MIRA: "zsh: killed" crash

[cwgao]

Hi,

I am a member of a lab doing a de novo assembly of Ion Torrent data for H. pylori on MIRA 3.4, and we have continually received a message in the command line, "zsh: killed", followed by a reiteration of our parameters, as the run crashes. The assembly log gives no fatal error messages; it was not a controlled stop.

We are running MIRA in BioLinux7 through a VirtualBox. The strange part is, I have gotten a successful run before, on a smaller virtual machine (1720 mb RAM, 16.0 GB VDI), using the exact same call parameters:

mira -project=hpylori -fastq -job=genome,denovo,accurate,iontor -notraceinfo

We thought originally that we may not have allocated enough RAM; however, another lab member (on a PC) gave his virtual machine 4.0 gb of RAM (way more than I did in my original, successful run), and it still showed "zsh: killed". This seems to be a particular problem for the Mac users in our lab - every single MIRA run on a Mac (even though it was through BioLinux on VirtualBox) has resulted in "zsh: killed". PC users have sometimes gotten successful runs, and sometimes received "zsh: killed", using the same call parameters.

The last few lines of one assembly log before the crash:
Hash analysis for proposed cutbacks:Localtime: Tue Mar 11 16:38:59 2014
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ..

And of another:
Localtime: Tue Mar 11 16:36:32 2014
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ..

These are the results from entering "ulimit -a":
zsh: killed mira --project=data --fastq --job=genome,denovo,accurate,iontor --notraceinfo
john@john-VirtualBox[MiraPath] ulimit -a [12:56PM]
-t: cpu time (seconds) unlimited
-f: file size (blocks) unlimited
-d: data seg size (kbytes) unlimited
-s: stack size (kbytes) 8192
-c: core file size (blocks) 0
-m: resident set size (kbytes) unlimited
-u: processes 7815
-n: file descriptors 1024
-l: locked-in-memory size (kb) 64
-v: address space (kb) unlimited
-x: file locks unlimited
-i: pending signals 7815
-q: bytes in POSIX msg queues 819200
-e: max nice 0
-r: max rt priority 0
-N 15: unlimited

Has anyone found a solution to the "zsh: killed" problem? Also, has anyone run MIRA on a Mac before through a VirtualBox Linux machine?

Thank you very much! If you need any more information about our attempted runs, please let me know.

[maubp]

This does sound like the (virtual) Linux OS is killing MIRA, probably due to running out of memory.

Have you considered running MIRA on the Mac directly instead? Also MIRA 3.4 is old now and replaced by MIRA 4.0, which should be more memory efficient (especially with Illumina data).

[cwgao]

We got MIRA 4.0 running directly on a Mac today, and it seems to be working now. It did give us more and shorter contigs compared to the previous runs through VirtualBox on PCs, but we figure that can probably be fixed by adjusting parameters. We will try replacing version 3.4 with 4.0 on the PCs as well.

Thank you very much for your advice!