BGFLOW error

[sadhanokar]

I have been working on BGCFLOW for both MacOS and Ubantu . But still, this error was showing.
Running Snakemake with command:

cd . && snakemake --snakefile workflow/Snakefile --use-conda --keep-going --rerun-incomplete --rerun-triggers mtime -c 4 --dryrun     --wms-monitor http://127.0.0.1:5000/
SyntaxError in file /home/arvind-kayande/my_bgcflow_dir/workflow/rules/common.smk, line 93:
invalid syntax. Perhaps you forgot a comma?:
        input_path = base_path / p.config["input_folder"].

[matinnuhamunada]

Hi @sadhanokar, can you go to the bgcflow directory and do this for me?

git fetch
git status
git diff

Can you then copy paste the stdout output here?

[sadhanokar]

Thank you for reply please find the query you asked.Thank you (bgcflow) ***@***.*** my_bgcflow_dir % git fetch remote: Enumerating objects: 13, done. remote: Counting objects: 100% (13/13), done. remote: Compressing objects: 100% (5/5), done. remote: Total 13 (delta 9), reused 10 (delta 8), pack-reused 0 (from 0) Unpacking objects: 100% (13/13), 1.28 KiB | 93.00 KiB/s, done. From https://github.com/NBChub/bgcflow 9ccecc7..c0a91be main -> origin/main 866d927..e274870 dev-1.1.2 -> origin/dev-1.1.2 (bgcflow) ***@***.*** my_bgcflow_dir % git status On branch main Your branch is behind 'origin/main' by 3 commits, and can be fast-forwarded. (use "git pull" to update your local branch) Changes not staged for commit: (use "git add/rm <file>..." to update what will be committed) (use "git restore <file>..." to discard changes in working directory) deleted: workflow/Report no changes added to commit (use "git add" and/or "git commit -a") (bgcflow) ***@***.*** my_bgcflow_dir % git diff *diff --git a/workflow/Report b/workflow/Report* *deleted file mode 100644* *index 43a7f03..0000000* *--- a/workflow/Report* *+++ /dev/null* @@ -1,37 +0,0 @@

…

-include: "rules/common.smk" - -##### 1. Extract information from config file

-DF_PROJECTS, DF_SAMPLES, PROKKA_DB_TABLE, PROKKA_DB_MAP, PEP_PROJECTS = extract_project_information(config) - -##### Target rules #####

-py_wildcards = []

-rpy_wildcards = []

-markdown = [] -

-rules_dict_path = "workflow/rules.yaml"

-with open(rules_dict_path, "r") as f: - rules_dict = yaml.safe_load(f) -

-metadata = []

-for name in PEP_PROJECTS.keys(): : Regards, *Akshay Dhanokar* Ph.D. Scholar C/O Dr. Arvind P.Singh Public Health and Genomics Lab, Department Of Microbiology, School Of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India

On Thu, Dec 5, 2024 at 12:29 PM Matin Nuhamunada ***@***.***> wrote: Hi @sadhanokar <https://github.com/sadhanokar>, can you go to the bgcflow directory and do this for me? git fetch git status git diff Can you then copy paste the stdout output here? — Reply to this email directly, view it on GitHub <#366 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BNOZXPYMVDB3O2S5C4M4IWL2D72VRAVCNFSM6AAAAABTBR3N2WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMJZGM4TQNZXGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[matinnuhamunada]

It seems you made a change to the workflow?

Can you do:

git stash
git pull
bgcflow run -n

[sadhanokar]

Thank you for mail. Please find the query results. % git stash Saved working directory and index state WIP on main: 9ccecc7 feat: use env variable to run antiSMASH fungi mode (bgcflow) ***@***.*** my_bgcflow_dir % git pull Updating 9ccecc7..c0a91be Fast-forward workflow/envs/r_notebook.yaml | 1 - workflow/rules/common.smk | 2 +- workflow/rules/roary.smk | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) (bgcflow) ***@***.*** my_bgcflow_dir % bgcflow run -n Monitoring BGCFlow jobs with Panoptes... DEBUG 05/12 14:22:30 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:30 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Running Panoptes to monitor BGCFlow jobs at http://127.0.0.1:5000 Panoptes job id: 12126 Connecting to Panoptes... DEBUG 05/12 14:22:30 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:30 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 1x * Serving Flask app 'panoptes.app' * Debug mode: off DEBUG 05/12 14:22:31 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:31 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 2x DEBUG 05/12 14:22:32 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:32 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 3x DEBUG 05/12 14:22:33 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:33 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 4x DEBUG 05/12 14:22:34 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:34 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 5x DEBUG 05/12 14:22:35 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:35 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 6x DEBUG 05/12 14:22:36 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:36 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 7x DEBUG 05/12 14:22:37 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:37 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 8x DEBUG 05/12 14:22:38 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:38 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 9x DEBUG 05/12 14:22:39 Starting new HTTP connection (1): 127.0.0.1:5000 DEBUG 05/12 14:22:39 http://127.0.0.1:5000 "GET /api/service-info HTTP/11" 403 0 Retrying to connect: 10x DEBUG: Using 8 out of 8 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 Problem with server: http://127.0.0.1:5000 Stopping panoptes server: PID 12126 (bgcflow) ***@***.*** my_bgcflow_dir % Regards, *Akshay Dhanokar* Ph.D. Scholar Department Of Microbiology, School Of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India

…

On Thu, Dec 5, 2024 at 1:01 PM Matin Nuhamunada ***@***.***> wrote: It seems you made a change to the workflow? Can you do: git stash git pull bgcflow run -n — Reply to this email directly, view it on GitHub <#366 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BNOZXP3XO5MA32BZXQGR75L2D76N5AVCNFSM6AAAAABTBR3N2WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMJZGQ2TMOBUHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[matinnuhamunada]

@sadhanokar did you manage to resolve your issue?

[sadhanokar]

No issue still remains the same. Regards, *Akshay Dhanokar* Ph.D. Scholar Department Of Microbiology, School Of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India

…

On Thu, Dec 5, 2024 at 6:37 PM Matin Nuhamunada ***@***.***> wrote: @sadhanokar <https://github.com/sadhanokar> did you manage to resolve your issue? — Reply to this email directly, view it on GitHub <#366 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BNOZXPZCTMZAKPSPFFYOLY32EBFYDAVCNFSM6AAAAABTBR3N2WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMRQGI3TQMBUGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>