Building custom database without gi_taxid_nucl.dmp

[fungs]

Hi,

I'm getting errors on version 0.10.5b when I prepare a fasta file as described in the manual and run kraken-build. First, kraken-build complains about a missing taxonomy/gi_taxid_nucl.dmp which is a 8 GiB file which not needed in this case. When I create this as an empty file, there is a mmap error.

Without gi_taxid_nucl.dmp:

kraken-build --db mydb --threads 20 --build
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 '81910966608'
K-mer set created. [2h4m52.942s]
Skipping step 2, no database reduction requested.
Sorting k-mer set (step 3 of 6)...
K-mer set sorted. [11h41m59.065s]
Creating GI number to seqID map (step 4 of 6)...
GI number to seqID map created. [4m29.637s]
Creating seqID to taxID map (step 5 of 6)...
make_seqid_to_taxid_map: unable to open taxonomy/gi_taxid_nucl.dmp: No such file or directory

With empty gi_taxid_nucl.dmp:

kraken-build --db mydb --threads 20 --build
Kraken build set to minimize disk writes.
Skipping step 1, k-mer set already exists.
Skipping step 2, no database reduction requested.
Skipping step 3, k-mer set already sorted.
Skipping step 4, GI number to seqID map already complete.
Creating seqID to taxID map (step 5 of 6)...
make_seqid_to_taxid_map: unable to mmap taxonomy/gi_taxid_nucl.dmp: Invalid argument

This could be changed.

[jenniferlu717]

This is no longer an issue for Kraken v1.0