ilnamkang commented 7 years ago

Hello, I'm running the latest version of kaiju (1.5.0) and have been trying to construct the reference database and index using makeDB.sh. But, it seems that the script terminates prematurely and no fmi file is generated.

Below is the stdout I got by makeDB.sh.

Start

memb-main@membmain-empty[kaijudb] makeDB.sh -e -t 12
Downloading file taxdump.tar.gz 2017-05-02 10:08:37 URL: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz [2752] -> ".listing" [1] 2017-05-02 10:09:20 URL: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz [39222156] -> "taxdump.tar.gz" [1] Extracting file taxdump.tar.gz Downloading file nr.gz 2017-05-02 10:09:25 URL: ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz [3725] -> ".listing" [1] 2017-05-02 13:14:40 URL: ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz [29460199431] -> "nr.gz" [1] Downloading file prot.accession2taxid.gz 2017-05-02 13:14:44 URL: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz [1623] -> ".listing" [1] 2017-05-02 14:04:00 URL: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz [2957842802] -> "prot.accession2taxid.gz" [1] Unpacking prot.accession2taxid.gz Converting NR file to Kaiju database Reading taxonomic tree from file nodes.dmp Reading taxa from file /mnt/Storage/Metagenome/kaiju/bin/taxonlist.tsv Reading accession to taxon id map from file prot.accession2taxid Processing NR file Creating BWT from Kaiju database

infilename= kaiju_db_nr_euk.faa

outfilename= kaiju_db_nr_euk

Alphabet= ACDEFGHIKLMNPQRSTVWY

nThreads= 12

length= 0.000000

checkpoint= 5

caseSens=OFF

revComp=OFF

term= *

revsort=OFF

help=OFF

Sequences read time = 522.420483s SLEN 36316848503 NSEQ 102635280 ALPH *ACDEFGHIKLMNPQRSTVWY SA NCHECK=0 Sorting done, time = 42943.242368s memb-main@membmain-empty[kaijudb]

End

The makeDB.sh terminates immediately after generating .bwt and .sa file. How can I solve this problem and get *.fmi file?

Thanks.

pmenzel commented 7 years ago

Weird, since you got the kaiju_db_nr_euk.bwt and kaiju_db_nr_euk.sa files, you can try to just make the fmi file using the mkfmi command:

/mnt/Storage/Metagenome/kaiju/bin/mkfmi kaiju_db_nr_euk