Running Java and Picard for the first time - so confused!

anandianandi StellenboschMember

Hi all.
Please bear with this newbie question. I am trying to run Picard MarkDuplicates with java and have read all the documentation I can find and still I'm getting strange errors!

1) I made a path for java by adding these lines to my .bash_profile:

$export JAVA_HOME=/usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java
$export JRE_HOME=/usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java
$export PATH=$PATH:$HOME/bin:JAVA_HOME:JRE_HOME

2) I am running the MarkDuplicates script as follows:

java -Xmx2g -jar /home/.apps/picard-tools/1.119/MarkDuplicates.jar INPUT=inputfile.bam OUTPUT=outputfile.bam METRICS_FILE=stats/filename.sorted AS=TRUE REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=SILENT TMP_DIR=temp/CREATE_INDEX=true

In the .out file I get the following error:
OpenJDK 64-Bit Server VM warning: You have loaded library /home/.apps/picard-tools/1.119/libIntelDeflater.so which might have disabled stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c ', or link it with '-z noexecstack'.

And in the .err file I get:
[Thu Aug 27 09:14:37 SAST 2015] picard.sam.MarkDuplicates INPUT=[home/anandie/BWA/7DLAetAln.bam] OUTPUT=7DLAetAln.sorted.markdup.bam METRICS_FILE=stats/7DLAetAln_Markdup.sorted REMOVE_DUPLICATES=false ASSUME_SORTED=true TMP_DIR=[temp/CREATE_INDEX=true] VALIDATION_STRINGENCY=SILENT PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Aug 27 09:14:37 SAST 2015] Executing as [email protected] on Linux 2.6.32-573.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_85-mockbuild_2015_07_15_13_21-b00; Picard version: 1.119(d44cdb51745f5e8075c826430a39d8a61f1dd832_1408991805) IntelDeflater
[Thu Aug 27 09:14:37 SAST 2015] picard.sam.MarkDuplicates done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: /home/anandie/BWA/home/anandie/BWA/7DLAetAln.bam
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:280)
at picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:171)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
at picard.sam.MarkDuplicates.main(MarkDuplicates.java:161)

I have tried running ValidateSamFile in a similar manner and also get the same error.

Can someone please point me in the right direction! Is it java or picardtools giving the problem? Where can I start my search!

Thanks for your time!

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @anandi
    Hi,

    From the error message "Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: /home/anandie/BWA/home/anandie/BWA/7DLAetAln.bam", it looks like the bam file you specified is not in the directory. Can you check that the bam file and the bam index file are both in /home/anandie/BWA/home/anandie/BWA/?

    Thanks,
    Sheila

  • thibaultthibault Broad InstituteMember, Broadie, Moderator, Dev ✭✭

    Pay careful attention to how you're specifying the input: I see the relative path home/anandie/BWA/7DLAetAln.bam with no leading slash but I strongly suspect that you want the absolute path /home/anandie/BWA/7DLAetAln.bam including the leading slash.

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