Closed AnyaKovalenko closed 2 years ago
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
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
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*
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.
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:
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.