bgcflow run -n command - Githubissues

coderbins commented 2 months ago

(bgcflow) [n@login01 bgcflow]$ bgcflow init -n
Usage: bgcflow init [OPTIONS]
Try 'bgcflow init -h' for help.

Error: No such option: -n
(bgcflow) [n@login01 bgcflow]$ bgcflow init
DEBUG   23/09 12:30:14   Found config file at: /home/n/bgcflow/bgcflow/config/config.yaml
DEBUG   23/09 12:30:14   Creating Project from file /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/project_config.yaml
DEBUG   23/09 12:30:14   Creating a Project from a YAML file: /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/project_config.yaml
DEBUG   23/09 12:30:14   Raw (/home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/project_config.yaml) config data: {'name': 'Lactobacillus_delbrueckii', 'pep_version': '2.1.0', 'description': 'Lactobacillus delbrueckii 27 01 2023', 'sample_table': 'samples.csv', 'rules': {'seqfu': True, 'mash': True, 'fastani': True, 'checkm': True, 'gtdbtk': False, 'prokka-gbk': True, 'antismash': True, 'query-bigslice': False, 'bigscape': True, 'bigslice': True, 'automlst-wrapper': True, 'arts': True, 'roary': False, 'eggnog': False, 'eggnog-roary': False, 'deeptfactor': True, 'deeptfactor-roary': False, 'cblaster-genome': True, 'cblaster-bgc': False, 'gecco': True, 'amrfinderplus': False}}
DEBUG   23/09 12:30:14   Adding attributes: name, pep_version, description, sample_table, rules
DEBUG   23/09 12:30:14   Ensuring absolute path for 'samples.csv'
DEBUG   23/09 12:30:14   config_dirpath: /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii
DEBUG   23/09 12:30:14   Expanded and/or made absolute: /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/samples.csv
DEBUG   23/09 12:30:14   Setting 'sample_table' to '/home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/samples.csv'
DEBUG   23/09 12:30:14   No 'subsample_table' section in configuration file: /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/project_config.yaml
DEBUG   23/09 12:30:14   No subsample_table specified
DEBUG   23/09 12:30:14   Sample data: OrderedDict([('genome_id', 'GCA_000056065.1'), ('source', 'ncbi'), ('organism', None), ('genus', None), ('species', None), ('strain', None), ('closest_placement_reference', None), ('input_file', None)])
DEBUG   23/09 12:30:14   Sample data: OrderedDict([('genome_id', 'GCA_000182835.1'), ('source', 'ncbi'), ('organism', None), ('genus', None), ('species', None), ('strain', None), ('closest_placement_reference', None), ('input_file', None)])
DEBUG   23/09 12:30:14   Sample data: OrderedDict([('genome_id', 'GCA_000191165.1'), ('source', 'ncbi'), ('organism', None), ('genus', None), ('species', None), ('strain', None), ('closest_placement_reference', None), ('input_file', None)])
DEBUG   23/09 12:30:14   Sample data: OrderedDict([('genome_id', 'GCA_000014405.1'), ('source', 'ncbi'), ('organism', None), ('genus', None), ('species', None), ('strain', None), ('closest_placement_reference', None), ('input_file', None)])
DEBUG   23/09 12:30:14   Checking existence: None
DEBUG   23/09 12:30:14   Checking existence: remove
DEBUG   23/09 12:30:14   Checking existence: append
DEBUG   23/09 12:30:14   Checking existence: duplicate
DEBUG   23/09 12:30:14   Checking existence: imply
DEBUG   23/09 12:30:14   No subsample_table found, skipping merge
DEBUG   23/09 12:30:14   Checking existence: derive
DEBUG   23/09 12:30:14   Checking existence: None
DEBUG   23/09 12:30:14   Setting sample_table index to: ['genome_id']
Available projects:
 - Lactobacillus_delbrueckii : /home/n/bgcflow/bgcflow/config/Lactobacillus_delbrueckii/samples.csv

Do a test run by: `bgcflow run -n`

(bgcflow) [n@login01 bgcflow]$ bgcflow run -n
Monitoring BGCFlow jobs with Panoptes...
DEBUG   23/09 12:30:32   Starting new HTTP connection (1): 127.0.0.1:5000
DEBUG   23/09 12:30:32   http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 200 21
Panoptes already running on http://127.0.0.1:5000
Connecting to Panoptes...
DEBUG   23/09 12:30:32   Starting new HTTP connection (1): 127.0.0.1:5000
DEBUG   23/09 12:30:32   http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 200 21
Panoptes status: running

