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cfg_file_130.yml
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cfg_file_130.yml
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---
A_General:
dir_files: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes'
dir_out: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output'
job_name: 29
names: Xam_CIO1.fasta,XooKACC10331_genome.fasta,Xcc_aw12879.fasta,XalGPE_PC73_genome.fasta,XooPXO99A_genome.fasta,Xca756C_genome.fasta,Xam_UA303.fasta,XooMAFF311018_genome.fasta,XamCIO151_Uniandes.fasta,Xvm_complete.fasta,Xam_cassavae.fasta,Xam_UG39.fasta,XvmNCPPB4381_genome.fasta,Xam_NCPPB1159.fasta,Xcv8510_genome.fasta,Xam_IBSBF320.fasta,XvvNCPPB702_genome.fasta,XooBLS256_update.fasta,Xam_IBSBF725.fasta,Xam_IBSBF1411.fasta,Xac306_genome.fasta,Xa_citrumeloF1.fasta,XccB100_genome.fasta,XccATCC33913_genome.fasta,Xam_UA226.fasta,Xam_IBSBF356.fasta,Xam_CFBP1851.fasta,Xam_IBSBF2346.fasta,Xcc8004_genome.fasta
num_genomes: ~
num_regions: ~
B_MAUVE:
path_mauve: '/datos-biologia/BioProgs/gainloss/MAUVE/'
C_MAUVE_output:
backbone: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.backbone'
tree: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.tree'
xmfa: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.xmfa'
D_ssLCBs:
length: 500
path_ssLCBs: '/datos-biologia/BioProgs/gainloss/MAUVE/utility/'
E_ssLCBs_output:
bbcols: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.xmfa.bbcols'
core: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.core_alignment.xmfa'
F_Blocksplit:
num_blocks: 1189
path_blocksplit: '/datos-biologia/BioProgs/gainloss/clonalorigin/warg/scripts/'
G_Result:
Binary_File: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.backbone.binary'
Summary_File: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.Rcomb.out'
General:
num_genomes: 29
num_regions: 1189
H_ClonalFrame:
burn_in: 100000000000
interval: 100000
iterations: 10000000000
others: ' -v -C '
parallel: 10
path_ClonalFrame: '/datos-biologia//BioProgs/gainloss/ClonalFrame/bin/'
threshold: 6.80e-01
I_ClonalFrame_output:
clonal_concensus: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.clonalframe.out.1'
J_ClonalTree:
path_clonaltree: '/datos-biologia/BioProgs/gainloss/clonalorigin/warg/scripts/'
K_ClonalTree_output:
final_tree: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.clonaltree.nwk'
L_Result:
Summary_File: '/biologia-scratch3/l.perlaza149/DeEP_Pro/130_genomes_output/29.Rcomb_6.80e-01.out'
M_window_acgt:
path_window: '/datos-biologia/BioProgs_SGE/glimmer3.02/bin/'
window_skip: 80
N_Rscript:
Rscript_path: '/biologia-scratch3/l.perlaza149/DeEP_Pro/DeEP_Scripts/R-3.1.1/bin/Rscript'
O_Results:
Summary_file: '//data/DeEP/Genom130_Output//gc_result_pvalue.txt'
P_Patterns:
file_binary: '//data/DeEP/Genom130_Output//XAM_130.backbone.binary'
file_pattern: '//data/DeEP/Genom130_Output//XAM_130.backbone_.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,_.matrix'
pattern: '.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,'
region_name: ~
Q_AutoBLAST:
blast_task: ~
dbtype: ~
output_format: ~
path_bin: '/datos-biologia/BioProgs_SGE//ncbi-blast-2.2.25+/bin'
path_queries: ~
reference_genomes: ~