Not getting sensitivity and specificity

[rafaeltiveron]

a-posteriori probability of viterbi path
----------------------------------------
a-posteriori probability of correct path

204516 times were the paths equally likely (identical).
sorted quotients of the rest:

0 quotients were between 1 and 10


*******      Evaluation of gene prediction     *******

---------------------------------------------\
                 | sensitivity | specificity |
---------------------------------------------|
nucleotide level |        -nan |           0 |
---------------------------------------------/

----------------------------------------------------------------------------------------------------------\
           |  #pred |  #anno |      |    FP = false pos. |    FN = false neg. |             |             |
           | total/ | total/ |   TP |--------------------|--------------------| sensitivity | specificity |
           | unique | unique |      | part | ovlp | wrng | part | ovlp | wrng |             |             |
----------------------------------------------------------------------------------------------------------|
           |        |        |      |              93084 |                  0 |             |             |
exon level |  93084 |      0 |    0 | ------------------ | ------------------ |        -nan |           0 |
           |  93084 |      0 |      |    0 |    0 | 93084 |    0 |    0 |    0 |             |             |
----------------------------------------------------------------------------------------------------------/

----------------------------------------------------------------------------\
transcript | #pred | #anno |   TP |   FP |   FN | sensitivity | specificity |
----------------------------------------------------------------------------|
gene level | 52910 |     0 |    0 | 52910 |    0 |        -nan |           0 |
----------------------------------------------------------------------------/

------------------------------------------------------------------------\
            UTR | total pred | CDS bnd. corr. |   meanDiff | medianDiff |
------------------------------------------------------------------------|
            TSS |      11836 |              0 |         -1 |         -1 |
            TTS |      10533 |              0 |         -1 |         -1 |
------------------------------------------------------------------------|
            UTR | uniq. pred |    unique anno |      sens. |      spec. |
------------------------------------------------------------------------|
                |  true positive = 1 bound. exact, 1 bound. <= 20bp off |
 UTR exon level |          0 |              0 |       -nan |       -nan |
------------------------------------------------------------------------|
 UTR base level |          0 |              0 |       -nan |       -nan |
------------------------------------------------------------------------/
nucUTP= 0 nucUFP=0 nucUFPinside= 0 nucUFN=0
# total time: 2.24e+04

Why zero and "nan" for everything? Running in L.Mint 20.04

[MarioStanke]

It reports 0 annotated genes in the reference annotation that you input. The nan comes from a division by 0. Compare your input .gb file with one in the examples folder. If the cause is not obvious, I suggest, you manually create a single gene version of your file and then step wise adjust it until it eventually is in the very same format as the example.