Failed to shrink the database...

[jeffreycapy]

Hi,
I used your script and built a kraken database. However, I failed when I tried to shrink the database. The error messages are:

Use of uninitialized value $shrink_block_offset in exec at kraken-master/scripts/kraken-build line 278.
db_shrink: offset count cannot be negative

The database seems to be all right since the messages from the building process contain no warnings or errors:

Kraken build set to minimize disk writes.
Creating k-mer set (step 1 of 6)...
Found jellyfish v1.1.11
Hash size not specified, using '42143697583'
K-mer set created. [9h56m25.432s]
Skipping step 2, no database reduction requested.
Sorting k-mer set (step 3 of 6)...
K-mer set sorted. [3h39m41.612s]
Creating GI number to seqID map (step 4 of 6)...
GI number to seqID map created. [9m33.546s]
Creating seqID to taxID map (step 5 of 6)...
27325 sequences mapped to taxa. [0.254s]
Setting LCAs in database (step 6 of 6)...
Finished processing 27325 sequences
Database LCAs set. [19h44m16.052s]
Database construction complete. [Total: 33h29m57.036s]

I am wondering if you have any suggestion on how to solve this problem?

Cheers,
Jeffrey