DEBUG: Using 8 out of 80 available cores

Running Snakemake with command:
cd . && snakemake --snakefile workflow/Snakefile --use-conda --keep-going --rerun-incomplete --rerun-triggers mtime -c 8 --dryrun   --wms-monitor http://127.0.0.1:5000
Traceback (most recent call last):

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py", line 974, in json
    return complexjson.loads(self.text, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None

json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 2155, in main
    success = args_to_api(args, parser)
            ^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 1896, in args_to_api
    log_handlers = setup_log_handlers(args, parser)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 1807, in setup_log_handlers
    wms_logger = logging.WMSLogger(
                ^^^^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py", line 148, in __init__
    self.create_workflow()

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py", line 199, in create_workflow
    id = response.json()["id"]
        ^^^^^^^^^^^^^^^

  File "/home/n/anaconda3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py", line 978, in json
    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)

requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

matinnuhamunada commented 2 months ago

Hi @coderbins, from the error message, I can see that you have successfully created a project configuration from the template but failed to run the project.

I cannot reproduce this error, but it's either an error reading the project config or problem with panoptes (the monitoring workflow).

What I can think about is:

Did you make any changes to the configuration files before running the workflow? If yes, can you share it here so we can debug it together?

In case there is an error in running panoptes, try running it using the vanilla snakemake command and see if it works?:

snakemake --snakefile workflow/Snakefile --use-conda --keep-going --rerun-incomplete --rerun-triggers mtime -c 8 --dryrun

Can you give me your system detail? Which linux version etc. And maybe export the conda environment and share it here (using conda env export > coderbins.yaml)

coderbins commented 2 months ago

thank you so much for replying

error: This is BGCflow version 1.1.1.

Checking dependencies... Found configuration setting to use antiSMASH 7 antismash from: workflow/envs/antismash.yaml

antismash will be installed from git+ https://github.com/antismash/antismash.git
antismash==7.1.0 bigslice from: workflow/envs/bigslice.yaml
bigslice will be installed from git+ https://github.com/NBChub/bigslice.git
bigslice==c0085de cblaster from: workflow/envs/cblaster.yaml
cblaster will be installed using pip
cblaster==1.3.18 prokka from: workflow/envs/prokka.yaml
prokka==1.14.6 eggnog-mapper from: workflow/envs/eggnog.yaml
eggnog-mapper==2.1.6 roary from: workflow/envs/roary.yaml
roary==3.13.0 seqfu from: workflow/envs/seqfu.yaml
seqfu==1.20.3 checkm from: workflow/envs/checkm.yaml
checkm==1.2.2 gtdbtk from: workflow/envs/gtdbtk.yaml
gtdbtk==2.3.0 gecco from: workflow/envs/gecco.yaml
gecco==0.9.10

Step 1. Extracting project information from config...

Step 2.1 Getting sample information from: config/Lactobacillus_delbrueckii/project_config.yaml

Processing project [config/Lactobacillus_delbrueckii/project_config.yaml]
Custom input directory: False
Getting input files from: /home/simrann/bgcflow/bgcflow/data/raw/fasta
Custom input format: False
Default input file type: fna

Step 3. Merging genome_ids across projects...

Step 4. Preparing list of final outputs...

Getting outputs for project: Lactobacillus_delbrueckii
WARNING: ignoring errors in rule_dictionary
Ready to generate all outputs.

Step 5. Checking for user-defined local resources...

Symlink for resources/bigslice/full_run_result has more than two levels, using only the first two... All resources set.

Checking GTDB API...

GTDB API | Grabbing metadata using GTDB release version: r214
GTDB API | Testing connection to: https://gtdb-api.ecogenomic.org/status/db
GTDB API | Database is online: True
GTDB API | Searching in offline mode: False Building DAG of jobs... CreateCondaEnvironmentException: The 'mamba' command is not available in the shell /usr/bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with conda activate base.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with conda install -n base -c conda-forge mamba. If you still prefer to use conda, you can enforce that by setting --conda-frontend conda.

On Mon, Sep 23, 2024 at 1:53 PM Matin Nuhamunada @.***> wrote:

Hi @coderbins https://github.com/coderbins, from the error message, I can see that you have successfully created a project configuration from the template but failed to run the project.

I cannot reproduce this error, but it's either an error reading the project config or problem with panoptes (the monitoring workflow).

What I can think about is:

Did you make any changes to the configuration files before running the workflow? If yes, can you share it here so we can debug it together?

