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    $\begingroup$ I think you misread the output. The only quantity proportional to a variance is the standard error of estimate, abbreviated Std.Err, and indeed it is non-negative, as it must be. Have you consulted your software documentation for information about what the output means? $\endgroup$ Commented Sep 23, 2020 at 14:04
  • $\begingroup$ @whuber it is producing the warning as lavaan WARNING: some estimated lv variances are negative. and also I have updated the value of loadings and the value is 3.58. $\endgroup$ Commented Sep 23, 2020 at 14:11
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    $\begingroup$ That's a completely different issue. As you know, a true variance cannot be negative, so when a program computes a variance and detects a negative value, it knows something has gone wrong. But exactly what has gone wrong depends on the program and on the details of what it is doing. Often, the important clues are in the exact details of the error message and when in your workflow it occurs. That's the kind of information that would help people give you good answers. $\endgroup$ Commented Sep 23, 2020 at 14:38