java.lang.NullPointerException for Picard SamToFastq OUTPUT_PER_RG=T on bam without read groups

hgibling

Hello,

When running Picard's SamToFastq with OUTPUT_PER_RG=T on a bam file without read group information, you get the following error:

Exception in thread "main" java.lang.NullPointerException
        at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:148)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
        at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:119)

Obviously the command shouldn't work if there is no read group information, but it would be nice if there was a more informative error provided, as the NullPointerException makes it seem like an issue with memory allocation.

hgibling

I.e., a check for read groups and a warning/error message if there are none and OUTPUT_PER_RG was set to true.

Sheila

@hgibling
Hi,

I totally understand the frustration. Let me put in a request to have the error message be more informative.

Thanks,
Sheila

hgibling

Thank you, Sheila. I appreciate it.

dekling

Greetings @hgibling:

You are correct that many of the error messages produced by GATK and Picard are not very informative. We are in the process of trying to provide as much information as we can for error messages. However, often the amount of information that can be output on the command line is limited due to a number of reasons which are largely technical. We will inform our software development group regarding this issue and request that additional documentation be added to the command line.

dekling

@hgibling: We also strongly recommend using ValidateSamFile prior to using Picard or GATK.

hgibling

Understandable, @dekling. And good advice on using ValidateSamFile.

Geraldine_VdAuwera

Bug reported to Picard here. Don't hold your breath though -- this is unlikely to be prioritized.

lyndaeldo

NullPointerException is a RuntimeException . Runtime exceptions are critical and cannot be caught at compile time. They crash the program at run time if they are not handled properly. When a class is instantiated, its object is stored in computer memory. The NullPointerExceptions occur when you try to use a reference that points to no location in memory (null) as though it were referencing an object. More about....NullPointerException

http://net-informations.com/java/cjava/null.htm

Anto

Geraldine_VdAuwera

@hgibling An informative error message was added to this tool. This will be available in the next release (or you can get it by building the jar from source yourself).