ATA/ATAPI low level question
Before any application layer commands are issues (e.g. IDENTIFY) there is a event sequence at the PHY layer which has to take place. So if you're looking at the bus with a logic analyzer you're probably seeing the PHY setup process take place. Assuming there's a drive present, the sequence is essentially:

            HOST                    DEVICE

STATE:      HR_RESET                DR_RESET
SIGNAL:                     ---&gt; (COMRESET)
STATE:      HR_AwaitCOMINIT         DR_COMINIT
SIGNAL:           (COMINIT) &lt;---
STATE:      HR_COMWAKE              DR_AwaitCOMWAKE
SIGNAL:                     ---&gt; (COMWAKE)
STATE:      HR_AwaitCOMWAKE         DR_COMWAKE
SIGNAL:           (COMWAKE) &lt;---
STATE:      HR_AwaitAlign           DR_SendALIGN
SIGNAL:             (ALIGN) &lt;---
STATE:      HR_SendAlign            DR_SendALIGN
SIGNAL:                     ---&gt; (ALIGN)
STATE:      HR_Ready                DR_Ready


(I skipped a bunch of optional, error, and transitory states). It's all part of the host/device negotiating the connection before any commands take place.

When you say "I see there are flying some READ commands", what do you mean by a 'READ command'?

Sources:


ATA dev wiki 
T13 ATAPI 7 (Volume 3 - Serial Transport Protocols and Physical
Interconnect)