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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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gatk IndelRealigner causing core dumps #241

Open BirdmanRidesAgain opened 2 years ago

BirdmanRidesAgain commented 2 years ago

I'm running Phyluce in a Miniconda3 environment operating on Python 2.7. I registered gatk v.3.8, because that was the version that was expected by Conda when I ran the conda install phyluce command. Most functions are working, but when I try to use the IndelRealigner tool, an error occurs with my java runtime environment. I was able to enable core dumping with

ulimit -c unlimited without exiting the Conda environment, which produced a log file (attached), and if it makes any difference, 'which java' points to a binary in the same folder as gatk and the various phyluce commands.

I assume that uninstalling and then reinstalling java might fix the problem, but I don't want to unintentionally break the Phyluce dependency chain by trying it completely blindly. Any input you have would be appreciated.

hs_err_pid25324.log

Code: gatk -T IndelRealigner -R tringa-nebularia-MK460251.1.fasta \ -I tringa-bi-all-inds-mtDNA.bam \ -targetIntervals merged.intervals \ -o tringa-bi-all-inds-mtDNA-realigned.bam

Error:

A fatal error has been detected by the Java Runtime Environment: # SIGSEGV (0xb) at pc=0x0000000101746f27, pid=25832, tid=0x0000000000001a03 # JRE version: OpenJDK Runtime Environment (8.0_152-b12) (build 1.8.0_152-release-1056-b12) Java VM: OpenJDK 64-Bit Server VM (25.152-b12 mixed mode bsd-amd64 compressed oops) Problematic frame: C [libgkl_compression2956090310289492122.dylib+0x6f27] deflate_medium+0x867 # Core dump written. Default location: /cores/core or core.25832 # An error report file with more information is saved as: /Users/catharus2021/Documents/mtDNA-analysis/raw-mitogenomes/Tringa-bi/hs_err_pid25832.log # If you would like to submit a bug report, please visit: http://bugreport.java.com/bugreport/crash.jsp The crash happened outside the Java Virtual Machine in native code. See problematic frame for where to report the bug. #

brantfaircloth commented 2 years ago

Note, that this is an older version of Phyluce and not supported any longer.

That said, you may simply need to give gatk more RAM. Something like gatk --java-options "-Xmx4G" <other parameters> may work for you. Otherwise, you can run gatk outside of phyluce by installing it anywhere you like and running with the inputs already created.

BirdmanRidesAgain commented 2 years ago

Oh. Sorry; I didn't realize that I wasn't running an up-to-date version of Phyluce. I did just try to run conda update phyluce, but it's still showing v.1.6.7 when I pull it up via conda list.

There doesn't seem to be a --java-options argument defined for how I'm calling gatk, so I'll take your advice and install it somewhere else.

brantfaircloth commented 2 years ago

No worries. There's definitely a way to do this with bioconda wrapper for GATK... checking to see if I can find it.

brantfaircloth commented 2 years ago

It may simply be gatk -Xmx4g <other parameters> where the 4G part should be the max RAM you can spare. By default, max RAM gets set to -Xmx1g.

BirdmanRidesAgain commented 2 years ago

I did try that, but it's still showing the same error. Or, at least, I assume it's the same error. I can't really make heads or tails of the log files that are being generated.

Anyways, thanks for your help!