Hello, I have installed hail using pycharm not from github nor conda. I was trying read 1k genome vcf data: hl.import_vcf(‘data/1kg.vcf.bgz’).write(‘data/1kg.mt’, overwrite=True) mt = hl.read_matrix_table(‘data/1kg.mt’) The error: /shire/zillur/learning/python/project1/venv/bin/python /shire/zi…

Based on error, my guess is that your version of the C++ standard library is incompatible with the version of Hail you have. Your system must have at least GCC 4.9 installed in order to have access to CXXABI_1.3.8. What is the output of gcc --version ?

Thank you John. gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36). How can I get newer version of gcc? Best, Zillur

Probably by running something like: sudo yum install gcc-c++ ? [Hope] how to install gcc 4.9.2 on RHEL 7.4 linux, gcc, g++, centos7 asked by Hope on 09:16AM - 08 Nov 17 UTC

@zillurbmb51 , Even if you get a recent version of gcc installed, you will need a newer version of RHEL. RHEL 4.8.5 was released in December 2004 and uses a version of the GNU C Standard Library with which Hail is incompatible. RHEL 7 should be sufficient for use with Hail.

Hello, Thank you. Now I have gcc 7 in centos 7 `gcc (GCC) 7.3.1 20180303 (Red Hat 7.3.1-5 ) I have reinstalled hail as follows: conda create -n hail python==3.6 conda activate hail sudo pip3 install hail sudo python3.6 -m pip install -U --force-reinstall hail Now I am getting following error:…

what platform are you running on? You’ll probably need to compile hail yourself: https://hail.is/docs/0.2/getting_started_developing.html#building-hail

Thank you. I have tried from the link you shared. Getting this: (hail) [zillur@dutillab hail]$ git clone https://github.com/hail-is/hail.git Cloning into 'hail'... remote: Enumerating objects: 43, done. remote: Counting objects: 100% (43/43), done. remote: Compressing objects: 100% (42…

ack that’s out of date. Should be install not install-wheel

Thank you. Still doesn’t work. (hail) [zillur@dutillab hail]$ sudo make install HAIL_COMPILE_NATIVES=1 SPARK_VERSION=2.4.1 [sudo] password for zillur: SPARK_VERSION is set to “2.4.1” which is different from old value “2.4.0” printf “2.4.1” > env/SPARK_VERSION echo ‘[Build Metadata]’ > src/main/…

You need to install lz4 . Anyway, it appears that you don’t have a recent version of libstdc++. What version of g++ do you have installed?

py4j.protocol.Py4JNetworkError: Answer from Java side is empty: hail, download files

Hail Query & hailctl

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py4j.protocol.Py4JNetworkError: Answer from Java side is empty: hail, download files

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