Total of 8 + 46 != 53 tRNA + rRNA features ?

[cmkobel]

I was running good old prokka 1.14.6 (from bioconda) on some mags. A nice saturday evening after a long snowy day. ☃️

I looked at the log, and randomly stumbled upon "[22:24:31] Total of 53 tRNA + rRNA features" Then I thought to myself. Wait. It says that it found 8 rRNAs and 46 tRNAs 8 + 46 = 54

But then again, it says that it only found 53?

Is there an off-by-one error or am I misunderstanding something trivial?

Here's a bit of my log:

[22:22:33] Found 46 tRNAs
[22:22:33] Predicting Ribosomal RNAs
[22:22:33] Running Barrnap with 4 threads
[22:22:35] 1 124469 481951 16S ribosomal RNA
[22:22:35] 2 124469 484170 23S ribosomal RNA
[22:22:35] 3 124469 487172 5S ribosomal RNA
[22:22:35] 4 135071 59661 5S ribosomal RNA
[22:22:35] 5 135071 59867 23S ribosomal RNA
[22:22:35] 6 135071 63352 16S ribosomal RNA
[22:22:35] 7 68148 1 23S ribosomal RNA (partial)
[22:22:35] 8 68148 1255 5S ribosomal RNA
[22:22:35] Found 8 rRNAs
[22:22:35] Scanning for ncRNAs... please be patient.
[22:22:35] Running: cmscan -Z 5.369396 --cut_ga --rfam --nohmmonly --fmt 2 --cpu 4 --tblout /dev/stdout -o /dev/null --noali /home/axodines/assemblycomparator2/conda_base/0c811240a515a9f4fea202f66f386e5c_/db/cm/Bacteria results_ac2\/samples\/Treatment_LowE\.metabat\.242\/prokka\/Treatment_LowE\.metabat\.242\.fna
[22:24:31] 1 ncRNA 1 11019 1..367
[22:24:31] 2 ncRNA 2 11019 1..179
[22:24:31] 3 ncRNA 3 11019 1..105
[22:24:31] 4 ncRNA 1 63149 1..97
[22:24:31] 5 ncRNA 1 124469 1..98
[22:24:31] Found 5 ncRNAs.
[22:24:31] Total of 53 tRNA + rRNA features

Or maybe, a feature is not the same as a gene call?

Best, Carl

[cmkobel]

I guess it is because the 7th rRNA is "partial"?

[22:22:35] 7 68148 1 23S ribosomal RNA (partial)