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HD data GB/min

 
ATAPI commands take up 14 bytes. (used to be 12?)
the rest is data if need be I guess.
assuming you are transferring 512bytes-4096 bytes of data per packet, let's say 512 bytes, the total byte size would be 14(readsector)+14(readbuf)+512(sectorbytes)=540 bytes. If you add in an extra Seek(14 bytes), it makes it 540+14(seek)=554 bytes.
For SATA, 34-48(packet)+512=546-560 bytes, assuming I have the structure correct (I may not - the SATA spec isn't a clear read with structures to look at - had to google the information).
Since the IDE/ATAPI cable is 2 bytes wide, we must take this into consideration and multiply the transfers/sec (MHz) by 2.
For SATA, this is serial, so it doesn't make any difference, it's just measures in MB/sec or Gb/sec. It is not known to me what the proper command structure is for SATA because I don't have a spec.

With SATA you have approximately 34-48-byte packets, and I don't know how many commands you have to send to do a full read because the spec seems slightly unreadable still (ATAPI spec was very clear & well laid out).
With ATAPI you have to send a Read Sector command and then a Read Buffer command, both of which take 14 bytes (7 bytes in and 7 bytes out). Seek command is also 14 bytes. that turns ATA33's 225.28GB/s to 219.59GB/s, not including seek time. SATA's structures are much larger than SCSI-2 but smaller than ATAPI in size in my opinion (SCSI-2 has at most 12-byte commands). Setup & handling time could also slow down the OS to some degree compared with ATA, but then again not all fields are always used with every command - up to 10 bytes can go unused with ATAPI (and that could also include SATA).

atapi calculated data rates

doing a virus scan with McAfee 2007 takes several days to complete with 163GB of data, 6GB of which are compressed files. [Update: now that I upgraded from 1GB to 3GB ram, a scan takes a little over 2 days.]
doing a hard disk upgrade with Acronis MigrateEasy takes about 1 hour, which involves an entire partition copy.
doing a partition move (really a copy) with gparted takes about 3-4 hours, 30 minutes of which is file system check.

Summary: ATA/IDE/APAPI is a faster protocol than SATA, but SATA's faster data rates are supposed to make up for it. however, since software is slow, setup time & handling for SATA's larger structures means a slightly slower OS.

OS overhead would include things like memory allocation of buffers, setting up disk I/O, handling disk I/O, handling errors, passing information back and forth to the driver, (and anything else I've missed).

Once the data gets to the OS, then there's the filesystem at a higher level to take care of, which has structures stored on disk, partially cached in memory...

ATA: relative simplicity. for a seek, specify LBA address, device, and whether it's LBA. sector count and features aren't set to anything send the command twice to send the address halves. ATAPI in LBA mode has a either a 28-bit (137GB) or 48-bit (144Petabyte) address, or can be accessed in obsolete CHS mode. actually, with the new large-sector drives that have 4k sectors, the maximum would be 4096x248=1,152,921,504,606,846,976 bytes (1.153 Exabytes).
Note: CHS mode is deprecated and may be removed from the spec at some point in time, some have suggested it. With ATAPI (and I think with SATA too), it appears you can write the entire drive (? well maybe maximum 64k for DMA) full of data as one long data set in one command if you wanted to. This might make clusters and blocks of sectors faster — if they implemented it right.