Question: Picard MarkDuplicates.jar error
0
gravatar for mark.rose
3.3 years ago by
mark.rose30
United States
mark.rose30 wrote:

Hi All

Anybody know why am getting this error. I get it with version 1.92 and 1.77.

$ /usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar I=mut1-1478822061-bowtie2.bam.sort.bam O=mut1-1478822061-bowtie2.bam.sort.rmdup.bam M=marked_dup_metrics.txt REMOVE_DUPLICATES=true
    /usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 1: PK: command not found
    /usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 2: ÁP´B: command not found
    /usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 3:ÀP´B©: command not found
    /usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 4: syntax error near unexpected token `)'
    /usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 4: `SªMETA-INF/MANIFEST.MFe½
    wÞÑ1Ú¦lj·ÆýV¯)©"ëз/£±ãùÉwNÎÎI¢ÝZåÕîàÔÆ7ä¥ð¦4gm@ dó5¢ÈUYÉW®eYiÕÞ/(:7ª
                                                                         gÝÄI>--hDáóØýbÇõ`

I also get it with just

$ /usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar
/usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 1: PK: command not found
/usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 2: ÁP´B: command not found
/usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 3:ÀP´B©: command not found
/usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 4: syntax error near unexpected token `)'
/usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar: line 4: `SªMETA-INF/MANIFEST.MFe½
wÞÑ1Ú¦lj·ÆýV¯)©"ëз/£±ãùÉwNÎÎI¢ÝZåÕîàÔÆ7ä¥ð¦4gm@ dó5¢ÈUYÉW®eYiÕÞ/(:7ª
                                                                     gÝÄI>--hDáóØýbÇõ`

Thanks for your help

error picard duplicates • 1.4k views
ADD COMMENTlink modified 3.3 years ago by Dan D7.0k • written 3.3 years ago by mark.rose30
1
gravatar for Dan D
3.3 years ago by
Dan D7.0k
Tennessee
Dan D7.0k wrote:

It appears that you're trying to execute the jar file directly. That's why it's failing. Instead you should preface your command with this:

java -Xmx2g -jar

Before attempting this, try simply typing java and pressing enter to verify that Java is installed. If it's not, use the package manager for your distro to install java. For example yum install java on CentOS/Redhat or apt-get install java on Ubuntu

-Xmx2g is simply indicating the amount of memory to allocate to the Java virtual machine which will run the program. My example provides 2 gigabytes but you can experiment with other values.

Here's the full command for your specific example:

java -Xmx2g -jar /usr/local/thirdparty/picard/picard-tools-1.92/MarkDuplicates.jar I=mut1-1478822061-bowtie2.bam.sort.bam O=mut1-1478822061-bowtie2.bam.sort.rmdup.bam M=marked_dup_metrics.txt REMOVE_DUPLICATES=true

As @d-cameron mentioned, you're using an old version of Picard tools. But the specific tool you're using in this case is very mature and should provide perfectly acceptable results.

ADD COMMENTlink written 3.3 years ago by Dan D7.0k

I will try this but what is surprising if this works is that I have run the command I specified successfully in the past. I only encountered this problem when switching to a new server.

ADD REPLYlink written 3.3 years ago by mark.rose30

Yes, that was it. Thanks

ADD REPLYlink written 3.3 years ago by mark.rose30
0
gravatar for Santosh Anand
3.3 years ago by
Santosh Anand5.0k
Santosh Anand5.0k wrote:

Did you run 'java -jar', with correct version of Java?

ADD COMMENTlink written 3.3 years ago by Santosh Anand5.0k
0
gravatar for d-cameron
3.3 years ago by
d-cameron2.1k
Australia
d-cameron2.1k wrote:

Picard tools version 1.77 was released on Jul 3, 2012, and 1.92 was released on May 20, 2013. There have been 66 releases of picard tools since 1.92 with the most recent version of picard tools being version 2.7.1. I strongly encourage you to update to a more recent version, especially since the release packaging format has changed since the versions you are using.

ADD COMMENTlink written 3.3 years ago by d-cameron2.1k
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