I am not familiar with Java so sorry if this is a basic error. When I run pilon 1.22 on a single BAM file I get the error below. It looks like the program is failing to create a moab.fasta file or is failing before it can create it.
/opt/moab
Rush_KPC_330_test_pilon
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.simontuffs.onejar.Boot.run(Boot.java:340)
at com.simontuffs.onejar.Boot.main(Boot.java:166)
Caused by: java.io.FileNotFoundException: Rush_KPC_330_test_pilon/opt/moab.fasta (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.(Unknown Source)
at java.io.FileOutputStream.(Unknown Source)
at java.io.FileWriter.(Unknown Source)
at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:134)
at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:101)
at org.broadinstitute.pilon.Pilon.main(Pilon.scala)
... 6 more
I am not familiar with Java so sorry if this is a basic error. When I run pilon 1.22 on a single BAM file I get the error below. It looks like the program is failing to create a moab.fasta file or is failing before it can create it.
/opt/moab Rush_KPC_330_test_pilon Exception in thread "main" java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: java.io.FileNotFoundException: Rush_KPC_330_test_pilon/opt/moab.fasta (No such file or directory) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.(Unknown Source)
at java.io.FileOutputStream.(Unknown Source)
at java.io.FileWriter.(Unknown Source)
at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:134)
at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:101)
at org.broadinstitute.pilon.Pilon.main(Pilon.scala)
... 6 more