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bioinformatics-centre / kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
http://kaiju.binf.ku.dk
GNU General Public License v3.0
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makeDB.sh -e :process killed #83

Closed gkong1 closed 5 years ago

gkong1 commented 6 years ago

Hi, I have tried to make the database using makeDB.sh -e. It finished downloading all the necessary files but killed itself when moving onto mkbwt step.

These are the files I got from the partial process of makeDB.sh -e: kaiju_db_nr_euk.faa
nodes.dmp
prot.accession2taxid prot.accession2taxid.gz merged.dmp
names.dmp
nr.gz
taxdump.tar.gz

So when I tried to run mkbwt -n 12 -a ACDEFGHIKLMNPQRSTVWY -o kaiju_db_nr_euk kaiju_db_nr_euk.faa:

# 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
Killed

Any clues as to why the process might have been killed? Thanks in advance!

pmenzel commented 6 years ago

It usually means that you are out of RAM; I think around 90GB ought to be enough for NR+euk database. Also decreasing the value of -n results in less RAM usage.