Question: Collect Alignment Summary Metrics won't run?
gravatar for frankie.north
20 months ago by
frankie.north10 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: -Xmx7680m -Xms256m Exception in thread "main" htsjdk.samtools.SAMException: Requesting earlier reference sequence: 8 < 11 at htsjdk.samtools.reference.ReferenceSequenceFileWalker.get( at picard.analysis.SinglePassSamProgram.makeItSo( at picard.analysis.SinglePassSamProgram.doWork( at picard.cmdline.CommandLineProgram.instanceMain( at picard.cmdline.PicardCommandLine.instanceMain( at picard.cmdline.PicardCommandLine.main(

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


ADD COMMENTlink modified 19 months ago • written 20 months ago by frankie.north10
gravatar for Jennifer Hillman Jackson
20 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Try sorting the input BAM dataset(s). This is how:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 20 months ago by Jennifer Hillman Jackson25k
gravatar for frankie.north
19 months ago by
frankie.north10 wrote:

Thank you Jen, this worked!

ADD COMMENTlink written 19 months ago by frankie.north10
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