This is a test version of Biostars. For the public version, visit https://www.biostars.org.
BWA Index killed

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
• 4,086 views • link
updated by Ram Ram • written by Anupama • Anupama

1 answer

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.

• 0 views • link
written by ATpoint ATpoint

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

• 0 views • link
written by Anupama • Anupama

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

• 0 views • link
written by ATpoint ATpoint

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.

• 0 views • link
written by ATpoint ATpoint 
                  total        used        free      shared  buff/cache   available
Mem:          3.7Gi       233Mi       3.4Gi       0.0Ki       102Mi       3.4Gi
Swap:         1.0Gi          0B       1.0Gi
• 0 views • link
updated by ATpoint ATpoint • written by Anupama • Anupama

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.

• 0 views • link
written by ATpoint ATpoint

Log in to answer this question.

More posts like this