Description
Dear Authors,
Question 1:
I am using mavis to annotate SV calls from delly and Manta. I ran mavis using the command below and ran into an error due to "Additional properties are not allowed ('summary.cluster_radius' was unexpected)" ?
snakemake -j 1 --configfile config.json --use-singularity -s Snakefile
My config.json
{
"libraries": {
"1T": {
"assign": ["delly","manta"],
"bam_file": "/shared_2/minhui/fyp/WES/bam/1T_WES.realn.bam",
"disease_status": "diseased",
"protocol": "genome"
}
},
"convert": {
"delly": {
"assume_no_untemplated": true,
"file_type": "delly",
"inputs": ["/shared_2/minhui/fyp/WES/MAVIS/OUTPUT/delly1.vcf"]
},
"manta": {
"assume_no_untemplated": true,
"file_type": "manta",
"inputs": ["/shared_2/minhui/fyp/WES/MAVIS/OUTPUT/manta1.vcf"]
},
},
"annotate.draw_fusions_only": false,
"skip_stage.validate": true,
"output_dir": "output_dir",
"reference.aligner_reference":["/shared_2/minhui/ref/GRCh38.d1.vd1.fa"],
"reference.annotations": ["/shared_2/minhui/fyp/WES/MAVIS/REF/ensembl79_hg38_annotations.v3.json"],
"reference.template_metadata": ["/shared_2/minhui/fyp/WES/MAVIS/REF/cytoBand.txt"],
"reference.reference_genome": ["/shared_2/minhui/fyp/WES/MAVIS/REF/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"],
"reference.masking": ["/shared_2/minhui/fyp/WES/MAVIS/REF/GRCh38_masking.tab"],
"reference.dgv_annotation": ["/shared_2/minhui/fyp/WES/MAVIS/REF/dgv_hg38_variants.tab"]
}
Snippet of what I think is the relevant error message (full log included as attachment):
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/mavis_config/__init__.py", line 71, in validate_config
os.path.join(os.path.dirname(__file__), f'{schema}.json'),
File "/usr/local/lib/python3.7/site-packages/snakemake/utils.py", line 150, in validate
raise WorkflowError("Error validating config file.", e)
snakemake.exceptions.WorkflowError: Error validating config file.
ValidationError: Additional properties are not allowed ('summary.cluster_radius' was unexpected)
It seems that mavis run via snakemake/ singularity is using mavis3.0.0, is there any possibility that there is some sort of incompatibility since the latest version is mavis3.1.0?
This was my command for installing mavis_config
python3.7 -m pip install -U setuptools pip wheel
python3.7 -m pip install mavis_config
Question 2:
What is the difference between the package from 'pip install mavis_config' VS this one https://pypi.org/project/mavis-config/ ? One is underscore and another one is a dash
Many thanks in advance,
Min