bgcflow run -n command #358
Comments
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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:
snakemake --snakefile workflow/Snakefile --use-conda --keep-going --rerun-incomplete --rerun-triggers mtime -c 8 --dryrun
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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:
1. 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?
2. 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
3. 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)
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Have you tried following the instruction in the error message?
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 |
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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
<#358 (comment)>,
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.
You are receiving this because you were mentioned.Message ID:
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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 |
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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_ Select jobs to execute... [Wed Sep 25 15:14:37 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ Select jobs to execute... [Wed Sep 25 15:14:41 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ Select jobs to execute... [Wed Sep 25 15:14:41 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ Select jobs to execute... [Wed Sep 25 15:14:41 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ Select jobs to execute... [Wed Sep 25 15:14:42 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:42 2024] [Wed Sep 25 15:14:45 2024] [Wed Sep 25 15:14:49 2024] [Wed Sep 25 15:14:37 2024] Select jobs to execute... [Wed Sep 25 15:14:37 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ Select jobs to execute... [Wed Sep 25 15:14:41 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ Select jobs to execute... [Wed Sep 25 15:14:41 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ Select jobs to execute... [Wed Sep 25 15:14:41 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ Select jobs to execute... [Wed Sep 25 15:14:42 2024] Activating conda environment: .snakemake/conda/6108734d128c0fa773849e795b21d0f5_ [Wed Sep 25 15:14:42 2024] [Wed Sep 25 15:14:45 2024] [Wed Sep 25 15:14:49 2024] [Wed Sep 25 15:14:49 2024] [Wed Sep 25 15:14:50 2024] Exiting because a job execution failed. Look above for error message [Wed Sep 25 15:14:49 2024] [Wed Sep 25 15:14:50 2024] Exiting because a job execution failed. Look above for error message |
|
Glad that it works! To make the report, you need to finish the analysis first. Which means you need to run |
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i did try on mamba but there were issues. is their a docker containerfor bgcflow? Monitoring BGCFlow jobs with Panoptes... DEBUG: Using 8 out of 80 available cores Running Snakemake with command: File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py", line 974, in json File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/init.py", line 346, in loads File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/decoder.py", line 337, in decode File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/json/decoder.py", line 355, in raw_decode 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 File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 1896, in args_to_api File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/cli.py", line 1807, in setup_log_handlers File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py", line 148, in init File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/snakemake/logging.py", line 199, in create_workflow File "/home/simrann/miniforge-pypy3/envs/bgcflow/lib/python3.11/site-packages/requests/models.py", line 978, in json requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0) |
|
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?
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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? We are still working on the Docker containerization, but don't expect it to be done before December |
|
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
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