In case there is an error in running panoptes, try running it using the vanilla snakemake command and see if it works?:

snakemake --snakefile workflow/Snakefile --use-conda --keep-going --rerun-incomplete --rerun-triggers mtime -c 8 --dryrun

Can you give me your system detail? Which linux version etc. And maybe export the conda environment and share it here (using conda env export > coderbins.yaml)

— Reply to this email directly, view it on GitHub https://github.com/NBChub/bgcflow/issues/358#issuecomment-2367529969, or unsubscribe https://github.com/notifications/unsubscribe-auth/BLQHJY3N4BZDVIZZGAXNZGDZX7FYDAVCNFSM6AAAAABOVOMV2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRXGUZDSOJWHE . You are receiving this because you were mentioned.Message ID: @.***>

matinnuhamunada commented 2 months ago

Have you tried following the instruction in the error message?

The 'mamba' command is not available in the shell /usr/bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with conda activate base.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with conda install -n base -c conda-forge mamba. If you still prefer to use conda, you can enforce that by setting --conda-frontend conda.

As described in the installation wiki: https://github.com/NBChub/bgcflow/wiki/00-Installation-Guide#conda-package-manager, we recommend using https://github.com/conda-forge/miniforge#mambaforge rather than anaconda or conda installer

coderbins commented 2 months ago

yes sir. I did.

(base) @.*** bgcflow]$ conda install -n base -c conda-forge mamba Channels:

conda-forge
defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: / warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE failed

LibMambaUnsatisfiableError: Encountered problems while solving:

nothing provides package_has_been_revoked needed by anaconda-navigator-2.6.0-py310h06a4308_1

