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SysBioChalmers / RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
http://sysbiochalmers.github.io/RAVEN/
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RAVEN 2.7.10 #459

Closed edkerk closed 1 year ago

edkerk commented 1 year ago

Main improvements in this PR:

I hereby confirm that I have:

github-actions[bot] commented 1 year ago

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 Running blastPlusTests . Done blastPlusTests %0A Running cdhitTests . Done cdhitTests %0A Running checkTasksTests PASS: [Gen e[s] from a[s]] Gen e[s] from a[s] FAIL: [Gen e[s] from a[s]] Gen e[s] from a[s] . Done checkTasksTests %0A Running diamondTests . Done diamondTests %0A Running fillGapsLargeTests . %0A Error occurred in fillGapsLargeTests/testLargeCobra and it did not run to completion. %0A Error ID: %0A '' %0A Error Details: %0A Error using setRavenSolver (line 19) COBRA toolbox is not initialized, run 'initCobraToolbox()' Error in fillGapsLargeTests>testLargeCobra (line 91) setRavenSolver('cobra'); %0A . Done fillGapsLargeTests %0A Running fillGapsSmallTests .. %0A Error occurred in fillGapsSmallTests/testSmallCobra and it did not run to completion. %0A Error ID: %0A '' %0A Error Details: %0A Error using setRavenSolver (line 19) COBRA toolbox is not initialized, run 'initCobraToolbox()' Error in fillGapsSmallTests>testSmallCobra (line 91) setRavenSolver('cobra'); %0A . Done fillGapsSmallTests %0A Running hmmerTests . Done hmmerTests %0A Running importExportTests .... Done importExportTests %0A Running mafftTests . Done mafftTests %0A Running miriamTests . Done miriamTests %0A Running modelAbilitiesTests ......Getting minimal and maximal fluxes... 0%25 complete 10%25 completeCOMPLETE .. Done modelAbilitiesTests %0A Running modelConversionTests . Done modelConversionTests %0A Running modelCurationTests .......... ........ Done modelCurationTests %0A Running modelSortingTests .. Done modelSortingTests %0A Running solverTests .. %0A Verification failed in solverTests/testCobra. %0A Framework Diagnostic: %0A verifyEqual failed. --> Path to failure: <Value>.rCost --> The numeric values are not equal using "isequaln". --> The error was not within absolute tolerance. --> Failure table: Index Actual Expected Error RelativeError AbsoluteTolerance %0A %0A %0A %0A %0A %0A 22 0.0611098309167365 -0.0611098309167366 0.122219661833473 -2 0.1 26 0.0916647463751048 -0.0916647463751048 0.18332949275021 -2 0.1 28 0.0916647463751048 -0.0916647463751048 0.18332949275021 -2 0.1 29 0.0700216812587606 -0.0700216812587606 0.140043362517521 -2 0.1 30 0.0687485597813286 -0.0687485597813286 0.137497119562657 -2 0.1 39 0.0521979805747125 -0.0521979805747125 0.104395961149425 -2 0.1 Actual double: 95x1 double Expected double: 95x1 double Actual Value: struct with fields: x: [95x1 double] f: -0.873921506968430 stat: 1 msg: 'Optimal solution found' sPrice: [72x1 double] rCost: [95x1 double] Expected Value: struct with fields: x: [95x1 double] f: -0.873921506968430 stat: 1 msg: 'Optimal solution found' sPrice: [72x1 double] rCost: [95x1 double] %0A Stack Information: %0A In /home/m/actions-runner/_work/RAVEN/RAVEN/testing/unit_tests/solverTests.m (testCobra) at 113 %0A . Done solverTests %0A Running tinitTests .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 20%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 20%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) PASS: [Gen e[s] from a[s]] Gen e[s] from a[s] Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 25%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. [Gen e[s] from a[s]] Gen e[s] from a[s]: Added 0 reaction(s), 0 reactions added in total .WARNING: "[Gen e[s] from a[s]] Gen e[s] from a[s]" could not be performed for any set of reactions . New genes added to the model: G10 G11 G5 G6 G7 G8 G9 No mets ids with prefix "m_" currently exist in the model. The first new id will be "m_0001" ...Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 20%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 20%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. New genes added to the model: G11 G12 G13 G14 No mets ids with prefix "m_" currently exist in the model. The first new id will be "m_0001" Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 11%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 11%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 20%25 completeCOMPLETE Step 5: Final work .Step 1: Gene rules Step 2: First simplification Step 3: Check tasks (~10 min) Step 4: Second simplification (~1 hour) Getting minimal and maximal fluxes... 0%25 complete 3%25 complete100%25 completeCOMPLETE Step 5: Final work ftINIT: Running step 1 MILP detected. ftINIT: Running step 2 MILP detected. ftINIT: Running step 1 MILP detected. . Done tinitTests %0A Failure Summary: Name Failed Incomplete Reason(s) %0A fillGapsLargeTests/testLargeCobra X X Errored. %0A fillGapsSmallTests/testSmallCobra X X Errored. %0A solverTests/testCobra X Failed by verification.

Note: In the case of multiple test runs, this post will be edited.