Picard MarkedDuplicates Error: Unable to access jarfile picard.jar

Question

[connorjfausto]

Hello,

I am trying to run MarkedDuplicates on Picard, but it says that it cannot open the java file.

My initial code is:

   java -jar picard.jar MarkDuplicates \
          I=BAM_SRR9049479.bam \
          O=BAM_SRR9049479_dedup.bam \
          M=BAM_SRR9049479_dedup_metrics.txt

And I receive this error:

Error: Unable to access jarfile picard.jar

When trying to troubleshoot whether I have correctly installed picard with:

java -jar $PICARD -h

I get the help menu output:

Usage: java [-options] class [args...]
           (to execute a class)
   or  java [-options] -jar jarfile [args...]
           (to execute a jar file)
where options include:
    -d32      use a 32-bit data model if available
    -d64      use a 64-bit data model if available
    -server   to select the "server" VM
                  The default VM is server,
                  because you are running on a server-class machine.


    -cp <class search path of directories and zip/jar files>
    -classpath <class search path of directories and zip/jar files>
                  A : separated list of directories, JAR archives,
                  and ZIP archives to search for class files.
    -D<name>=<value>
                  set a system property
    -verbose:[class|gc|jni]
                  enable verbose output
    -version      print product version and exit
    -version:<value>
                  Warning: this feature is deprecated and will be removed
                  in a future release.
                  require the specified version to run
    -showversion  print product version and continue
    -jre-restrict-search | -no-jre-restrict-search
                  Warning: this feature is deprecated and will be removed
                  in a future release.
                  include/exclude user private JREs in the version search
    -? -help      print this help message
    -X            print help on non-standard options
    -ea[:<packagename>...|:<classname>]
    -enableassertions[:<packagename>...|:<classname>]
                  enable assertions with specified granularity
    -da[:<packagename>...|:<classname>]
    -disableassertions[:<packagename>...|:<classname>]
                  disable assertions with specified granularity
    -esa | -enablesystemassertions
                  enable system assertions
    -dsa | -disablesystemassertions
                  disable system assertions
    -agentlib:<libname>[=<options>]
                  load native agent library <libname>, e.g. -agentlib:hprof
                  see also, -agentlib:jdwp=help and -agentlib:hprof=help
    -agentpath:<pathname>[=<options>]
                  load native agent library by full pathname
    -javaagent:<jarpath>[=<options>]
                  load Java programming language agent, see java.lang.instrument
    -splash:<imagepath>
                  show splash screen with specified image

However I can't open the actual MarkedDuplicates file. With this input

java -jar $PICARD MarkDuplicates

I get:

Error: Unable to access jarfile MarkDuplicates

Please let me know!