This implies MetaboAnalyst failed to execute the command.
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Parameter issue: adjust parameters and try again;
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Data issue: in many cases, the problem is associated with sample size. In particular, if the sample size is very small (below 10), some unpredictable error may happen. For instance, by default PCA and PLSDA will try to generate summary/classification/permutation plot for the top 5 components, if the sample size is too small, it will fail to do so;
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Program issue: if you believe the issue is unlikely caused by issues described above, please provide details (data + steps) that can reproduce the issue