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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Unknown Exception #33

Closed kevlim83 closed 7 years ago

kevlim83 commented 7 years ago

Hi,

I have tried pilon to polish our pacbio assembly using illumina reads.

The first time I tried it with a canu assembly it worked with no problems. The second time was with a falcon assembly, it threw some exceptions which I could not figure: 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 com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: java.lang.ArithmeticException: / by zero at org.broadinstitute.pilon.GenomeFile.contigRegions(GenomeFile.scala:71) at org.broadinstitute.pilon.GenomeFile$$anonfun$2.apply(GenomeFile.scala:53) at org.broadinstitute.pilon.GenomeFile$$anonfun$2.apply(GenomeFile.scala:53) at scala.collection.immutable.List.map(List.scala:277) at org.broadinstitute.pilon.GenomeFile.(GenomeFile.scala:53) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:98) at org.broadinstitute.pilon.Pilon.main(Pilon.scala) ... 6 more

Please let me know if you have ideas how to resolve this.

Thanks.

w1bw commented 7 years ago

Sorry for the delay in responding, but I'm finally catching up on pilon support. It looks as if this could only happen if there are zero-length contigs in the assembly. That's bizarre...does Falcon generate such things?