The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

☞ Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

☞ Formatting tip!

Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ` ) each to make a code block.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

CountTerminusEvent and Output

Member Posts: 3

Hi,
I was trying to use the CountTerminusEvent walker and put the following in my bash:

java -Xmx4g -jar /Users/jacquelyn/GenomeAnalysisTK.jar -R /Users/jacquelyn/Sequencing/chr1.fa -T CountTerminusEvent -I /Users/jacquelyn/Desktop/10.NA12878/R_2013_06_24_09_51_35_user_NCR-42-Killary10NA12878r_Auto_user_NCR-42-Killary10NA12878r_43.bam -L /Users/jacquelyn/DeepSeqData/IAD33712_Designed.bed -o /Users/jacquelyn/Desktop/10.NA12878TerminusEvent.txt

I kept getting the error that the argument "o" was not defined. When I queried "CountTerminusEvent -h" in my bash to get help, "--out" wasn't even listed as an argument. I feel stupid asking this question, but what am I doing wrong?
Jacquelyn

Tagged:

Hi there,

I checked and -o/--out is listed, both in the tech doc and in the console output (see screenshot). You may have missed it because it's all the way after the engine arguments.

Any chance you have two spaces instead of one before after the -o in your command line?

Geraldine Van der Auwera, PhD

• Member Posts: 3

That was the first thing I checked when I got the error. I went back in my console output and re-searched for the -o (even pasted it into TextEdit and did a Find command there). I hate to paste it all but I feel that is the only way you can see exactly what I am seeing (see below). I have never had this issue before. I even used the previous command I did that worked and just changed the walker, leaving the output as the same from the previous entry that worked and it didn't work this time, giving me the same error that the "o" argument isn't defined. I am at a loss for what to do. The documentation on the website clearly states that -o is an argument, and its always clearly worked for me, but when i look at the arguments on the version I am running, -o isn't an option. Sorry for the trouble.
Jacquelyn