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enasequence / cramtools

CRAM format specification and java API for read data.
http://www.ebi.ac.uk/ena/about/cram_toolkit
Apache License 2.0
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cram to bam conversion error #70

Open blueagave opened 7 years ago

blueagave commented 7 years ago

I have a user who is attempting to convert a cram file into a bam file, but getting the error below. Do you have any suggestions?

Environment:

RHEL 7.1 openjdk 1.8.0_101 cramtools-3.0

Command and resulting error:

$ java -jar /usr/local/packages/cramtools/cramtools-3.0.jar bam -I 21136_1#1.cram -R /local/projects-t3/SerreDLab-3/kima7/genomes/p_vivax_P01/PlasmoDB-29_PvivaxP01_Genome.fasta -O test.bam Exception in thread "main" java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at net.sf.cram.CramTools.invoke(CramTools.java:91) at net.sf.cram.CramTools.main(CramTools.java:121) Caused by: java.lang.NullPointerException at htsjdk.samtools.cram.build.CramIO.readFormatDefinition(CramIO.java:168) at htsjdk.samtools.cram.build.CramIO.readCramHeader(CramIO.java:189) at net.sf.cram.Cram2Bam.main(Cram2Bam.java:113) ... 6 more

Thanks Tom

jkbonfield commented 7 years ago

This is one of our (Sanger's) CRAM files, produced by Scramble. So I thought I'd double check it just incase.

I can decode our local copy just fine with both Scramble and Cramtools (Version 3.0-b208). The local copy of this cram file has this md5sum:

36c622c3f0b65e684c35efdaa808c851  21136_1#1.cram

I'm not sure b208 is the latest cramtools, but it's what I had checked out. It'd help Vadim perhaps if you quoted the exact version of yours (it's at the top of the usage help).