'...
remote: Enumerating objects: 224, done.
remote: Total 224 (delta 0), reused 0 (delta 0), pack-reused 224 (from 1)
Receiving objects: 100% (224/224), 24.10 MiB | 16.57 MiB/s, done.
Resolving deltas: 100% (111/111), done.
Updating files: 100% (23/23), done.
Checking Mantis setup.
Checking installation
Using custom MANTIS.cfg: /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/config/binny_mantis.cfg
Default references folder:
/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/References/
Resources folder:
/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/
Custom references folder:
/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/References/Custom_references/
------------------------------------------
# Custom references:
/bioinf/home/lgallucc/databases/binni//hmms/checkm_tf/
/bioinf/home/lgallucc/databases/binni//hmms/checkm_pf/
#  Weights:
checkm_filtered_tf:0.5, checkm_filtered_pf:1.0

Metadata file missing: /bioinf/home/lgallucc/databases/binni//hmms/checkm_tf/metadata.tsv
Metadata file missing: /bioinf/home/lgallucc/databases/binni//hmms/checkm_pf/metadata.tsv
Cython needs to be compiled!
Checking extra files
Passed installation check on: /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/essential_genes
Failed installation check on [files missing]: /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/NCBI/gc.prt.dmp
Checking references installation
Passed installation check on: /bioinf/home/lgallucc/databases/binni//hmms/checkm_tf/
Passed installation check on: /bioinf/home/lgallucc/databases/binni//hmms/checkm_pf/
Installation check failed on:
/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/NCBI/

------------------------------------------
--------INSTALLATION CHECK FAILED!--------
------------------------------------------
#  Setting up databases
Using custom MANTIS.cfg: /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/config/binny_mantis.cfg
Default references folder:
/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/References/
Resources folder:
/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/
Custom references folder:
/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/References/Custom_references/
------------------------------------------
# Custom references:
/bioinf/home/lgallucc/databases/binni//hmms/checkm_tf/
/bioinf/home/lgallucc/databases/binni//hmms/checkm_pf/
#  Weights:
checkm_filtered_tf:0.5, checkm_filtered_pf:1.0

Compiling /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/cython_src/get_non_overlapping_hits.pyx because it changed.
[1/1] Cythonizing /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/cython_src/get_non_overlapping_hits.pyx
running build_ext
building 'mantis.cython_src.get_non_overlapping_hits' extension
creating build/temp.linux-x86_64-cpython-310/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/cython_src
/bioinf/home/lgallucc/software/miniconda3/envs/binny/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /bioinf/home/lgallucc/software/miniconda3/envs/binny/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /bioinf/home/lgallucc/software/miniconda3/envs/binny/include -fPIC -I/bioinf/home/lgallucc/software/miniconda3/envs/binny/include/python3.10 -c /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/cython_src/get_non_overlapping_hits.c -o build/temp.linux-x86_64-cpython-310/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/cython_src/get_non_overlapping_hits.o
creating /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/cython_src/mantis/cython_src
/bioinf/home/lgallucc/software/miniconda3/envs/binny/bin/x86_64-conda-linux-gnu-cc -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -Wl,-rpath-link,/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -L/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -Wl,-rpath-link,/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -L/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -Wl,-rpath-link,/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -L/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /bioinf/home/lgallucc/software/miniconda3/envs/binny/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /bioinf/home/lgallucc/software/miniconda3/envs/binny/include build/temp.linux-x86_64-cpython-310/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/cython_src/get_non_overlapping_hits.o -o /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/cython_src/mantis/cython_src/get_non_overlapping_hits.cpython-310-x86_64-linux-gnu.so
Database will be setup with 1 workers!
/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/NCBI/gc.prt
#  Finished downloading all data!
#  Will now split data into chunks!
Checking which HMMs need to be split, this may take a while...
Will split:  []
Database will be split with 1 workers!
Checking which custom hmms need to be pressed
HMMs will be pressed with 1 workers!
Preparing NLP Resources!
Traceback (most recent call last):
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/__main__.py", line 224, in binny_setup
    check_installation(mantis_config=mantis_cfg, no_taxonomy=True)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/assembler.py", line 27, in check_installation
    mantis.check_installation(check_sql=check_sql)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/assembler.py", line 628, in check_installation
    raise InstallationCheckNotPassed
mantis.exceptions.InstallationCheckNotPassed: Installation check not passed! Make sure you've setup the databases