Could not solve for environment specs The following packages are incompatible ├─ anaconda-navigator 2.6.0. is installable with the potential options │ ├─ anaconda-navigator 2.6.0 would require │ │ └─ pyqtwebengine >=5.15.10,<6.0a0 with the potential options │ │ ├─ pyqtwebengine 5.15.10 would require │ │ │ └─ qt-webengine >=5.15.9,<5.16.0a0 with the potential options │ │ │ ├─ qt-webengine 5.15.9 would require │ │ │ │ └─ libxml2 >=2.10.3,<2.11.0a0 with the potential options │ │ │ │ ├─ libxml2 2.10.4 would require │ │ │ │ │ └─ icu >=73.1,<74.0a0 with the potential options │ │ │ │ │ ├─ icu 73.2, which can be installed; │ │ │ │ │ └─ icu 73.1 conflicts with any installable versions previously reported; │ │ │ │ ├─ libxml2 [2.10.3|2.9.14] would require │ │ │ │ │ └─ icu >=70.1,<71.0a0 , which conflicts with any installable versions previously reported; │ │ │ │ ├─ libxml2 [2.10.3|2.10.4] would require │ │ │ │ │ └─ icu >=72.1,<73.0a0 , which conflicts with any installable versions previously reported; │ │ │ │ └─ libxml2 [2.10.3|2.10.4|2.9.14] would require │ │ │ │ └─ icu >=58.2,<59.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ qt-webengine 5.15.9 would require │ │ │ └─ libxml2 >=2.9.14,<2.10.0a0 but there are no viable options │ │ │ ├─ libxml2 [2.10.3|2.9.14], which cannot be installed (as previously explained); │ │ │ ├─ libxml2 [2.10.3|2.10.4|2.9.14], which cannot be installed (as previously explained); │ │ │ └─ libxml2 2.9.14 would require │ │ │ └─ icu 69. , which conflicts with any installable versions previously reported; │ │ ├─ pyqtwebengine 5.15.10 would require │ │ │ └─ python >=3.10,<3.11.0a0 , which can be installed; │ │ ├─ pyqtwebengine 5.15.10 would require │ │ │ └─ python >=3.11,<3.12.0a0 , which can be installed; │ │ ├─ pyqtwebengine 5.15.10 would require │ │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ │ └─ pyqtwebengine 5.15.10 would require │ │ └─ python >=3.9,<3.10.0a0 , which can be installed; │ ├─ anaconda-navigator 2.6.0 would require │ │ └─ python >=3.10,<3.11.0a0 , which can be installed; │ ├─ anaconda-navigator 2.6.0 would require │ │ └─ package_has_been_revoked, which does not exist (perhaps a missing channel); │ ├─ anaconda-navigator 2.6.0 would require │ │ └─ python >=3.11,<3.12.0a0 , which can be installed; │ ├─ anaconda-navigator 2.6.0 would require │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ └─ anaconda-navigator 2.6.0 would require │ └─ python >=3.9,<3.10.0a0 , which can be installed; ├─ conda-token is installable with the potential options │ ├─ conda-token 0.5.0 would require │ │ └─ conda >=4.6,!=23.10.0,!=23.11.0 with the potential options │ │ ├─ conda [22.11.0|22.11.1|...|4.14.0] would require │ │ │ └─ python >=3.10,<3.11.0a0 , which can be installed; │ │ ├─ conda [22.11.1|22.9.0|...|24.7.1] would require │ │ │ └─ python >=3.11,<3.12.0a0 , which can be installed; │ │ ├─ conda [22.11.0|22.11.1|...|4.9.2] would require │ │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ │ ├─ conda [22.11.0|22.11.1|...|4.9.2] would require │ │ │ └─ python >=3.9,<3.10.0a0 , which can be installed; │ │ ├─ conda [23.9.0|24.1.0|...|24.7.1], which can be installed; │ │ ├─ conda [22.11.0|22.11.1|...|4.9.2] would require │ │ │ └─ python >=3.7,<3.8.0a0 , which can be installed; │ │ ├─ conda [4.10.0|4.10.1|...|4.9.2] would require │ │ │ └─ python >=3.6,<3.7.0a0 , which can be installed; │ │ └─ conda [4.3.21|4.3.22|...|4.8.4] would require │ │ └─ python [2.7 |>=2.7,<2.8.0a0 ], which can be installed; │ └─ conda-token [0.1.2|0.1.3|0.2.0|0.3.0|0.4.0] would require │ └─ conda >=4.3,<23.9 with the potential options │ ├─ conda [22.11.0|22.11.1|...|4.14.0], which can be installed (as previously explained); │ ├─ conda [22.11.1|22.9.0|...|24.7.1], which can be installed (as previously explained); │ ├─ conda [22.11.0|22.11.1|...|4.9.2], which can be installed (as previously explained); │ ├─ conda [22.11.0|22.11.1|...|4.9.2], which can be installed (as previously explained); │ ├─ conda [22.11.0|22.11.1|...|4.9.2], which can be installed (as previously explained); │ ├─ conda [4.10.0|4.10.1|...|4.9.2], which can be installed (as previously explained); │ ├─ conda [4.3.21|4.3.22|...|4.8.4], which can be installed (as previously explained); │ ├─ conda [4.3.21|4.3.22|...|4.5.9] would require │ │ └─ python [3.5 |>=3.5,<3.6.0a0 ], which can be installed; │ ├─ conda [4.3.21|4.3.22|...|4.5.1] would require │ │ └─ python 3.6 , which can be installed; │ └─ conda [4.3.29|4.3.30] would require │ └─ python >=3.4,<3.5.0a0 , which can be installed; ├─ mamba is installable with the potential options │ ├─ mamba [1.5.2|1.5.3|1.5.7|1.5.8] would require │ │ └─ libmambapy [1.5.2 py312hd9e9ff6_1|1.5.3 py312hd9e9ff6_1|1.5.3 py312hd9e9ff6_2|1.5.7 py312hd9e9ff6_0|1.5.8 py312hd9e9ff6_0], which requires │ │ └─ libmamba [1.5.2 had39da4_1|1.5.3 had39da4_1|1.5.3 had39da4_2|1.5.7 had39da4_0|1.5.8 had39da4_0], which requires │ │ └─ libarchive >=3.7.2,<3.8.0a0 but there are no viable options │ │ ├─ libarchive 3.7.2 would require │ │ │ └─ libxml2 >=2.11.5,<3.0.0a0 but there are no viable options │ │ │ ├─ libxml2 [2.11.5|2.11.6|...|2.12.7] would require │ │ │ │ └─ icu >=73.2,<74.0a0 , which can be installed; │ │ │ ├─ libxml2 2.11.5 would require │ │ │ │ └─ icu >=72.1,<73.0a0 , which conflicts with any installable versions previously reported; │ │ │ ├─ libxml2 2.12.7 would require │ │ │ │ └─ icu >=75.1,<76.0a0 , which conflicts with any installable versions previously reported; │ │ │ └─ libxml2 2.13.1 conflicts with any installable versions previously reported; │ │ ├─ libarchive [3.7.2|3.7.4] would require │ │ │ └─ libxml2 [>=2.12.2,<3.0.0a0 |>=2.12.7,<3.0a0 ] but there are no viable options │ │ │ ├─ libxml2 [2.11.5|2.11.6|...|2.12.7], which cannot be installed (as previously explained); │ │ │ ├─ libxml2 2.12.7, which cannot be installed (as previously explained); │ │ │ └─ libxml2 2.13.1 conflicts with any installable versions previously reported; │ │ └─ libarchive 3.7.4 would require │ │ └─ libxml2 >=2.13.1,<2.14.0a0 , which conflicts with any installable versions previously reported; │ ├─ mamba [0.0.10|0.0.7|0.0.8|0.0.9|0.1.0] would require │ │ └─ python >=2.7,<2.8.0a0 , which can be installed; │ ├─ mamba [0.0.10|0.0.7|...|0.9.2] would require │ │ └─ python >=3.6,<3.7.0a0 , which can be installed; │ ├─ mamba [0.0.10|0.0.7|...|0.9.2] would require │ │ └─ python >=3.7,<3.8.0a0 , which can be installed; │ ├─ mamba [0.1.2|0.10.0|...|1.5.8] would require │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ ├─ mamba [0.10.0|0.11.1|...|1.5.9] would require │ │ └─ python >=3.9,<3.10.0a0 , which can be installed; │ ├─ mamba [0.18.1|0.18.2|...|1.5.9] would require │ │ └─ python >=3.10,<3.11.0a0 , which can be installed; │ ├─ mamba [1.0.0|1.1.0|...|1.5.9] would require │ │ └─ python >=3.11,<3.12.0a0 , which can be installed; │ ├─ mamba [1.5.10|1.5.9] would require │ │ └─ libmambapy [1.5.10 py312h7fb9e8e_0|1.5.9 py312h7fb9e8e_0], which requires │ │ └─ libmamba [1.5.10 h4cc3d14_0|1.5.9 h4cc3d14_0], which requires │ │ └─ libarchive >=3.7.4,<3.8.0a0 , which cannot be installed (as previously explained); │ └─ mamba [1.5.4|1.5.5|1.5.6] would require │ └─ conda >=23.11,<23.12 with the potential options │ ├─ conda [22.11.0|22.11.1|...|4.14.0], which can be installed (as previously explained); │ ├─ conda [22.11.1|22.9.0|...|24.7.1], which can be installed (as previously explained); │ ├─ conda 23.11.0 conflicts with any installable versions previously reported; │ ├─ conda [22.11.0|22.11.1|...|4.9.2], which can be installed (as previously explained); │ └─ conda [22.11.0|22.11.1|...|4.9.2], which can be installed (as previously explained); └─ pin-1 is not installable because it requires └─ python 3.12. , which conflicts with any installable versions previously reported.

