Hi! I am very new to bioinformatics and am trying to follow the centrifuge tutorial (https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-example). I am having issues building an index using Centrifuge build.
I am trying to run this code from the tutorial on Centrifuge 1.0.4 Beta:
centrifuge-build -p 4 --conversion-table seqid2taxid.map \
--taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp \
input-sequences.fna abv
My output looks like this:
Settings:
Output files: "abv.*.cf"
Line rate: 7 (line is 128 bytes)
Lines per side: 1 (side is 128 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
input-sequences.fna
Reading reference sizes
Time reading reference sizes: 00:10:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Killed
Any help would be greatly appreciated. Thank you!
Are you running out of memory? How much memory do you have available?
Hi! I don't think I am running out of memory. I've requested 45000 from our server, and the file is only 86 GB. I can request more memory if you think that would help! Thank you!
Is that 45G? Then you should try asking for more.
Hi, I think it's actually 4.5Gb. I've just been given a green light for 320G so I'm going to give that a whack. Thank you so much!