We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Java FileNotFoundError while executing gatk4

I have install gatk on ubuntu 16.04 LTS, 64 bit following the steps mentioned at this link and I have checked that the instlallation is good (everything checked till step#4 on the above provided lnk)

Now , when I run gatk --list, I encounter below error message:

(gatk) [email protected]:~/gatk-$ gatk --list
Using GATK jar /home/bioinfo/gatk-
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/bioinfo/gatk- --help
Traceback (most recent call last):
  File "/home/bioinfo/gatk-", line 477, in <module>
  File "/home/bioinfo/gatk-", line 152, in main
    runGATK(sparkRunner, sparkSubmitCommand, dryRun, gatkArgs, sparkArgs, javaOptions)
  File "/home/bioinfo/gatk-", line 328, in runGATK
    runCommand(cmd, dryrun)
  File "/home/bioinfo/gatk-", line 382, in runCommand
  File "/home/bioinfo/miniconda2/envs/gatk/lib/python3.6/subprocess.py", line 286, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/home/bioinfo/miniconda2/envs/gatk/lib/python3.6/subprocess.py", line 267, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/home/bioinfo/miniconda2/envs/gatk/lib/python3.6/subprocess.py", line 707, in __init__
    restore_signals, start_new_session)
  File "/home/bioinfo/miniconda2/envs/gatk/lib/python3.6/subprocess.py", line 1333, in _execute_child
    raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: 'java'
(gatk) [email protected]:~/gatk-$ java -version

Best Answers


Sign In or Register to comment.