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medbioinf / pia

:books: :microscope: PIA - Protein Inference Algorithms
https://github.com/medbioinf/pia
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Problem when running CMD #164

Closed cksakura closed 10 months ago

cksakura commented 3 years ago

Hello,

I encountered this problem when I use the CMD to run the PIA:

2021-03-22 23:13:47,855 ERROR PIAIntermediateJAXBHandler - Error while parsing PIA XML file com.ctc.wstx.exc.WstxUnexpectedCharException: Unexpected character 'f' (code 102) in prolog; expected '<' at [row,col {unknown-source}]: [1,1] at com.ctc.wstx.sr.StreamScanner.throwUnexpectedChar(StreamScanner.java:653) at com.ctc.wstx.sr.BasicStreamReader.nextFromProlog(BasicStreamReader.java:2133) at com.ctc.wstx.sr.BasicStreamReader.next(BasicStreamReader.java:1181) at com.ctc.wstx.sr.BasicStreamReader.nextTag(BasicStreamReader.java:1204) at de.mpc.pia.intermediate.xmlhandler.PIAIntermediateJAXBHandler.parseXMLFile(PIAIntermediateJAXBHandler.java:188) at de.mpc.pia.intermediate.xmlhandler.PIAIntermediateJAXBHandler.parse(PIAIntermediateJAXBHandler.java:162) at de.mpc.pia.modeller.PIAModeller.parseIntermediate(PIAModeller.java:296) at de.mpc.pia.modeller.PIAModeller.loadFileName(PIAModeller.java:175) at de.mpc.pia.modeller.PIAModeller.(PIAModeller.java:119) at de.mpc.pia.modeller.PIAModeller.processExecuteXMLFile(PIAModeller.java:799) at de.mpc.pia.modeller.PIAModeller.parseParameterXMLFile(PIAModeller.java:786) at de.mpc.pia.modeller.PIAModeller.main(PIAModeller.java:733)

I just generated the parameter file by the "-paramOutFile" command. Thanks for your help.

julianu commented 3 years ago

Apologies for the late reply, but could you elaborate, how you called PIA from the CLI? Could you maybe also post the param file here, so I can double check it?

The generation of an "analysis pipeline file" via the command line is discouraged and, I am afraid, a bit out of date, if you tried this way. More effort went into the KNIME nodes lately and an update of the CLI is lacking behind.

julianu commented 10 months ago

You should use the json file to run a CLI analysis by now.