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/bin/binny", line 10, in <module>
    sys.exit(main())
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/__main__.py", line 293, in main
    binny_setup(arguments)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/__main__.py", line 227, in binny_setup
    setup_databases(mantis_config=mantis_cfg, no_taxonomy=True, chunk_size=1200, cores=args.threads)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/assembler.py", line 21, in setup_databases
    mantis.setup_databases()
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/utils.py", line 610, in wrapper
    res = f(self, *args, **kwargs)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/database_generator.py", line 109, in setup_databases
    UniFunc_wrapper.__init__(self)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/mantis/unifunc_wrapper.py", line 25, in __init__
    UniFunc.__init__(self)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/Resources/UniFunc/unifunc/source.py", line 1082, in __init__
    self.tagger = PerceptronTagger()
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/nltk/tag/perceptron.py", line 183, in __init__
    self.load_from_json(lang)
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/nltk/tag/perceptron.py", line 273, in load_from_json
    loc = find(f"taggers/averaged_perceptron_tagger_{lang}/")
  File "/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/nltk/data.py", line 579, in find
    raise LookupError(resource_not_found)
LookupError:
**********************************************************************
  Resource averaged_perceptron_tagger_eng not found.
  Please use the NLTK Downloader to obtain the resource:

  >>> import nltk
  >>> nltk.download('averaged_perceptron_tagger_eng')

  For more information see: https://www.nltk.org/data.html

  Attempted to load taggers/averaged_perceptron_tagger_eng/

  Searched in:
    - '/home/lgallucc/nltk_data'
    - '/bioinf/home/lgallucc/software/miniconda3/envs/binny/nltk_data'
    - '/bioinf/home/lgallucc/software/miniconda3/envs/binny/share/nltk_data'
    - '/bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/nltk_data'
    - '/usr/share/nltk_data'
    - '/usr/local/share/nltk_data'
    - '/usr/lib/nltk_data'
    - '/usr/local/lib/nltk_data'
**********************************************************************

[ohickl]

Strange. What if you just did python -c "import nltk;nltk.download('averaged_perceptron_tagger_eng')" with the binny env activated and the tried the setup + test again, as a workaround?

[l-gallucci]

That actually worked to get out the -setup command, thank you!!

I still have these warning, but maybe is normal for the setup command (?)

[Tue Jun 24 19:57:42 2025]
Job 1: binny: Running Python Binny.
Reason: Missing output files: /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/test/out/binny.done; Input files updated by another job: /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/test/out/intermediary/mantis_out/consensus_annotation.tsv, /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/test/out/intermediary/assembly.contig_depth.txt, /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/test/out/intermediary/assembly.formatted.fa, /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/test/out/intermediary/annotation.filt.gff

[Tue Jun 24 19:57:42 2025]
localrule ALL:
    input: /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/test/out/binny.done
    jobid: 0
    reason: Input files updated by another job: /bioinf/home/lgallucc/software/miniconda3/envs/binny/lib/python3.10/site-packages/binny/test/out/binny.done
    resources: tmpdir=/tmp

Job stats:
job                          count    min threads    max threads
-------------------------  -------  -------------  -------------
ALL                              1              1              1
annotate                         1              1              1
binny                            1              1              1
call_contig_depth                2              1              1
format_assembly                  1              1              1
mantis_checkm_marker_sets        1              1              1
merge_contig_depths              1              1              1
prepare_input_data               1              1              1
total                            9              1              1

Reasons:
    (check individual jobs above for details)
    input files updated by another job:
        ALL, annotate, binny, call_contig_depth, format_assembly, mantis_checkm_marker_sets, merge_contig_depths
    missing output files:
        annotate, binny, call_contig_depth, format_assembly, mantis_checkm_marker_sets, merge_contig_depths, prepare_input_data

This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.

[ohickl]

Sorry, i overlooked this! It looks just fine for a dry-run.