On Mon, Sep 23, 2024 at 3:57 PM Matin Nuhamunada @.***> wrote:

Have you tried following the instruction in the error message?

The 'mamba' command is not available in the shell /usr/bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with conda activate base.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with conda install -n base -c conda-forge mamba. If you still prefer to use conda, you can enforce that by setting --conda-frontend conda.

As described in the installation wiki: https://github.com/NBChub/bgcflow/wiki/00-Installation-Guide#conda-package-manager, we recommend using https://github.com/conda-forge/miniforge#mambaforge rather than anaconda or conda installer

— Reply to this email directly, view it on GitHub https://github.com/NBChub/bgcflow/issues/358#issuecomment-2367809083, or unsubscribe https://github.com/notifications/unsubscribe-auth/BLQHJY3KJZIEIJKENYUUQNTZX7UJXAVCNFSM6AAAAABOVOMV2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRXHAYDSMBYGM . You are receiving this because you were mentioned.Message ID: @.***>

matinnuhamunada commented 2 months ago

Hi, this is likely an issue from Anaconda. Please refer to the mamba installation here: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html

I would personally uninstall Anaconda and replace it with miniforge as suggested in the Wiki.

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-Linux-x86_64.sh"
bash Miniforge-pypy3-Linux-x86_64.sh

coderbins commented 2 months ago

Thank you so much. Its working with mamba. but when i try to use 'bgcflow build report'. i am facing certain errors again.

