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:
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!