Parameters of tool "Analyzer" (Analyzer, version: 1.7.1):
t - truth (the true annotation, type = gff,gff3,gff.gz,gff3.gz)	= /Users/dev/Downloads/GeMoMa 2/GCF_000001735.4_TAIR10.1_genomic.gff
	The following parameter(s) can be used multiple times:
	n - name (can be used to distinguish different predictions, OPTIONAL)	= null
	p - predicted annotation (GFF file containing the predicted annotation, type = gff,gff3,gff.gz,gff3.gz)	= /Users/dev/Downloads/GeMoMa 2/out/Transcript_Predictions_14.gff3
c - CDS (if true CDS features are used otherwise exon features, default = true)	= true
w - write (write detailed table comparing the true and the predicted annotation, range={NO, YES}, default = NO)	= NO
    No parameters for selection "NO"
    Parameters for selection "YES":
    	ca - common attributes (Only gff attributes of mRNAs are included in the result table, that can be found in the given portion of all mRNAs. Attributes and their portion are handled independently for truth and prediction. This parameter allows to choose between a more informative table or compact table., valid range = [0.0, 1.0], default = 0.5)	= 0.5
r - reliable (additionally evaluate sensitivity for reliable transcripts, range={NO, YES}, default = NO)	= NO
    No parameters for selection "NO"
    Parameters for selection "YES":
    	f - filter (A filter for deciding which transcript from the truth are reliable or not. The filter is applied to the GFF attributes of the truth. You probably need to run AnnotationEvidence on the truth GFF. The default filter decides based on the completeness of the prediction (start=='M' and stop=='*'), no premature stop codons (nps==0), RNA-seq coverage (tpc==1) and intron evidence (isNaN(tie) or tie==1)., default = start=='M' and stop=='*' and nps==0 and (tpc==1 and (isNaN(tie) or tie==1)), OPTIONAL)	= start=='M' and stop=='*' and nps==0 and (tpc==1 and (isNaN(tie) or tie==1))
outdir - The output directory, defaults to the current working directory (.)	= analyzer_test
selected feature: CDS

reading true annotation and removing duplicate transcripts
removed 5738 empty transcripts
removed 7321 duplicates

reading predicted annotation: /Users/dev/Downloads/GeMoMa 2/out/Transcript_Predictions_14.gff3
removed 190 empty transcripts
comparing true and predicted annotation
NC_037304.1
NC_003076.8
NC_000932.1
NC_003074.8
NC_003075.7
NC_003070.9
NC_003071.7

category	/Users/dev/Downloads/GeMoMa 2/out/Transcript_Predictions_14.gff3

number of true transcripts	40947

number of predicted transcripts	15318
number of perfectly predicted transcripts	12100

number of true genes	27565

number of predicted genes	1
number of perfectly predicted genes	10946

transcript sensitivity	0.29550394412289055
transcript precision	0.7899203551377464

gene sensitivity	0.39709776890984944
gene precision	10946.0

