search

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
338 stars 60 forks source link

Error Pilon - Array #89

Open KristinaGagalova opened 5 years ago

KristinaGagalova commented 5 years ago

Hi, I am running Pilon on a large genome (20G) and I have short reads alignments. I am correcting only snps and short indels in a list of targets.

After running for quite a long time and having the contigs corrected I have the following error:

Corrected 0 snps; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
Finished processing Ps-1r180608s00017228:112301-116371
Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at com.simontuffs.onejar.Boot.run(Boot.java:340)
    at com.simontuffs.onejar.Boot.main(Boot.java:166)
Caused by: java.lang.ArrayIndexOutOfBoundsException

Any hints of what that could be?

aaronphillips7493 commented 4 years ago

I am also having the same issue. I am hoping that by commenting here I can get the ball rolling on a solution as it seems to have stalled :)