search

SysBioChalmers / RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
http://sysbiochalmers.github.io/RAVEN/
Other
100 stars 52 forks source link

Can fast tINIT integrate data from bulk RNA-seq? #518

Closed yangjingyu1108 closed 7 months ago

yangjingyu1108 commented 9 months ago

Current behavior:

We used fast tINIT to integrate different bulk RNA-seq (Hart2015_RNAseq; K562, GEO: GSE71299). Both failed to run successfully and showed the same results as shown in figures. 图片1

图片2

Expected feature/value/output:

I want to know why.

Reproducing these results:

Anything else:

mihai-sysbio commented 8 months ago

I'll transfer this issue to RAVEN where potentially similar issues have been resolved:

edkerk commented 8 months ago

@yangjingyu1108 Which solver do you use?

yangjingyu1108 commented 8 months ago

@yangjingyu1108 Which solver do you use?

RAVEN.

mihai-sysbio commented 8 months ago

@yangjingyu1108 Which solver do you use?

RAVEN.

The RAVEN toolbox can work with different solvers. This info is shown in the output of the command checkInstallation. Could you paste that output here please?

yangjingyu1108 commented 8 months ago

@yangjingyu1108 Which solver do you use?

RAVEN.

The RAVEN toolbox can work with different solvers. This info is shown in the output of the command checkInstallation. Could you paste that output here please?

checkInstallation

THE RAVEN TOOLBOX

Checking RAVEN release 2.7.5 Checking for latest RAVEN release Fail Cannot reach GitHub for release info Checking MATLAB release 2023a Set RAVEN in MATLAB path Pass

=== Model import and export ===

Add Java paths for Excel format Pass Checking libSBML version 5.19.0 Checking model import and export Import Excel format Pass Export Excel format Pass Import SBML format Pass Export SBML format Pass

=== Model solvers ===

Checking for LP solvers glpk Pass gurobi Pass cobra Pass Checking for MILP solvers glpk Pass While passing here, we do not recommended glpk for MILPs due to occasional inconsistent results gurobi Pass cobra Pass Set RAVEN solver gurobi

=== Essential binary executables ===

Checking BLAST+ Pass Checking DIAMOND Pass Checking HMMER Pass

=== Compatibility ===

Checking function uniqueness Fail Duplicate functions in C:\Users\jjyan\Documents\GitHub\Human-GEM\code\GPRs getGenesFromGrRules.m Duplicate functions in C:\Users\jjyan\Documents\GitHub\Human1_Publication_Data_Scripts\tINIT_GEMs\figures compareMultipleModels.m Duplicate functions in C:\Users\jjyan\Documents\GitHub\yjy\code simplifyModel.m Duplicate functions in C:\Users\jjyan\Documents\GitHub\ftINIT-Human-GEM\code\GPRs getGenesFromGrRules.m Resolve conflicting functions to ensure RAVEN functionality

checkInstallation complete

mihai-sysbio commented 8 months ago

@yangjingyu1108 the version of RAVEN you are using looks surprisingly old - 2.7.5 was released Jun 28, 2022. Could you please update to the latest 2.8.6 https://github.com/SysBioChalmers/RAVEN/wiki/Installation#installation ? I kind of lost track of what was done in which release, but this is an easy thing to check. Could you also please share the version of Gurobi you are using? It's normally included in the license file.

edkerk commented 8 months ago

Indeed, there are some significant changes related to the solver and ftINIT that might have to do with the error you encounter. So please update your RAVEN version, and if the error persist, then also report the Gurobi version.

edkerk commented 7 months ago

I can report first-hand that using bulk-RNAseq with ftINIT should work, so it is likely that the error is caused by using an older RAVEN release. I will close this issue, can be reopened if the problem persists in release 2.8.6+.