Trying to run doubleGeneDeeletion script on PALM.jl

[ali-kishk]

I have only both the model.mat and KO script 'Macrophage_KO.m' in the test directory.

PALM(modelDir, "$(joinpath(dirname(pathof(COBRA)), "../test/Macrophage_KO.m"))",
nMatlab=nWorkers, outputFile="modelCharacteristics.mat",
varsCharact=varsCharact, cobraToolboxDir=installDir)

but I am getting this error:

Every worker will run 17 model(s).
Load sharing is ideal.

-- Load distribution --

• Number of models: 17

• Number of workers: 1

• True load (models/worker): 17.0

• Realistic load (quotient): 17

• Remaining load (remainder): 0

┌ Info: Directory with 17 models read successfully.
└ @ COBRA
~/COBRA.jl/src/PALM.jl:247

The poolsize is equal to 1. PALM.jl is meant to be used in parallel, not serial or sequential.

Stacktrace:
[1] error(::String) at ./error.jl:33
[2] PALM(::String, ::String; nMatlab::Int64, outputFile::String, varsCharact::Array{String,1}, cobraToolboxDir::String, printLevel::Int64, useCOBRA::Bool) at ~/COBRA.jl/src/PALM.jl:257
[3] top-level scope at In[122]:1

[rmtfleming]

Hi it may be that COBRA.jl needs to be updated to point to the new location of the models repo: https://github.com/opencobra/COBRA.models Alternatively, add that missing model to the new repo. Regards, Ronan

…

On Mon, 23 Mar 2020 at 12:43, ali-kishk ***@***.***> wrote: I have only both the model.mat and KO script 'Macrophage_KO.m' in the test directory. PALM(modelDir, "$(joinpath(dirname(pathof(COBRA)), "../test/Macrophage_KO.m"))", nMatlab=nWorkers, outputFile="modelCharacteristics.mat", varsCharact=varsCharact, cobraToolboxDir=installDir) but I am getting this error: Every worker will run 17 model(s). Load sharing is ideal. -- Load distribution -- - Number of models: 17 - Number of workers: 1 - True load (models/worker): 17.0 - Realistic load (quotient): 17 - Remaining load (remainder): 0 ┌ Info: Directory with 17 models read successfully. └ @ COBRA ~/COBRA.jl/src/PALM.jl:247 The poolsize is equal to 1. PALM.jl is meant to be used in parallel, not serial or sequential. Stacktrace: [1] error(::String) at ./error.jl:33 [2] PALM(::String, ::String; nMatlab::Int64, outputFile::String, varsCharact::Array{String,1}, cobraToolboxDir::String, printLevel::Int64, useCOBRA::Bool) at ~/COBRA.jl/src/PALM.jl:257 [3] top-level scope at In[122]:1 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#74>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQMEOUKGNGPSK7L7SZCDW3RI5KPPANCNFSM4LR25QFQ> .

-- -- Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D. ---------------------------------------------------------------------------- Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway. ---------------------------------------------------------------------------- Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 873 413 072 Skype: ronan.fleming ---------------------------------------------------------------------------- (This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)