MiSeq v3 (2X300PE) 16S sequencing, no values for clusters PF

[guesswhat]

We recently have problems with 16S runs. We have been following the illumina protocol for v3-v4 regions, but have difficulties to get the optimum cluster density and >Q30 values.

We multiplexed 96 samples with Nextera XT v2 set A. Loaded 4pM lib+20% 4pM PhiX.

Now we see another problem, after 25 cycles there was values for cluster density 507K/mm2, but no values for Clusters PF and >Q30.

Is there anyone had the same problem? There was no error or warning message, the run is still going on.

[guesswhat]

I got reply from Illumina tech support. They said that the MiSeq control software can be slow at loading data sometimes. My run is finished and PF%, Q30 values turned up at very late stage. In case someone encounter the same problem, just wait patiently :-)