Hi Dian,
I was trying to run MZmine with command line on a Linux machine. It is a
remote machine and it does not support X server. Therefore, I prepared the
input xml file on a local computer and copied it over to the Linux machine. I
did "startMZmine_Linux.sh myfile.xml" and got the following error. Is java VM
really needed for command-line mode?
Java VM is certainly needed, because the whole MZmine code is written in Java.
If not is there a way to disable it? If java VM is indeed needed, how do I
increase the heap size?
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
As Matthias already suggested, check the HEAP_SIZE variable in the startup
script.
The above error means that the Java VM tried to allocate more memory than what
was available from the OS.
How much memory does your Linux machine have? Is it running 32-bit or 64-bit
kernel?
Another question is, does this startMZmine script execute all three steps: mass
detection, chromatogram building and perk deconvolution?
The batch script will execute all modules that you put into your batch, in the
same order as they appear in the batch.
Is it possible to manually run them one by one (by option/flag)?
Sorry, that is not possible. But you can prepare different batches according to
your needs.
Tomas
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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