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Question: picard collectwgsmetrics error
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gravatar for hkhoja
2.9 years ago by
hkhoja • 0
United States
hkhoja • 0 wrote:

 

Hi..I am trying to use the picard collectwgsmetrics on a bam file generated from a whole genome sequencing with a hg38 as the reference sequence. I keep getting the following error; Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Exception in thread "main" java.lang.NullPointerException at htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:87  

Any ideas on what it means and how I can avoid it?

Thank you

 

 

 
software error • 949 views
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written 2.9 years ago by hkhoja • 0

Hello,

This same problem was reported just a few days ago and our team is reviewing. Feedback/resolution may occur after the holiday.

Thank you for reporting the problem, Jen, Galaxy team

ADD REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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