Error in running the pipeline

[inquisithustler]

Hi I configured a virus config with "Virus_Pathogen" which includes a virus_pathogen_database.fna and I have been getting the following error message persistently: VPIPE_BASEDIR = /my_path_to/V-pipe/workflow
Using base configuration virus VIRUS_PATHOGEN
AttributeError in file /my_path_to/V-pipe/workflow/rules/common.smk, line 252:
'str' object has no attribute 'setdefault'
File "/my_path_to/V-pipe/workflow/Snakefile", line 15, in
File "/my_path_to/V-pipe/workflow/rules/common.smk", line 286, in
File "/my_path_to/V-pipe/workflow/rules/common.smk", line 252, in process_config
File "/home/miniconda3/lib/python3.10/site-packages/jsonschema/validators.py", line 450, in validate
File "/home/miniconda3/lib/python3.10/site-packages/jsonschema/validators.py", line 384, in iter_errors
File "/home/miniconda3/lib/python3.10/site-packages/jsonschema/_keywords.py", line 296, in properties
File "/home/miniconda3/lib/python3.10/site-packages/jsonschema/validators.py", line 432, in descend

Please kindly me solve!
Thanks

[DrYak]

Hi!

This error message is generated by the Schema validator.
Some how, the configuration files are invalid.
But without seeing them I can't help much.

Could you provide all the concerned yaml/json files
Thank you!

Also how did you create Virus_Pathogen? Could you provide those files too?

[inquisithustler]

Hi!

I have attached the concerned config file, the corresponding Virus_pathogen config file.

To add, I created a directory "virus_pathogen" in the resource directory and added my reference files in the "virus_pathogen" directory

Here are the files:
virus_pathogen.txt

config.txt

[DrYak]

I've noticed two things in the files you have posted:

In the config.yaml, there is a syntax error in the YAML syntax:

preprocessing:
    extra = -ns_max_n 4 -min_qual_mean 30 -trim_qual_left 30 -trim_qual_right 30 -trim_qual_window 30 
    #    ^^^- error here

as you might have already guessed by the syntax highlight of GitHub, the = isn't recognized, YAML syntax uses : instead.
(What happens then is that snakemake loads the whole line extra = -ns_max 4… as a single string instead of a key:value pair containing option names as keys and their values as, well values)

The correct syntax should have been:

preprocessing:
    extra: -ns_max_n 4 -min_qual_mean 30 -trim_qual_left 30 -trim_qual_right 30 -trim_qual_window 30 
    #    ^^^- fixed.

In the virus_pathogen.yaml file, there are these two path:

input:
    reference: "V-pipe/resources/virus_pathogen/virus_pathogen_database.fasta"
    
bwa_QA:
    ref_panel: "V-pipe/resources/virus_pathogen/pprv.fasta"

Realtive paths in V-pipe are always relative to the current working directory (which if I am following correctly is in /data/ICMR_BS/work, right?). The way you've writtent virus_pathogen, it looks for a sub-directory called "V-pipe", in the current directory (i.e.: /data/ICMR_BS/work/V-pipe/resources/virus_pathogen/pprv.fasta). If you want to refere to files that you've stored into V-pipe's own resource directory, you can use a macro (like, e.g., hiv.yaml does):

input:
    reference: "{VPIPE_BASEDIR}/../resources/virus_pathogen/virus_pathogen_database.fasta"
    
bwa_QA:
    ref_panel: "{VPIPE_BASEDIR}/../resources/virus_pathogen/pprv.fasta"

(Note that the macro points to the directory holding the Snakefile, i.e.: V-pipe/workflow/, hence the ../resources/ to reach the correct directory).