Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Exit codes in GATK 4.0

RMuletRMulet BarcelonaMember

Hi,

In my BASH scripts I often use "$?" to monitor the exit status of a process and normally stop if there is an error. However, I am using the latest version of GATK (4.0.0.0) and some tools return 0 exit status even if they fail. Instead, they display the following message to STDOUT:

Tool returned:
1

Though inconvenient for error handling in BASH scripts, this might be an intended behaviour, but not all tools exhibit it. To mention a few, MarkDuplicates, CollectMultipleMetrics, CollectGcBiasMetrics always have a 0 exit status, whereas VariantsToTable or CountVariants do return 1 if they encounter an error.

A similar issue had been reported in the past for previous versions of GATK (https://gatkforums.broadinstitute.org/gatk/discussion/8618/error-handling-end-exit-codes-in-gatk).

Best regards,

Roger

Issue · Github
by Sheila

Issue Number
4433
State
closed
Last Updated
Assignee
Array
Closed By
cmnbroad

Best Answers

Answers

Sign In or Register to comment.