BWA mem reference genome index
hi...I am trying to run the Chip-Seq analysis pipeline...
bwa mem2 for reference genome GRCm39 download from https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27 as .fna (genbank)
#index genome
cd /media/j/Data/BWA-MEM2
bwa-mem2-2.0pre2_x64-linux/bwa-mem2 index "/media/j/Data/reference_genome/GCA_000001635.9_GRCm39_genomic.fna"
output
[bwa_index] Pack FASTA... 6.45 sec
init ticks = 204276126157
ref seq len = 5456444902
binary seq ticks = 108645462914
build index ticks = 4181642648109
ref_seq_len = 5456444902
count = 0, 1585357357, 2728222451, 3871087545, 5456444902
BWT[2307856312] = 4
CP_SHIFT = 5, CP_MASK = 31
sizeof CP_OCC = 64
Killed
As far as I understood, it is a problem of memory, but I checked and should have enough space (8T)
Any suggestions? thanks in advance!
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Disk space is not memory, and no or barely any machine in the world has 8T of memory. Type
free -hmto learn how much memory you have.sorry, I misunderstood! so I checked it and it is a total mem 62G...
you have 8Tb of memory in your server? I think you might be confusing it with storage/disk space .
can you add/post the specs of the server/laptop/pc you are trying to run this on?