Question

BWA Index killed

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2.8 years ago

Anupama • 0

I'm trying to build an index by using this command

bwa index -p hg19bwaidx -a bwtsw hg19.fa

However, the process keeps getting killed after ~10 minutes. I have 1TB of memory. Here's the error message

[bwa_index] Pack FASTA... Killed

What could be the reason?

Fastq BWA Index • 2.8k views

ADD COMMENT • link updated 2.8 years ago by Ram 44k • written 2.8 years ago by Anupama • 0

ATpoint · Answer 1 · 2022-03-03

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2.8 years ago

ATpoint 85k

1TB of memory, can you confirm that it is memory and not disk space? Is this a cluster job/node, if so please show the submission script. Maybe it is simply not allocated properly.

ADD COMMENT • link 2.8 years ago by ATpoint 85k

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1TB is the external hard drive. No, it's not a cluster job.

ADD REPLY • link 2.8 years ago by Anupama • 0

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Hard drive space != memory. What is the output of free -hm? Meaning how much memory (aka RAM) do you have?

ADD REPLY • link 2.8 years ago by ATpoint 85k

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Turs out you asked the same before (and apparently deleted it?) and a user already told you it's a memory problem. probably same issue, you confuse memory and disk space BWA Index Killed

It is 99.9% sure simply not enough memory available on your machine.

ADD REPLY • link 2.8 years ago by ATpoint 85k

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                  total        used        free      shared  buff/cache   available
Mem:          3.7Gi       233Mi       3.4Gi       0.0Ki       102Mi       3.4Gi
Swap:         1.0Gi          0B       1.0Gi

ADD REPLY • link updated 2.8 years ago by ATpoint 85k • written 2.8 years ago by Anupama • 0

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4GB of RAM is by far not enough. 8GB or better more will be required, see memory consumption of bwa-mem

You need to upgrade your machine or switch to a workstation/server with adequate memory. With 4GB you are not going to do any meaningful analysis these days. Even something like bowtie2 which has a low memory footprint will likely not run on it.