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 in main #75

Closed dUmich closed 6 years ago

dUmich commented 6 years ago

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

dUmich commented 6 years ago

FIXED: The variable I used as input to the --output option was a bash internal variable for "/opt/moab"