I recently upgraded my MacOSX system to Catalina and several files were placed automatically into "Relocated items" folder on my Desktop. I recently tried to run the following code which had previously worked:
qualimap bamqc -bam Sample1_sorted.bam -c -outdir QualiMap/Sample1_sorted
and received the following error:
Java HotSpot(TM) 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
Error: Unable to initialize main class org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain
Caused by: java.lang.NoClassDefFoundError: org/apache/commons/cli/ParseException
I have seen many other posts related to this error but am unsure how to even go about trying some of the suggested solutions. I do not work directly with some of the applications/files mentioned in these forums, such as JAVA, Maven, AppAssembler, and the pom.xml file (I could not even find that file). As a result, I wished to ask about this error from the perspective of a biologist using qualimap.
How can I fix this error (with little knowledge of the above applications/files)? I can certainly work with these applications/files, but I would probably need more detailed/basic/low-level advice on how to access and modify them. Thank you!
