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.
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.
Comment