minimap2 gets killed, but it doesn't explain why
2
0
Entering edit mode
6 weeks ago

I've been using bowtie2 fine aligning some reads to chr4.

I'm now trying to align to a custom reference that includes several thousand synthetic sequences. It works fine locally when I run it on my own machine, but it fails when I run it remotely on my server (aws t2.large, 8 GB RAM).

Here's the output I get:

$ minimap2 -ax map-ont --sam-hit-only --MD -Y "$REF" "$R1" > "${OUT}/${FN}.sam"
[M::mm_idx_gen::12.568*1.61] collected minimizers
[M::mm_idx_gen::28.109*1.34] sorted minimizers
[M::main::28.120*1.34] loaded/built the index for 70014 target sequence(s)
[M::mm_mapopt_update::28.120*1.34] mid_occ = 1000000
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 70014
[M::mm_idx_stat::28.120*1.34] distinct minimizers: 607 (1.65% are singletons); average occurrences: 353381.712; average spacing: 3.393; total length: 727835538
Killed

I've tried reading around, and also can't find a method to run it in a more verbose mode. I suspect it's hitting a ceiling in processing power? Can anyone help me work out what the issue is, and how to resolve?

bowtie2 • 470 views
ADD COMMENT
1
Entering edit mode

You're running minimap2 not bowtie, but anyway, you are likely running out of memory because 8GB isn't much especially with larger reference. You need a larger instance. Also, when a process is killed by the kernel you never get an explanation, but it is almost always because of RAM issues.

ADD REPLY
0
Entering edit mode

Yes, sorry minimap2!

ADD REPLY
1
Entering edit mode
6 weeks ago
ATpoint 81k

It's minimap2, not bowtie2, and you might simply run out of memory. Check memory usage locally, then you know.

ADD COMMENT
0
Entering edit mode

The other point to make here is that its not telling you why it has been killed because the "Killed" message is coming from the operation system, not minimap2.

ADD REPLY
0
Entering edit mode
6 weeks ago

It's a RAM problem, as others have said. 8 GB is too little. I use 30-60 GB for my minimap2 processes for long reads vs plant genomes.

You can check RAM usage on your server using a variety of tools, like htop, glances, and my current fave bottom https://github.com/ClementTsang/bottom .

ADD COMMENT

Login before adding your answer.

Traffic: 1516 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6