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Installation running errors
Sina Majidian edited this page Jun 19, 2024
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If you face this when running nextflow, you need to have proper a java installed.
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.UnsupportedClassVersionError: nextflow/cli/Launcher has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:756)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:473)
at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:621)
which is related to java version
$ java -version
openjdk version "1.8.0_372"
OpenJDK Runtime Environment (build 1.8.0_372-b07)
OpenJDK 64-Bit Server VM (build 25.372-b07, mixed mode)
Nextflow (and FastOMA) needs version 11.
You can install openjdk using conda (openjdk is the free version of java).
conda install conda-forge::openjdk
then you will have
$ java -version
openjdk version "11.0.13" 2021-10-19
OpenJDK Runtime Environment JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21)
OpenJDK 64-Bit Server VM JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21, mixed mode)
If it still shows you the other java previously had been installed on your system, you probably need to add the path
JAVA_HOME="/path/to/jdk-17"
NXF_JAVA_HOME="/path/to/jdk-17"
export PATH="/path/to/jdk-17/bin:$PATH"
or
JAVA_CMD="$(which java)"
Traceback (most recent call last):
File " software/miniconda/envs/f4/bin/fastoma-collect-subhogs", line 8, in <module>
sys.exit(fastoma_collect_subhogs())
File " software/miniconda/envs/f4/lib/python3.8/site-packages/FastOMA/collect_subhogs.py", line 140, in fastoma_collect_subhogs
write_hog_orthoxml(conf_collect_subhogs.pickle_folder, conf_collect_subhogs.out, conf_collect_subhogs.gene_id_pickle_file,
File " software/miniconda/envs/f4/lib/python3.8/site-packages/FastOMA/collect_subhogs.py", line 194, in write_hog_orthoxml
ET.indent(orthoxml_file, space=' ', level=0)
AttributeError: module 'xml.etree.ElementTree' has no attribute 'indent'
Probably you are using python 3.8. Try python 3.9!
Traceback (most recent call last):
File "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/f39p/bin/omamer", line 8, in <module>
sys.exit(main())
File "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/f39p/lib/python3.9/site-packages/omamer/main.py", line 33, in main
from tables import PerformanceWarning
File "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/f39p/lib/python3.9/site-packages/tables/__init__.py", line 44, in <module>
from .utilsextension import get_hdf5_version as _get_hdf5_version
File "tables/utilsextension.pyx", line 1, in init tables.utilsextension
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
Install numpy version 1.23
using pip install numpy==1.23
To make sure it is solved you can run omamer -h
You could install like this
conda create -n fasto python=3.10
conda activate fasto
git clone https://github.com/DessimozLab/FastOMA.git
conda install bioconda::fasttree
conda install bioconda::mafft
conda install conda-forge::openjdk
pip install .[report,nextflow]
pip install numpy==1.23