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:37 2024] Error in rule mkdocs_py_report: jobid: 23 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/deeptfactor.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/deeptfactor.md log: logs/report/deeptfactor-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/deeptfactor.ipynb --no-input --output deeptfactor.md 2>> logs/report/deeptfactor-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:37 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/checkm.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/checkm.md log: logs/report/checkm-report-Lactobacillus_delbrueckii.log jobid: 9 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/checkm.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/checkm.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=checkm resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:41 2024] Error in rule mkdocs_py_report: jobid: 15 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/bigscape.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/bigscape.md log: logs/report/bigscape-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/bigscape.ipynb --no-input --output bigscape.md 2>> logs/report/bigscape-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:41 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.md log: logs/report/prokka-gbk-report-Lactobacillus_delbrueckii.log jobid: 11 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=prokka-gbk resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:41 2024] Error in rule mkdocs_py_report: jobid: 27 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/gecco.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/gecco.md log: logs/report/gecco-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/gecco.ipynb --no-input --output gecco.md 2>> logs/report/gecco-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:41 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/seqfu.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/seqfu.md log: logs/report/seqfu-report-Lactobacillus_delbrueckii.log jobid: 1 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/seqfu.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/seqfu.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=seqfu resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:41 2024] Error in rule mkdocs_py_report: jobid: 13 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/antismash.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/antismash.md log: logs/report/antismash-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/antismash.ipynb --no-input --output antismash.md 2>> logs/report/antismash-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:41 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/bigslice.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/bigslice.md log: logs/report/bigslice-report-Lactobacillus_delbrueckii.log jobid: 17 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/bigslice.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/bigslice.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=bigslice resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:42 2024] Error in rule mkdocs_py_report: jobid: 21 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/arts.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/arts.md log: logs/report/arts-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/arts.ipynb --no-input --output arts.md 2>> logs/report/arts-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:42 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/cblaster-genome.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/cblaster-genome.md log: logs/report/cblaster-genome-report-Lactobacillus_delbrueckii.log jobid: 25 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/cblaster-genome.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/cblaster-genome.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=cblaster-genome resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:42 2024] Error in rule mkdocs_py_report: jobid: 5 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/mash.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/mash.md log: logs/report/mash-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/mash.ipynb --no-input --output mash.md 2>> logs/report/mash-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:42 2024] Error in rule mkdocs_py_report: jobid: 7 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/fastani.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/fastani.md log: logs/report/fastani-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/fastani.ipynb --no-input --output fastani.md 2>> logs/report/fastani-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:45 2024] Error in rule mkdocs_rpy_report: jobid: 19 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/automlst-wrapper.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/automlst-wrapper.md log: logs/report/automlst-wrapper-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/51620c99e7ffd92732a8d9f8a0d02483 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/automlst-wrapper.ipynb --no-input --output automlst-wrapper.md 2>> logs/report/automlst-wrapper-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:49 2024] Error in rule mkdocs_py_report: jobid: 9 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/checkm.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/checkm.md log: logs/report/checkm-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/checkm.ipynb --no-input --output checkm.md 2>> logs/report/checkm-report-Lactobacillus_delbrueckii.loActivating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_

[Wed Sep 25 15:14:37 2024] Error in rule mkdocs_py_report: jobid: 23 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/deeptfactor.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/deeptfactor.md log: logs/report/deeptfactor-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/deeptfactor.ipynb --no-input --output deeptfactor.md 2>> logs/report/deeptfactor-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:37 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/checkm.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/checkm.md log: logs/report/checkm-report-Lactobacillus_delbrueckii.log jobid: 9 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/checkm.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/checkm.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=checkm resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:41 2024] Error in rule mkdocs_py_report: jobid: 15 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/bigscape.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/bigscape.md log: logs/report/bigscape-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/bigscape.ipynb --no-input --output bigscape.md 2>> logs/report/bigscape-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:41 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.md log: logs/report/prokka-gbk-report-Lactobacillus_delbrueckii.log jobid: 11 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=prokka-gbk resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:41 2024] Error in rule mkdocs_py_report: jobid: 27 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/gecco.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/gecco.md log: logs/report/gecco-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/gecco.ipynb --no-input --output gecco.md 2>> logs/report/gecco-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:41 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/seqfu.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/seqfu.md log: logs/report/seqfu-report-Lactobacillus_delbrueckii.log jobid: 1 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/seqfu.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/seqfu.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=seqfu resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:41 2024] Error in rule mkdocs_py_report: jobid: 13 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/antismash.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/antismash.md log: logs/report/antismash-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/antismash.ipynb --no-input --output antismash.md 2>> logs/report/antismash-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:41 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/bigslice.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/bigslice.md log: logs/report/bigslice-report-Lactobacillus_delbrueckii.log jobid: 17 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/bigslice.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/bigslice.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=bigslice resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:42 2024] Error in rule mkdocs_py_report: jobid: 21 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/arts.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/arts.md log: logs/report/arts-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/arts.ipynb --no-input --output arts.md 2>> logs/report/arts-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute... Execute 1 jobs...

