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problem with picard

Hello, I have been running into an error that i can not figure out why.

Here is the error message:

Fatal error: Exit code 1 ()
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/017/962/17962822/_job_tmp -Xmx7g -Xms256m
Exception in thread "main" htsjdk.samtools.SAMFormatException: For sequence 0, text and binary have different lengths in file /galaxy-repl/main/jobdir/017/962/17962822/working/RmDup_on_data_275
at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:543)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:177)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:132)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:293)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:145)
at picard.sam.SortSam.doWork(SortSam.java:91)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105

Here is what i did:

      1. run BWA-MEM with a reference genome on Galaxy (all default settings for read group,  output settings: -M For Picard, defaults for others)

      2. try to sort the BAM with Picard->SortSam on Coordinates.  This will fail and generate the above errors.

Thank You!

Answers

  • Update: I run ValidateSamFile, the runs finished, but with empty result.

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @eagle_009,

    Are you saying that ValidateSamFile validates your file? Just to be sure, can you post your ValidateSamFile command and standard out message (the message that prints to the screen)?

    I see you're using Galaxy to run SortSam. Did you also run ValidateSamFile on Galaxy? What I would suggest is you download the Picard program jar to run on your system directly. You can download the latest picard.jar from https://github.com/broadinstitute/picard/releases. Be sure your Unix/Linux system is running Java 1.8.

    Assuming your SAM validates, then the sort command you would run will look something like:

    java -jar picard.jar SortSam I=input.bam O=sorted.bam SORT_ORDER=coordinate CREATE_INDEX=true
    

    I've not seen the error:

    For sequence 0, text and binary have different lengths in file

    before. Searching the web with your error, I find this thread. Did you by chance change the reference you are using at some point in your processing?

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