Hello,
Let me preface my question by saying that I am new to using MZmine and it may
be that I am misunderstanding how the “batch” functionality works. I was under
the impression that the subsequent steps in the batch act on the result of the
previous line(s), however, I seem to have found an instance where that is not
the case. When I try run a simple batch with the following commands:
Raw data import
Targeted peak detection
Export to CSV file
The following error is thrown: “Unhandled exception in task Batch of 3 steps:
java.lang.ArrayIndexOutOfBoundsException: 0 (CSVExportTask.java:50)
I tracked down my problem to the fact that the “Targeted peak detection”
command is NOT generating a peak list which could then be exported. For
example, if I run the following 2 step batch no peak list is generated (but no
error is thrown either):
Raw data import
Targeted peak detection
The “Targeted peak detection” functionality works fine when not invoked in
batch mode -i.e. I can generate the correct peak list file navigating through
Raw data methods->Peak detection ->Targeted peak detection. Also, a peak list
is generated if I run a batch with “Mass detection" followed by “Chromatogram
builder”.
I also have one very curious observation…If already have a raw data file
already imported, and then run the following batch:
Raw data import
Targeted peak detection
a peak list corresponding to that called in the “Target peak detection” is
generated BUT form the file that is already open! (note: for this to work the
already open raw data file needs to be highlighted, if it is not then no peak
list in generated). So it would seem that the “Target peak detection” function
in the batch command looks at to a raw data file that is highlighted and NOT
that called in previous batch lines. I would be curious to know if (1) this is
a bug (2) if there are any work arounds you could think of like modifying the
batch xml file?
Thanks for you help!
here is my system info:
MZmine 2.10
running of OS X 10.9.1
java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)
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