gatk-launch file missing

Question

[sruthi]

Hi, Basically I need to run the below command for converting bed file to target file(tsv):

gatk-launch --javaOptions "-Xmx4g" ConvertBedToTargetFile  --input targets.bed --output targets.tsv

I have downloaded GATK 4.1.2.0 and when unzipped the folder, all files except gatk-launch are available. I tried downloading gatk-launch file separately and saved it in the respective folder, but gatk-launch command doesn't work. Is there any alternative to this?

TIA

[Pierre Lindenbaum]

try to use 'gatk' instead of gatk-launch

[sruthi]

Thanks Pierre. 'gatk' command works but --javaOptions command is not found when I try the command mentioned in the question. Kindly help.

[WouterDeCoster]

What about --java-options?

[sruthi]

So, my command was :

gatk --javaOptions "Xmx4g" ConvertBedToTargetFile --input targets.bed --output targets.tsv

It says, JavaOptions command not found.

[WouterDeCoster]

What about --java-options?

[sruthi]

I tried --java-options, now it says ConvertBedToTargetFile command not found

[WouterDeCoster]

Please give the full, exact command you used and the full error you received.

[vaish01kv]

Hi, I get the same error.

The command I have given is

gatk --java-options "Xmx4G" ConvertBedToTargetFile --input targets.bed --output targets.tsv

and the below error shows up

A USER ERROR has occurred: 'ConvertBedToTargetFile' is not a valid command.

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

[WouterDeCoster]

Syntax should be gatk --java-options "-Xmx4G" [program arguments]. Not Xmx4G. Please read documentation carefully.

[vaish01kv]

Thanks Wouter. I edited my syntax with "-Xmx4G"

I still get the same error.

[WouterDeCoster]

gatk --list will return all commands with are valid. See also this post on the GATK forum https://gatkforums.broadinstitute.org/gatk/discussion/comment/45203/#Comment_45203

Which guidelines are you following?

[sruthi]

I already did and there is no ConvertBedToTargetFile command in the list. I read the post on GATK forum few minutes ago and yes they have removed the command. Guidelines as in?

Thanks for the information :)

[vaish01kv]

I tried running PreprocessIntervals command:

 gatk PreprocessIntervals \ -R hg38.fa \ -L file.bed \ -- padding 0 \ -O preprocessed.interval_list

and the error I get is

A USER ERROR has occurred: Invalid argument ' -R'.

How should I work further? TIA

[WouterDeCoster]

There is a space in front of your -R argument, as you can see from the error message. Try the command without extra spaces and without backslashes \.

[sruthi]

Hey, I removed the space in the command and executed again, it runs. But it is now asking for a dictionary file of reference genome, while creating one using below gatk command:

gatk --java-options "-Xmx4G" CreateSequenceDictionary R= hg38.fasta O= hg38.dict

I get the following error:

Invalid argument 'R='

How should I go about it?

[WouterDeCoster]

From here there are two options:

1. Either you start reading the documentation more carefully, for example on this page. My previous answer shows you that spaces matter.
2. Alternatively, you just keep on asking questions (because it is easier for you to have someone else read the documentation and you are lazy), and in that case you should remove the space between R= and hg38.fasta

[sruthi]

I do get your point. But it is sad to know that such comments are passed without knowing what the person on other end is doing. 1. I did check it with no space between the options and values. It still didn't work. 2. as far as "not reading the documentation correctly is considered" which you had already mentioned for "-Xmx4G" if you could just scroll up and look at the main question, it is properly written. I had missed it while writing it in the trail post, my bad and I apologise. Says who is lazy. 3. Just have a look at it there are spaces between options and values. 4. Me asking questions alternatively is because I'm new to NGS analysis and there are so many tools to look at and it's all confusing. Being a new user I have a limit of 5 posts/6 hrs and I have to finish a task by 6pm IST every day and I have access to this account only from 10am -6pm IST . Writing this to you hoping you would understand.

[WouterDeCoster]

Thanks for your reply, and I do understand. Maybe it's now my time to apologize, so I'm sorry. I'm happy to help here, but at the same time, you must know that I also don't know these things by heart. I also have to search for the documentation. Of course, it is harder if you are new to this, and I should have taken that into account.

One thing to keep in mind for GATK syntax is that the tool has changed quite a bit the past few years. The post you linked, for example, is from 2012 and uses a rather different syntax: java -jar CreateSequenceDictionary.jar, and not gatk CreateSequenceDictionary.

Second, the most up to date help you can get is on the command line itself: gatk CreateSequenceDictionary -h, which will show you that you need either -R or --REFERENCE.

[sruthi]

Thanks for the reply. I totally understand. Will keep these trivial things(versions, command line options etc.) in mind before starting an analysis, as these play a major role.