[Wed Sep 25 15:14:42 2024] localrule mkdocs_py_report: input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/cblaster-genome.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/cblaster-genome.md log: logs/report/cblaster-genome-report-Lactobacillus_delbrueckii.log jobid: 25 reason: Missing output files: data/processed/Lactobacillus_delbrueckii/docs/cblaster-genome.md; Input files updated by another job: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/cblaster-genome.ipynb wildcards: name=Lactobacillus_delbrueckii, bgcflow_rules_py=cblaster-genome resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:42 2024] Error in rule mkdocs_py_report: jobid: 5 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/mash.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/mash.md log: logs/report/mash-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/mash.ipynb --no-input --output mash.md 2>> logs/report/mash-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:42 2024] Error in rule mkdocs_py_report: jobid: 7 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/fastani.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/fastani.md log: logs/report/fastani-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/fastani.ipynb --no-input --output fastani.md 2>> logs/report/fastani-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:45 2024] Error in rule mkdocs_rpy_report: jobid: 19 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/automlst-wrapper.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/automlst-wrapper.md log: logs/report/automlst-wrapper-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/51620c99e7ffd92732a8d9f8a0d02483 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/automlst-wrapper.ipynb --no-input --output automlst-wrapper.md 2>> logs/report/automlst-wrapper-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:49 2024] Error in rule mkdocs_py_report: jobid: 9 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/checkm.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/checkm.md log: logs/report/checkm-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/checkm.ipynb --no-input --output checkm.md 2>> logs/report/checkm-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:49 2024] Finished job 17. 17 of 30 steps (57%) done [Wed Sep 25 15:14:50 2024] Finished job 25. 18 of 30 steps (60%) done [Wed Sep 25 15:14:50 2024] Error in rule mkdocs_py_report: jobid: 1 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/seqfu.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/seqfu.md log: logs/report/seqfu-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/seqfu.ipynb --no-input --output seqfu.md 2>> logs/report/seqfu-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:50 2024] Error in rule mkdocs_py_report: jobid: 11 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.md log: logs/report/prokka-gbk-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.ipynb --no-input --output prokka-gbk.md 2>> logs/report/prokka-gbk-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-25T145500.383306.snakemake.log WorkflowError: At least one job did not complete successfully. g

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:49 2024] Finished job 17. 17 of 30 steps (57%) done [Wed Sep 25 15:14:50 2024] Finished job 25. 18 of 30 steps (60%) done [Wed Sep 25 15:14:50 2024] Error in rule mkdocs_py_report: jobid: 1 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/seqfu.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/seqfu.md log: logs/report/seqfu-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/seqfu.ipynb --no-input --output seqfu.md 2>> logs/report/seqfu-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Wed Sep 25 15:14:50 2024] Error in rule mkdocs_py_report: jobid: 11 input: data/processed/Lactobacillus_delbrueckii/metadata/dependency_versions.json, data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.ipynb output: data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.md log: logs/report/prokka-gbk-report-Lactobacillusdelbrueckii.log (check log file(s) for error details) conda-env: /home/simrann/bgcflow/.snakemake/conda/6108734d128c0fa773849e795b21d0f5 shell:

        jupyter nbconvert --to markdown --execute data/processed/Lactobacillus_delbrueckii/docs/prokka-gbk.ipynb --no-input --output prokka-gbk.md 2>> logs/report/prokka-gbk-report-Lactobacillus_delbrueckii.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-25T145500.383306.snakemake.log WorkflowError: At least one job did not complete successfully.

matinnuhamunada commented 2 months ago

Glad that it works!

To make the report, you need to finish the analysis first. Which means you need to run bgcflow run without the -n (--dry-run). Is that the case?

coderbins commented 2 months ago

i did try on mamba but there were issues. is their a docker containerfor bgcflow? now it is showing this: (bgcflow) [simrann@login01 bgcflow]$ bgcflow run

Monitoring BGCFlow jobs with Panoptes... DEBUG 28/09 15:15:47 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 28/09 15:15:47 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 200 21 Panoptes already running on http://127.0.0.1:5000 Connecting to Panoptes... DEBUG 28/09 15:15:47 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 28/09 15:15:47 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 200 21 Panoptes status: running

DEBUG: Using 8 out of 80 available cores

Running Snakemake with command: cd . && snakemake --snakefile workflow/Snakefile --use-conda --keep-going --rerun-incomplete --rerun-triggers mtime -c 8 --wms-monitor http://127.0.0.1:5000 Traceback (most recent call last):

