Lost result file type! (huh?)

[wsnoble]

I tried running this command:

java -jar ~/software/PDV-2.2.0/PDV-2.2.0.jar -s one.mgf -st 1

but I got this inscrutable output:

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/net/noble/vol1/home/noble/software/PDV-2.2.0/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/net/noble/vol1/home/noble/software/PDV-2.2.0/lib/logback-classic-1.2.3.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
Lost result file type! (mzID: 1, pepXML: 2, proBAM: 3, txt: 4, maxQuant: 5)

What does that last line mean? I think it would be good to catch errors like this, so the user doesn't see all the SLF4 warnings, and just provide an informative error message.

I also think you should reorganize the help message to list all the required arguments first, followed by the optional arguments. And for all the optional ones, you should specify what the default value is.

I suspect that, in my particular case, the problem is that I haven't provided an annotation for this spectrum. I was hoping that PDV would go ahead and make a picture without any sequence annotation, but maybe that's not supported?

Anyway, I am now considering how to provide the annotation. I have one spectrum in an annotated MGF file (see below). According to the help message, there is apparently a .txt format for providing the annotation. Is there any documentation on what that format should look like?

Here is the MGF file (one.mgf):

BEGIN IONS
TITLE=Theoretical spectrum for MQLTVKALQGRE
PEPMASS=687.38211125376
CHARGE=2+
SEQ=MQLTVKALQGRE
132.04776137976 1.0 
150.05832606346002 1.0 
260.10633888504003 1.0 
278.11690356874 1.0 
373.19040286217 1.0 
391.20096754587 1.0 
474.23808133058003 1.0 
492.24864601428004 1.0 
573.30649524357 1.0 
591.3170599272701 1.0 
701.4014582575701 1.0 
719.41202294127 1.0 
772.43857204228 1.0 
790.44913672598 1.0 
885.52263601941 1.0 
903.5332007031101 1.0 
1013.5812135246899 1.0 
1031.59177820839 1.0 
1070.60267724526 1.0 
1088.61324192896 1.0 
1226.70378826886 1.0 
1244.7143529525601 1.0 
END IONS

[wenbostar]

If you just want to annotate one spectrum stored in an MGF file, you can use "One PSM" function:

[wenbostar]

You could launch the GUI interface in Mac by running the following command line:

java -jar ~/software/PDV-2.2.0/PDV-2.2.0.jar

[wsnoble]

I got this far, but the start button doesn't do anything.

[wenbostar]

Could you upload your mgf file here?

[wenbostar]

It works in my ubuntu system: