Hi everyone,
I have been trying qualscore 1.0.2, but having quite a few problems
getting it to work properly. I followed Frank Posthast's suggestion to
include -Xms750m to solve the outofmemory issue, and it worked. The
error msg for the latest problem that I encountered is as follows:
[Thu Jun 11 15:18:26 2009] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/
data/Proteominer/Cartridge1Solv1; java -Xms750m -Xmx750m -jar C:
\Inetpub\tpp-bin\qualscore_v1.0_2.jar -c 1.5 -p 0.2
cart1solv1_newtandem_interact.pep.xml
OUTPUT:
XML
WARNING: Output directory 'cart1solv1_newtandem_interact.pep.qdir'
exists. DTAs will be written to existing dir.
Loading interact data:
1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000
12000 13000 14000 15000 16000 17000 18000 19000 20000 21000
22000 23000 24000 25000 26000 27000 28000 29000 30000 31000
32000 33000 34000 35000 36000 37000 38000 39000 40000 41000
42000 43000 44000 45000 46000 47000 48000 49000 50000 50580
Interact data file contains 50579 entries.
0 +1 were removed.
Enumerating scans:
processing RNP00186S00209FR05.mzXML... 500 1000 1500 2000 2500
processing RNP00186S00209FR07.mzXML... 3000 3500 4000 4500 5000
5500
processing RNP00186S00209FR01.mzXML... 6000 6500 7000
processing RNP00186S00209FR10.mzXML... 7500 8000 8500 9000 9500
10000 10500 11000
processing RNP00186S00209FR08.mzXML... 11500 12000 12500 13000
13500 14000
processing RNP00186S00209FR15.mzXML... 14500 15000 15500 16000
16500 17000 17500
processing RNP00186S00209FR02.mzXML... 18000 18500 19000 19500
20000
processing RNP00186S00209FR14.mzXML... 20500 21000 21500 22000
22500 23000 23500
processing RNP00186S00209FR03.mzXML... 24000 24500 25000 25500
26000 26500
processing RNP00186S00209FR16.mzXML... 27000 27500 28000 28500
29000 29500
processing RNP00186S00209FR04.mzXML... 30000 30500 31000 31500
32000 32500 33000
processing RNP00186S00209FR09.mzXML... 33500 34000 34500 35000
35500 36000 36500
processing RNP00186S00209FR12.mzXML... 37000 37500 38000 38500
39000 39500 40000
processing RNP00186S00209FR13.mzXML... 40500 41000 41500 42000
42500 43000 43500
processing RNP00186S00209FR11.mzXML... 44000 44500 45000 45500
46000 46500 47000
processing RNP00186S00209FR06.mzXML... 47500 48000 48500 49000
49500 50000 50500 50579
Features calculated for: 50579 (202211 ms)
Training set: 5707/33361 (good/bad)
Unassigned spectra: 39463
Quality score calculation time: 391 ms
Writing classifier co-efficients to file:
cart1solv1_newtandem_interact.pep.qdir.coef
java.lang.ArrayIndexOutOfBoundsException: 0
at org.isb.mzxml.MzXML.rap(MzXML.java:120)
at org.systemsbiology.qualscore.commandline.Main.extractDTAsFromMzXML
(Main.java:448)
at org.systemsbiology.qualscore.commandline.Main.<init>(Main.java:
384)
at org.systemsbiology.qualscore.commandline.Main.main(Main.java:1041)
0 dtas written to cart1solv1_newtandem_interact.pep.qdir.
Time: 211
END OUTPUT
RETURN CODE:0
I have absolutely no idea what this error is all about. It seems that
qualscore could perform all its calculations properly until the last
few steps. Would appreciate any advice on this. Thanks!
Bernard
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