dbespiatykh / rdscan

A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples

Hi there 👋🏻

I'm a bioinformatician working in the field of microbial genomics. Specifically, my research focuses on challenges in genomics, phylogenomics, and transcriptomics of infectious organisms such as Mycobacterium tuberculosis, Staphylococcus aureus, and Klebsiella pneumoniae.

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rdscan's Issues

Unable to execute RDscan..

Looking for: ['snakemake', 'snakedeploy', 'biopython']

Encountered problems while solving:

• package snakedeploy-0.1.1-pyhdfd78af_1 requires python >=3.8, but none of the providers can be installed

How to execute properly without any error?

Error in rule compute_coverage:

Error in rule compute_coverage:
jobid: 16
output: bed/ERR386816.bed
conda-env: /mnt/e/Karthisir_mtb/mtb/RDscan/.snakemake/conda/f1da7f6336cc754e535647fdb7c37a30
shell:

    parallel bedtools genomecov -bga -ibam ::: mapped/ERR386816.bam         | awk '$4<'$(samtools depth  -aa mapped/ERR386816.bam |  awk '{sum+=$3} END {print sum/4411532*0.1}')''            | bedtools merge -d 1500 | bedtools subtract -f 0.30 -a stdin -b config/IS6110.bed -A > bed/ERR386816.bed

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Input when running RDscan

What is the exact input to provide to the command below when trying to determine the RD regions of a sample? Is the working directory to contain the files to be analyzed? Please provide examples if possible. Thanks,

snakemake --conda-frontend mamba --use-conda -j {Number of cores}

AmbiguousRuleException: Rules calculate_proportion and compute_coverage are ambiguous for the file results/bed/28 /test/reads/28_1.fastq.gz.proportion.bed.

RDscan end with this error with our data, and dry run give probably the results

Dry run
/mnt/f/RD/RDscan/workflow/rules/novel_discovery.smk:52: SyntaxWarning: invalid escape sequence '\w'
input:
Building DAG of jobs...
Nothing to be done (all requested files are present and up to date).

Our data

AmbiguousRuleException:
Rules calculate_proportion and compute_coverage are ambiguous for the file results/bed/28 /test/reads/28_1.fastq.gz.proportion.bed.
Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
Wildcards:
calculate_proportion: sample=28 /test/reads/28_1.fastq.gz
compute_coverage: sample=28 /test/reads/28_1.fastq.gz.proportion
Expected input files:
calculate_proportion: results/mosdepth_bed/28 /test/reads/28_1.fastq.gz.regions.bed.gz
compute_coverage: results/mapped/28 /test/reads/28_1.fastq.gz.proportion.bam resources/IS6110.bed
Expected output files:
calculate_proportion: results/bed/28 /test/reads/28_1.fastq.gz.proportion.bed
compute_coverage: results/bed/28 /test/reads/28_1.fastq.gz.proportion.bed