BWA mem reference genome index
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20 months ago
Maka ▴ 20

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!

chipseq Index BWA analysis • 1.6k views
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Disk space is not memory, and no or barely any machine in the world has 8T of memory. Type free -hm to learn how much memory you have.

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sorry, I misunderstood! so I checked it and it is a total mem 62G...

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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?

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