Error: cannot find or fail to load the main class de.hu.berlin.wbi.stuff.dbSNPParser.xml.ParseXMLToFile when Parse dbSNP-XML dump

rockt / SETH

SNP Extraction Tool for Human Variations

rockt.github.com/SETH

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Error: cannot find or fail to load the main class de.hu.berlin.wbi.stuff.dbSNPParser.xml.ParseXMLToFile when Parse dbSNP-XML dump #36

Closed QQ-Peng closed 2 years ago

Erechtheus commented 2 years ago

Please explain in more detail what you were trying to do. Did you use bash?

QQ-Peng commented 2 years ago

I followed the readme “https://rockt.github.io/SETH/” to Parse dbSNP-XML file，but failed. the command line is "java -cp seth.jar -Djdk.xml.totalEntitySizeLimit=0 -DentityExpansionLimit=0 de.hu.berlin.wbi.stuff.dbSNPParser.xml.ParseXMLToFile"

Erechtheus commented 2 years ago

Unable to reproduce.

git clone https://github.com/rockt/SETH.git
cd SETH
mvn clean compile assembly:single
mv ./target/seth-1.3.2-Snapshot-jar-with-dependencies.jar seth.jar
java -cp seth.jar -Djdk.xml.totalEntitySizeLimit=0 -DentityExpansionLimit=0 de.hu.berlin.wbi.stuff.dbSNPParser.xml.ParseXMLToFile

works for me

QQ-Peng commented 2 years ago

thanks for your instruction, but it still failed to work. After adding "import de.hu.berlin.wbi.stuff.dbSNPParser.xml.*;" in the SETH.java, it works successfully. from Qianqian Peng(HZAU BioNLP Lab)