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- Step One - Clone the repository
Clone the repository to the desired location on your system using the following command:
git clone https://github.com/wen1112/SinProVirP-v1.0.git
- Step Two - Create a new conda environment
Create a new conda environment via the following command, replacing /full/path/to/cloned/repo with the appropriate path to your cloned repository:
conda env create -n SinProVirP_env --file /full/path/to/cloned/repo/SinProVirP_env.yaml
Activate the environment by executing:
conda activate SinProVirP_env
If you have trouble creating the environment using the above commands, you can alternatively follow the instructions to create a enviroment.
conda create -n SinProVirP_env python=3.11
conda activate SinProVirP_env
conda install bioconda::snakemake
conda install samtools=1.6
conda install bedtools=2.31.0
conda install diamond=2.0.14
conda install biopython
If you do not already have conda installed, please install using the instructions provided here.
If you have some problem with snakemake install, please install using the instructions provided here
-
If the input file is Paired-end, then it will 'cat R1.fq R2.fq > R1R2.fq' as the final input file because of diamond required SE reads input.
-
The input file each col should split by '\t'.
-
Paired-end reads
sample_id fq1 fq2 s1 s1.R1.fq.gz s1.R2.fq.gz s2 s2.R1.fq.gz s2.R2.fq.gz s3 s3.R1.fq.gz s3.R2.fq.gz s4 s4.R1.fq.gz s4.R2.fq.gz -
Also you can 'cat R1.fq R2.fq > R1R2.fq' before you input file.
sample_id fq s1 s1.R1R2.fq.gz s2 s2.R1R2.fq.gz s3 s3.R1R2.fq.gz s4 s4.R1R2.fq.gz -
Single-end reads
sample_id fq1 fq2 s1 s1.R1.fq.gz s2 s2.R1.fq.gz s3 s3.R1.fq.gz s4 s4.R1.fq.gz
- We need three file: 'work.sh', 'config.yaml' and 'sample_file.txt'
- Please remeber to change the path in it.
cd /full/path/to/cloned/repo/test_data
bash work.sh
- work.sh:
conda activate SinProVirP_env
snakemake -s /full/path/to/cloned/repo/Snakefile.py \
--configfile /full/path/to/cloned/repo/test_data/config.yaml \
--jobs 99 --cores 8
- config.yaml
pipeline_directory: /full/path/to/cloned/repo
# Sample file specifies sample names and names of files containing sample reads
# Format: Tab-delimited, two columns
# sample_name reads_R1R2file
# See example (samp_file.txt) in the testing folder
sample_file: /full/path/to/sample/file
# In which directory should results be outputted?
outdir: /full/path/to/output/directory
- sample_file.txt - split each col by "\t".
sample1 /full/path/to/cloned/repo/test_data/test1_R1R2.fastq
sample2 /full/path/to/cloned/repo/test_data/test2_R1R2.fastq
- The script output log may just like this:
Building DAG of jobs...
Relative file path './test2_R1R2.fastq' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Using shell: /bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 add_taxonomy
1 all
1 calculate_relative_abudance
1 diamond_blastx
1 filter_mapped_reads
1 get_marker_coverage
1 index_bam_file
1 reads_per_marker_protein
1 sam_to_bam
1 sort_bam_file
10
2024-05-30 22:03:25.334570
The sample ./test_data/sample1/sample1.sorted.bam.idxstats.addTaxonomy.final.abundance.txt of SinProVirP pipline is done!
./
├── sample1.bam
├── sample1.sam
├── sample1.sorted.bai
├── sample1.sorted.bam
├── sample1.sorted.bam.coverage
├── sample1.sorted.bam.filter.coverage.idxstats
├── sample1.sorted.bam.idxstats
├── sample1.sorted.bam.idxstats.abundance
└── sample1.sorted.bam.idxstats.addTaxonomy.final.abundance.txt
0 directories, 9 files
-
*.final.abundance.txt
VCID Relative_abundance VC_lineage VC_lifestyle VC_host_lineage VC_3803_0 0.0123774546010874 Viruses;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;; Temperate Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Ruminococcus; VC_2046_0 0.0362526365705308 Viruses;Uroviricota;Caudoviricetes;Caudovirales;Myoviridae;; Temperate Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Faecalibacterium; VC_2673_0 0.0140144228362927 Viruses;Uroviricota;Caudoviricetes;;;; Unknown Bacteria;Firmicutes;Clostridia;Eubacteriales;Oscillospiraceae;Oscillibacter; VC_6076_0 0.0063759751235582 Viruses;Uroviricota;Caudoviricetes;Caudovirales;Myoviridae;; Virulent Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;
- If you want to adjust the parameters about SinProVirP pipeline used, you could change the 'config.yaml' file.
# The value setting
threads: 8 # see usage instructions - can increase if you have more threads available
IDENTITY: 90 # diamond balst used identity
COVERAGE: 80 # diamond balst used coverage
MARKER_COVERAGE: 0.7 # SinProVirP profiling used marker coverage
MARKER_RATIO: 0.5 # SinProVirP profiling used marker ratio