HISAT2-build killed: 9 macOS

Question

[datascientist28]

I'm getting the most random error on my genome build the output is killer 9, i've seen very conflicting reports on stackexchange and the goggles, does anyone have advice on what this means and how i can fix or look into this??

It outputs .ht2 files but is missing some of them. It only outputs the 1,2,3,4,7,8 .ht2 files (missing 5

D-128-95-53-182:mm9 rehlab$ /Applications/hisat2//hisat2-build -p 4 genome.fa --ss genome.ss --exon genome.exon test/genome_tran
Settings:
  Output files: "test/genome_tran.*.ht2"
  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
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 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:
  genome.fa
Reading reference sizes
  Time reading reference sizes: 00:00:33
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:18
  Time to read SNPs and splice sites: 00:00:02
Killed: 9

Answer 1

[datascientist28]

It was a memory issue because -ss and --exon require 200GB of memory. Removing those flags caused it to work.