messersc
commented
2 years ago This looks like a problem with two java installations in the conda env, where we have 1.7 and 1.8 at the same time and picard does not use the correct one. We will need to untangle that.
Dec 01 15:08:36 ..... started STAR run Dec 01 15:08:36 ..... loading genome Dec 01 15:08:53 ..... started mapping Dec 01 15:31:21 ..... finished mapping Dec 01 15:31:23 ..... finished successfully
** NOTE: Picard's command line syntax is changing.
** For more information, please see: ** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
** The command line looks like this in the new syntax:
** MarkDuplicates -I mapping/star/4_Hypo_OP13/all_mates/out/star.4_Hypo_OP13.all_mates.bam -O mapping/star/4_Hypo_OP13/all_mates/out/4_Hypo_OP13.mdup.bam -M mapping/star/4_Hypo_OP13/all_mates/out/4_Hypo_OP13.metrics.out -TMP_DIR mapping/star/4_Hypo_OP13/all_mates/out
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. Exception in thread "main" java.lang.ExceptionInInitializerError at picard.cmdline.CommandLineProgram.getCommandLineParserForArgs(CommandLineProgram.java:398) at picard.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:348) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:223) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113) Caused by: java.lang.UnsupportedOperationException: No class provided, and an appropriate one cannot be found. at org.apache.logging.log4j.LogManager.callerClass(LogManager.java:576) at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:601) at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:588) at org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParser.(LegacyCommandLineArgumentParser.java:97)
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