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Question: Collect Alignment Summary Metrics won't run?
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gravatar for frankie.north
2.1 years ago by
frankie.north • 10
frankie.north • 10 wrote:

Hi all,

I am trying to run Collect Alignment Summary Metrics on my RNA Seq data and every time it keeps coming up with the error below. Prior to this I have aligned using BWA for Illumina and used the same reference genome which is UCSC Main hg19 imported into my history.

Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch -Xmx7680m -Xms256m Exception in thread "main" htsjdk.samtools.SAMException: Requesting earlier reference sequence: 8 < 11 at htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:81) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:110) at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:53) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

If anyone has any ideas on what this error means or how I can solve it, it would be greatly appreciated.

Thanks.
rna-seq software error alignmentsummary • 895 views
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modified 2.1 years ago • written 2.1 years ago by frankie.north • 10
1
gravatar for Jennifer Hillman Jackson
2.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Try sorting the input BAM dataset(s). This is how: https://github.com/jennaj/support-prior-qa/wiki/Sort-your-inputs

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for frankie.north
2.1 years ago by
frankie.north • 10
frankie.north • 10 wrote:

Thank you Jen, this worked!
ADD COMMENT • link written 2.1 years ago by frankie.north • 10
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