diff --git a/CIValidations/MaCh3CLI b/CIValidations/MaCh3CLI
index e041cd3..fd2a356 100755
--- a/CIValidations/MaCh3CLI
+++ b/CIValidations/MaCh3CLI
@@ -47,12 +47,12 @@ run_fitter_validations() {
   ${MaCh3Tutorial_ROOT}/CIValidations/FitterValidations
   ${MaCh3_ROOT}/bin/ProcessMCMC ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml MCMC_Test.root
   # Chain diagnostic
-  ${MaCh3_ROOT}/bin/DiagMCMC MCMC_Test.root ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml
+  ${MaCh3_ROOT}/bin/DiagMCMC ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml MCMC_Test.root
   ${MaCh3_ROOT}/bin/RHat 2 MCMC_Test.root MCMC_Test.root MCMC_Test.root MCMC_Test.root
   ${MaCh3_ROOT}/bin/RHat_HighMem 10 MCMC_Test.root MCMC_Test.root MCMC_Test.root MCMC_Test.root
   ${MaCh3_ROOT}/bin/PlotMCMCDiag MCMC_Test_MCMC_Diag.root "test_plot_1" MCMC_Test_MCMC_Diag.root "test_plot_2"
   ${MaCh3_ROOT}/bin/CombineMaCh3Chains -o MergedChain.root MCMC_Test.root MCMC_Test.root MCMC_Test.root MCMC_Test.root
-  ${MaCh3_ROOT}/bin/GetPenaltyTerm MCMC_Test.root ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml
+  ${MaCh3_ROOT}/bin/GetPenaltyTerm ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml MCMC_Test.root
   # Fancy plotting
   ${MaCh3_ROOT}/bin/MatrixPlotter ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml MCMC_Test_drawCorr.root
   ${MaCh3_ROOT}/bin/GetPostfitParamPlots MCMC_Test_drawCorr.root
@@ -157,8 +157,8 @@ run_multicanoical_validations() {
 run_CLI_validations() {
   mach3 tutorial TutorialConfigs/FitterConfig.yaml --MCMCSteps 10000
   mach3 process ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml Test.root --corr --MakeCredibleIntervals
-  mach3 diag Test.root ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml
-  mach3 penterm Test.root ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml
+  mach3 diagnostics mcmc ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml Test.root 
+  mach3 penaltyterm ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml Test.root 
 }
 
 
diff --git a/README.md b/README.md
index 2c5dae5..b9e3622 100644
--- a/README.md
+++ b/README.md
@@ -658,7 +658,7 @@ The latter class deals with actual event reweighting and general heavy lifting.
 ## MCMC Diagnostic
 A crucial part of MCMC is diagnosing whether a chain has converged or not. You can produce chain diagnostics by running:
 ```bash
-mach3 diag Test.root bin/TutorialDiagConfig.yaml
+mach3 diagnostics mcmc bin/TutorialDiagConfig.yaml Test.root
 ```
 This will produce a plethora of diagnostic information. One of most important of these are the autocorrelations for each of the parameters. Autocorrelation indicates how correlated MCMC steps are when they are n-steps apart in the chain.
 Generally speaking, we want the autocorrelation to drop to 0 fast and stay around there (like in the plot below). You can read about other diagnostics [here](https://mach3-software.github.io/MaCh3/MCMCconvergance.html), but it is sufficient for now to focus on autocorrelation.