Error: <Workflow defines configfile config.yaml but it is not present or accessible.>

[AnyaKovalenko]

hi to everyone. Please could somebody help me with my issue? After the installation I ran the following command:

snakemake -s workflow/Snakefile all

and this error comes to me:

WorkflowError in line 8 of /home/artic/ncov-tools/workflow/rules/common.smk:
Workflow defines configfile config.yaml but it is not present or accessible.
  File "/home/artic/ncov-tools/workflow/Snakefile", line 6, in <module>
  File "/home/artic/ncov-tools/workflow/rules/common.smk", line 8, in <module>

I can not find out why the tool does not see my config.yaml file. It seems I missed something. Please could somebody help me with this. Many thanks in advance.

[jts]

Hi @AnyaKovalenko,

I believe the workflow assumes that config.yaml is present in the current working directory. Can you confirm whether that file is in the directory that you ran ncov-tools from?

Jared

[AnyaKovalenko]

Hi Jared, thank you so much for the quick response. You was right - it my case the config.yaml was in the workflow folder, now I moved it upper to the ncov-tools folder. So now it works. But a new one error.. Please see below:

Building DAG of jobs...
MissingInputException in line 96 of /home/artic/ncov-tools/workflow/rules/annotation.smk:
Missing input files for rule run_snpeff:
    output: qc_annotation/NB01_CAMB-AA83E9.ann.vcf
    wildcards: sample=NB01_CAMB-AA83E9
    affected files:
        /home/artic/ncov-qc_analysis/run/NB01_CAMB-AA83E9.pass.vcf.gz

please could you help with this error? thank you

[rdeborja]

Hi Anya,

ncov-tools expects all the results from the ARTIC pipeline in a single directory defined in the config.yaml file as parameter:

data_root: /path/to/data/directory

Can you run the following and let me know the output:

ls /home/artic/ncov-qc_analysis/run/*.vcf*

[AnyaKovalenko]

Hi Richard. Thank you so much for helping. Oh true! I did not have all seq results in that folder, only consensus and bam files for each barcode. So now included all the seq results and everything is working great :) Amazing plots! Brilliant work! Many thanks for this tool! My best to you and team.