Long Read Assembly Issue

[peflanag]

Hi All,

I've tried to run a long read assembly on unicycler on a linux machine and got the following error. Anyone know what it means?

Cheers,

P

linux-biostation@Linux-BioStation:~$ unicycler -l '/home/linux-biostation/Documents/Peter F Work/MinION_Unicycler_Test/Guppy_BC6.fastq' -o '/home/linux-biostation/Documents/Peter F Work/MinION_Unicycler_Test/Unicycler/Guppy_BC6'

Starting Unicycler (2019-05-24 08:28:10) Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you provided only long reads, Unicycler will assemble the reads with miniasm and then run repeated polishing rounds using Racon. For more information, please see https://github.com/rrwick/Unicycler

Command: /home/linux-biostation/.local/bin/unicycler -l "/home/linux-biostation/Documents/Peter F Work/MinION_Unicycler_Test/Guppy_BC6.fastq" -o "/home/linux-biostation/Documents/Peter F Work/MinION_Unicycler_Test/Unicycler/Guppy_BC6"

Unicycler version: v0.4.8-beta Using 8 threads

The output directory already exists and files may be reused or overwritten: /home/linux-biostation/Documents/Peter F Work/MinION_Unicycler_Test/Unicycler/Guppy_BC6

Dependencies: Program Version Status
spades.py not used racon 1.3.3 good
makeblastdb 2.2.31+ good
tblastn 2.2.31+ good
bowtie2-build not used bowtie2 not used samtools not used java not used pilon not used bcftools not used

Loading reads (2019-05-24 08:28:10) 2,866,569 / 3,372,434 (85.0%) - 3,680,092,087 bpKilled linux-biostation@Linux-BioStation:~$

[dswan]

Most likely you ran out of memory When you see "Killed" like that, it's often the OOM (out of memory) Killer has reaped the process before it grinds the system to a halt.

Try dmesg | less and look for information about the killed process.

[peflanag]

Oh right, yea I see this at the end of that command:

[770224.653862] Out of memory: Kill process 9055 (unicycler) score 530 or sacrifice child [770224.653866] Killed process 9055 (unicycler) total-vm:9255508kB, anon-rss:9156896kB, file-rss:64kB, shmem-rss:0kB [770225.063522] oom_reaper: reaped process 9055 (unicycler), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB

Is there anything I can do to stop it from happening? The machine has an i7 intel chip and 16GB of ram

[dswan]

I don't know much about your dataset, but fewer reads would be a good place to start if you can't move to a machine with more memory.

[peflanag]

Unfortunately I can't. We are limited in our resources and waiting on a HPC to be up and runnig that went down a few days! Cheers though. Was the first time using unicycler for long minion reads only! I'll wait till the HPC cluster is back up and running!

[stevenjdunn]

Have you checked out Climb? They offer free access to servers for academic institutions.