CAMISIM: Configurating config.init

ndreey commented 1 year ago

Configuration File

MAIN

seed: Sets seed to bee consistent with RNG.
phase: Full run (0), Only community design (1), Read Simulation (2)
max_processors: Number of cores to run on
dataset_id: ID for created sample data
output_directory: Set path to output directory. Will create if it does not exist.
temp_directory: Set path to store tmp files.
gsa: True/Yes or False/No to create gold standard assembly for each sample.
pooled_gsa: True/Yes or False/No to greater GSA for all samples combined.
anonymous: Set to No/False as it is not relevant for this project.
compress: Set value between 0-9, 0 is No compression, 9 is max. Recommended to set at least 1.

ReadSimulator

readsim: ART comes with CAMISIM, set path to path/tools/art_illumina-2.3.6/art_illumina
error_profiles: Path to the error profiles, set path/tools/art_illumina-2.3.6/profiles
samtools: SAMtools v1.3 comes with CAMISIM, set path to path/tools/samtools-1.3/samtools
profile: Select error profile, recommended mbarc.
size: Size of each sample in Gigabasepairs (Gbp). One Gbp equaled one GB in size for the rhizosphere mock data
type: set to art
fragments_size_mean: Mean size of the fragments. Set 270.
fragments_size_standard_deviation: SD of fragments. Set 27.

CommunityDesign

distribution_file_paths: Path to each abundanceX.tsv file as a list. ['path/abundance0.tsv', 'path/abundance1.tsv', 'path/abundance2.tsv'
ncbi_taxdump: database containing the hierarchical classification of all known organisms. Set to path/tools/ncbi-taxonomy_20170222.tar.gz
strain_simulation_template: Path to a template.tree for the sgEvolver from the mauve suite. scripts/StrainSimulationWrapper/sgEvolver/simulation_dir
number_of_samples: Must match the number of abundance profiles.

community0

metadata: Path to the metadata.tsv
id_to*genome_file: Path to the genome_to_ids.tsv
id_to_gff_file: Optional, set it to nothing.
genomes_total: Total number of simulated genomes.
genomes_real: Number of genomes used as input.
max_strains_per_otu: Max number of strains drawn from genomes belonging to single OTU.
ratio: Ratio between different communities. Set to 1.
mode: Either replicates or differential should be used for the project.
log_mu=1
log_sigma=2
gauss_mu=1: Used with timeseries, so set to 1.
gauss_sigma=1: Used with timeseries, so set to 1.
view: Set to False as we don't need to see the distribution of genomes.

ndreey commented 1 year ago

_Configuration file for March 13th_

NOTABLE CHANGES

max_processors=4: So i can give it a go on my PC to see if it runs.
output_directory=data/CAMISIM_run/platanthera_mock/run: updating paths, this is not permanent and will likely change once we get up to Mjölnir.
gsa=True: We want GSA for each sample as i wont co-assemble these.
pooled_gsa=False: Not needed as we will not co-assemble.
anonymous=False: Not needed.
profile=hi150: To simulate HiSeq2500L150 NGS data (150bp reads).
size=5.0: Raw data for forward and reverse is 2.5GB each. CAMISIM will place both forward and reverse in same fq. Thus, i set it to ca 5GB.

[Main]
seed=13371337
phase=0
max_processors=4
dataset_id=P_mock
output_directory=data/CAMISIM_run/platanthera_mock/run
temp_directory=/tmp
gsa=True
pooled_gsa=False
anonymous=False
compress=1

[ReadSimulator]
readsim=PATH/bin/CAMISIM/tools/art_illumina-2.3.6/art_illumina
error_profiles=PATH/bin/CAMISIM/tools/art_illumina-2.3.6/profiles
samtools=PATH/bin/CAMISIM/tools/samtools-1.3/samtools
profile=hi150
size=5.0
type=art
fragments_size_mean=270
fragment_size_standard_deviation=27

[CommunityDesign]
distribution_file_paths=['data/CAMISIM_run/platanthera_mock/abundance/abundance0.tsv', 'data/CAMISIM_run/platanthera_mock/abundance/abundance1.tsv', 'data/CAMISIM_run/platanthera_mock/abundance/abundance2.tsv', 'data/CAMISIM_run/platanthera_mock/abundance/abundance3.tsv', 'data/CAMISIM_run/platanthera_mock/abundance/abundance4.tsv']

ncbi_taxdump=PATH/bin/CAMISIM/tools/ncbi-taxonomy_20170222.tar.gz
strain_simulation_template=PATH/bin/CAMISIM/scripts/StrainSimulationWrapper/sgEvolver/simulation_dir
number_of_samples=5

[community0]
metadata=data/CAMISIM_run/platanthera_mock/abundance/metadata.tsv
id_to_genome_file=data/CAMISIM_run/platanthera_mock/abundance/genome_to_id.tsv
id_to_gff_file=
genomes_total=894
genomes_real=894
max_strains_per_otu=3
ratio=1
mode=differential
log_mu=1
log_sigma=2
gauss_mu=1
gauss_sigma=1
view=False

ndreey commented 1 year ago

The config used to generate a subsample of the data locally on my laptop.

[Main]
seed=13371337
phase=2
max_processors=6
dataset_id=orchid_mock
output_directory=platanthera_mock/01_output
temp_directory=/tmp
gsa=True
pooled_gsa=True
anonymous=False
compress=1

[ReadSimulator]
readsim=/mnt/c/Users/andbo/thesis_andbo/CAMISIM/tools/art_illumina-2.3.6/art_illumina
error_profiles=/mnt/c/Users/andbo/thesis_andbo/CAMISIM/tools/art_illumina-2.3.6/profiles
samtools=/mnt/c/Users/andbo/thesis_andbo/CAMISIM/tools/samtools-1.3/samtools
profile=hi150
base_profile_name=
profile_read_length=
size=2.5
type=art
fragments_size_mean=270
fragment_size_standard_deviation=27

[CommunityDesign]
distribution_file_paths=platanthera_mock/01_abundance/0_hc_abundance.tsv,platanthera_mock/01_abundance/0.5_hc_abundance.tsv,platanthera_mock/01_abundance/0.8_hc_abundance.tsv,platanthera_mock/01_abundance/0.95_hc_abundance.tsv,platanthera_mock/01_abundance/0.98_hc_abundance.tsv
ncbi_taxdump=/mnt/c/Users/andbo/thesis_andbo/CAMISIM/tools/ncbi-taxonomy_20170222.tar.gz
strain_simulation_template=/mnt/c/Users/andbo/thesis_andbo/CAMISIM/scripts/StrainSimulationWrapper/sgEvolver/simulation_dir
number_of_samples=5

[community0]
metadata=platanthera_mock/01_simulation/metadata.tsv
id_to_genome_file=platanthera_mock/01_simulation/01genome_to_id.tsv
id_to_gff_file=
genomes_total=100
num_real_genomes=100
max_strains_per_otu=2
ratio=1
mode=differential
log_mu=1
log_sigma=2
gauss_mu=1
gauss_sigma=1
view=False

ndreey / ghost-magnet

CAMISIM: Configurating config.init #21