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Finally found a case where user errors were being masked behind other errors and could debug. It turns out that the checkForMaskedUserErrors() method needs to run recursively over all levels (calling exception.getCause()) to check for the original cause.

This commit is contained in:
Eric Banks 2012-11-21 15:57:05 -05:00
parent 2e1a055aca
commit ed50814ccb
1 changed files with 13 additions and 8 deletions
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21
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -118,17 +118,24 @@ public class CommandLineGATK extends CommandLineExecutable {
public static final String DISK_QUOTA_EXCEEDED_ERROR = "Disk quota exceeded";
private static void checkForMaskedUserErrors(final Throwable t) {
// masked out of memory error
if ( t instanceof OutOfMemoryError )
exitSystemWithUserError(new UserException.NotEnoughMemory());
// masked user error
if ( t instanceof UserException || t instanceof TribbleException )
exitSystemWithUserError(new UserException(t.getMessage()));
// no message means no masked error
final String message = t.getMessage();
if ( message == null )
return;
// we know what to do about the common "Too many open files" error
// too many open files error
if ( message.contains("Too many open files") )
exitSystemWithUserError(new UserException.TooManyOpenFiles());
// malformed BAM looks like a SAM file
if ( message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) ||
message.contains(PICARD_TEXT_SAM_FILE_ERROR_2) )
if ( message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) || message.contains(PICARD_TEXT_SAM_FILE_ERROR_2) )
exitSystemWithSamError(t);
// can't close tribble index when writing
@ -138,12 +145,10 @@ public class CommandLineGATK extends CommandLineExecutable {
// disk is full
if ( message.contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || message.contains(DISK_QUOTA_EXCEEDED_ERROR) )
exitSystemWithUserError(new UserException.NoSpaceOnDevice());
if ( t.getCause() != null && (t.getCause().getMessage().contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || t.getCause().getMessage().contains(DISK_QUOTA_EXCEEDED_ERROR)) )
exitSystemWithUserError(new UserException.NoSpaceOnDevice());
// masked out of memory error
if ( t.getCause() != null && t.getCause() instanceof OutOfMemoryError )
exitSystemWithUserError(new UserException.NotEnoughMemory());
// masked error wrapped in another one
if ( t.getCause() != null )
checkForMaskedUserErrors(t.getCause());
}
/**