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py", line 974, in json return complexjson.loads(self.text, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/init.py", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None

json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 2155, in main success = args_to_api(args, parser) ^^^^^^^^^^^^^^^^^^^^^^^^^

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 1896, in args_to_api log_handlers = setup_log_handlers(args, parser) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 1807, in setup_log_handlers wms_logger = logging.WMSLogger( ^^^^^^^^^^^^^^^^^^

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py", line 148, in init self.create_workflow()

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py", line 199, in create_workflow id = response.json()["id"] ^^^^^^^^^^^^^^^

File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py", line 978, in json raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)

requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

coderbins commented 1 month ago

Yes, it does. thank you .

i did try on mamba but there were issues. is their a docker containerfor bgcflow? now it is showing this:

(bgcflow) @.*** bgcflow]$ bgcflow run

Monitoring BGCFlow jobs with Panoptes...
DEBUG 28/09 15:15:47 Starting new HTTP connection (1): 127.0.0.1:5000
DEBUG 28/09 15:15:47 http://127.0.0.1:5000 "GET /api/service-info HTTP/11"
200 21
Panoptes already running on http://127.0.0.1:5000
Connecting to Panoptes...
DEBUG 28/09 15:15:47 Starting new HTTP connection (1): 127.0.0.1:5000
DEBUG 28/09 15:15:47 http://127.0.0.1:5000 "GET /api/service-info HTTP/11"
200 21
Panoptes status: running

DEBUG: Using 8 out of 80 available cores

Running Snakemake with command:
cd . && snakemake --snakefile workflow/Snakefile --use-conda --keep-going
--rerun-incomplete --rerun-triggers mtime -c 8 --wms-monitor
http://127.0.0.1:5000
Traceback (most recent call last):

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py",
line 974, in json
return complexjson.loads(self.text, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/init.py",
line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/decoder.py",
line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/decoder.py",
line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None

json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py",
line 2155, in main
success = args_to_api(args, parser)
^^^^^^^^^^^^^^^^^^^^^^^^^

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py",
line 1896, in args_to_api
log_handlers = setup_log_handlers(args, parser)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py",
line 1807, in setup_log_handlers
wms_logger = logging.WMSLogger(
^^^^^^^^^^^^^^^^^^

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py",
line 148, in init
self.create_workflow()

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py",
line 199, in create_workflow
id = response.json()["id"]
^^^^^^^^^^^^^^^

File
"/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py",
line 978, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)

requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char
0)

On Wed, Sep 25, 2024 at 3:38 PM Matin Nuhamunada @.***> wrote:

Glad that it works!

To make the report, you need to finish the analysis first. Which means you need to run bgcflow run without the -n (--dry-run). Is that the case?

— Reply to this email directly, view it on GitHub https://github.com/NBChub/bgcflow/issues/358#issuecomment-2373644729, or unsubscribe https://github.com/notifications/unsubscribe-auth/BLQHJY7Z6BBZFESFAP4KRV3ZYKDTLAVCNFSM6AAAAABOVOMV2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZTGY2DINZSHE . You are receiving this because you were mentioned.Message ID: @.***>

matinnuhamunada commented 1 month ago

Hi @coderbins , sorry I was a bit occupied with other stuff.

This seems like a panoptes issue, have you already tried running it without the monitoring workflow?

snakemake --snakefile workflow/Snakefile --use-conda --keep-going
--rerun-incomplete --rerun-triggers mtime -c 8

We are still working on the Docker containerization, but don't expect it to be done before December

coderbins commented 1 month ago

Thabk you for replying. I can understand you must be very busy. Yes, i did try this command.

On Fri, 11 Oct 2024 at 2:42 PM, Matin Nuhamunada @.***> wrote:

Hi @coderbins https://github.com/coderbins , sorry I was a bit occupied with other stuff.

This seems like a panoptes issue, have you already tried running it without the monitoring workflow?

snakemake --snakefile workflow/Snakefile --use-conda --keep-going --rerun-incomplete --rerun-triggers mtime -c 8

We are still working on the Docker containerization, but don't expect it to be done before December

— Reply to this email directly, view it on GitHub https://github.com/NBChub/bgcflow/issues/358#issuecomment-2406982459, or unsubscribe https://github.com/notifications/unsubscribe-auth/BLQHJYZV2OD7ZUCVXPBILITZ26I7XAVCNFSM6AAAAABOVOMV2GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBWHE4DENBVHE . You are receiving this because you were mentioned.Message ID: @.***>

NBChub / bgcflow

bgcflow run -n command #358