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wshuai294 / PStrain

Pstrain profiles strains in metagenomics data. It infers strain abundance and genotype for each species. Also, it has a single species mode; where given a BAM and VCF, it can phase the variants for any species.
MIT License
8 stars 2 forks source link

Java version for GATK? #7

Closed yuxiangtan closed 3 years ago

yuxiangtan commented 3 years ago

I got the following the error, which should be at the GATK step:

[Sun May 23 22:52:52 CST 2021] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2155872256

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: HaplotypeCaller
ERROR ------------------------------------------------------------------------------------------

I googled and someone said it is because of the Java version, so what't the java version should be?

Best,

Yuxiang

yuxiangtan commented 3 years ago

I install the GATK3.8 from conda in which the java version works for the GATK3.5 provided by the author.

wshuai294 commented 3 years ago

That's Great.

The java version I used is 

openjdk version "1.8.0_282"
OpenJDK Runtime Environment (build 1.8.0_282-b08)
OpenJDK 64-Bit Server VM (build 25.282-b08, mixed mode)