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Timing Issues Error/normal HSQLDB/ Java doubt

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Well I am a bit confused if its a hsqldb question or java question but still if some one can answer; here it goes:
Test run approx gave me the time to run second query each time (code: read_2 string - for table2) is some Milli seconds. Isnt it too much time
Full run:
Time approx: 5 days (estimate based on the output for approx 3 days)
Size of table1: 2,355,459 rows, 9 fields, all varchar
Size of table2: 7,392,872 rows 17 fields, all varchar [am using Indexing]
Tables created were cached tables

1 issue definitely is I am calling a query from a query and the second query is on a large table but still main issue is if this time for reading data from 2nd query isn't too much? I have tried with prepared statement too but the performance increment is not that great.
Besides I today tried the same thing thing with mySQL and it was extremely fast (sample: hsqldb- 1 hour; mysql- 17 mins). So can I conclude that HSQLDB isnt that good for large DBs..???

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Please take immediate note of the private message I just sent you
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