Multi-copy GMP model

[zhongxiangSu]

您好：我在运行如下脚本时报错了：
脚本：
from models.MultiGMPmodel import MultiCopyGMPmodel
from models.MultiGGHPmodel import MultiCopyGGHPmodel
from util.calculatedCRBrateAndEstimationAccuracy import calculatedCRBrateAndEstimationAccuracy
from util.cutCircularChromosomes import cutCircularChromosomes

"""
Inferring ancestor species for Gramineae species.
Ancestor 4: Multi-copy GGHP model, result in outdutdata/Gramineae/Ancestor4
Ancestor 3: Multi-copy GMP model, result in outdutdata/Gramineae/Ancestor3
Ancestor 2: Multi-copy GMP model, result in outdutdata/Gramineae/Ancestor2
Ancestor 1: Multi-copy GMP model, result in outdutdata/Gramineae/Ancestor1

"""

please use your path

path = '/prepare/gene_filter'

workdir = path + '/finalBlocks/'

"""
Inferring ancestor species for Gramineae species.
Ancestor 2 using Multi-copy GMP model
"""
species_file_list = [
workdir + 'D_drimm.final.block',
workdir + 'G_drimm.final.block',
workdir + 'P_drimm.final.block',
]
guided_species_for_matching = workdir + 'P_drimm.final.block'
ancestor_target_copy_number = 1
outAncestor2dir = path + '/'
ancestor_name = 'AEO'
MultiCopyGMPmodel(species_file_list, outAncestor2dir, guided_species_for_matching, ancestor_name, ancestor_target_copy_number)

Evaluation

matching_target_file = workdir + 'P_drimm.final.block'
matching_target_copy_number = ancestor_target_copy_number
matching_target_name = 'P'
speciesAndCopyList = [

[workdir + 'D_drimm.final.block',ancestor_target_copy_number,'D'],
[workdir + 'G_drimm.final.block',ancestor_target_copy_number,'G'],
[workdir + 'P_drimm.final.block',ancestor_target_copy_number,'P'],

]

model_type = 'MultiCopyGMP'
calculatedCRBrateAndEstimationAccuracy(matching_target_file, matching_target_copy_number, matching_target_name,
speciesAndCopyList, outAncestor2dir, model_type)

报错：
Using license file /gpfs/hpc/home/kib_unit/leiyunting/gurobi.lic
Gurobi Optimizer version 9.1.2 build v9.1.2rc0 (linux64)
Thread count: 192 physical cores, 192 logical processors, using up to 32 threads
Optimize a model with 7104 rows, 11669 columns and 15001 nonzeros
Model fingerprint: 0x229938d7
Model has 1667 quadratic constraints
Model has 5001 general constraints
Variable types: 0 continuous, 11669 integer (0 binary)
Coefficient statistics:
Matrix range [1e+00, 1e+00]
QMatrix range [1e+00, 1e+00]
QLMatrix range [1e+00, 1e+00]
Objective range [1e+00, 1e+00]
Bounds range [1e+03, 1e+03]
RHS range [1e+00, 1e+00]
Presolve removed 1673 rows and 1605 columns
Presolve time: 0.00s

Explored 0 nodes (0 simplex iterations) in 0.00 seconds
Thread count was 1 (of 192 available processors)

Solution count 0

Model is infeasible
Best objective -, best bound -, gap -
Encountered an attribute error
Traceback (most recent call last):
File "orch.py", line 33, in
MultiCopyGMPmodel(species_file_list, outAncestor2dir, guided_species_for_matching, ancestor_name, ancestor_target_copy_number)
File "IAGS/models/MultiGMPmodel.py", line 29, in MultiCopyGMPmodel
adjacency_matrix = gmp.ancestor_adjacency_matrix()
File "IAGS/inferringAncestorGenomeStructure/GMP.py", line 196, in ancestor_adjacency_matrix
result.append(v.x)
File "src/gurobipy/var.pxi", line 125, in gurobipy.Var.getattr
File "src/gurobipy/var.pxi", line 153, in gurobipy.Var.getAttr
File "src/gurobipy/attrutil.pxi", line 100, in gurobipy.__getattr
AttributeError: Unable to retrieve attribute 'x'