methyPrior： all is "NaN"

[pei-wang111]

Dear Dr. Liu,
In the case of the example BAM file BH01.chr22.bam, the first and second steps can run successfully. However, when using my own BAM file for testing, the first step runs successfully, but the second step throws an error. Upon checking, for BH01.chr22.CpgMultiMetricsStats.hg19.details.bed.gz, the 12th column methyPrior contains both numerical values and NaN values. However, for my own BAM file result CS84.22.CpgMultiMetricsStats.hg19.details.bed.EPICv2.gz, the 12th column methyPrior consists entirely of NaN values. Could this be the reason why the second step fails for my own BAM file?

Here is the command I used for the second step:
java -Xmx100G -cp "$FinaleMe/target/FinaleMe-0.58-jar-with-dependencies.jar:$FinaleMe/lib/jahmm-0.6.2.jar" \
org.cchmc.epifluidlab.finaleme.hmm.FinaleMe
$outpath/test.FinaleMe.mincg7.model
$outpath/CS84.22.CpgMultiMetricsStats.hg19.details.bed.EPICv2.gz
$outpath/test.FinaleMe.mincg7.prediction.bed.gz
-miniDataPoints 7 -gmm -covOutlier 3

The following error occurs:
log4j:WARN No appenders could be found for logger (org.cchmc.epifluidlab.finaleme.hmm.FinaleMe).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
HMM training new ....
GMMLearner...
Exception in thread "main" org.apache.commons.math3.exception.NotStrictlyPositiveException: 0 is smaller than, or equal to, the minimum (0)
at org.apache.commons.math3.distribution.fitting.MultivariateNormalMixtureExpectationMaximization.estimate(MultivariateNormalMixtureExpectationMaximization.java:308)
at org.cchmc.epifluidlab.finaleme.hmm.ClustersGMM.(GMMLearner.java:346)
at org.cchmc.epifluidlab.finaleme.hmm.GMMLearner.(GMMLearner.java:87)
at org.cchmc.epifluidlab.finaleme.hmm.FinaleMe.buildInitNhmmByGMM(FinaleMe.java:1403)
at org.cchmc.epifluidlab.finaleme.hmm.FinaleMe.trainHmm(FinaleMe.java:791)
at org.cchmc.epifluidlab.finaleme.hmm.FinaleMe.doMain(FinaleMe.java:236)
at org.cchmc.epifluidlab.finaleme.hmm.FinaleMe.main(FinaleMe.java:170)