Last active
July 30, 2020 06:36
-
-
Save shadiakiki1986/366a61df58475e667aa84101ff337b1a to your computer and use it in GitHub Desktop.
mpi3snp error on plink example.ipynb
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| { | |
| "nbformat": 4, | |
| "nbformat_minor": 0, | |
| "metadata": { | |
| "colab": { | |
| "name": "mpi3snp error on plink example.ipynb", | |
| "provenance": [], | |
| "collapsed_sections": [], | |
| "authorship_tag": "ABX9TyNJAiBtEn12VbPd4B+WhG3j", | |
| "include_colab_link": true | |
| }, | |
| "kernelspec": { | |
| "name": "python3", | |
| "display_name": "Python 3" | |
| }, | |
| "accelerator": "GPU" | |
| }, | |
| "cells": [ | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "id": "view-in-github", | |
| "colab_type": "text" | |
| }, | |
| "source": [ | |
| "<a href=\"https://colab.research.google.com/gist/shadiakiki1986/366a61df58475e667aa84101ff337b1a/mpi3snp-error-on-plink-example.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "id": "R-YJpQ8ebS1P", | |
| "colab_type": "text" | |
| }, | |
| "source": [ | |
| "Notebook demonstrating error: `Error in example/wgas1.tped:1: invalid nucleotide value '0' at position 265`\n", | |
| "\n", | |
| "Reported at https://github.com/UDC-GAC/mpi3snp/issues/7" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "8_DUBRfeanFV", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 204 | |
| }, | |
| "outputId": "be4edc31-942c-4f99-93bb-521137424dd5" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# download example files from plink\n", | |
| "wget -q https://www.cog-genomics.org/static/bin/plink/example.zip\n", | |
| "unzip example.zip" | |
| ], | |
| "execution_count": 1, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "Archive: example.zip\n", | |
| " creating: example/\n", | |
| " inflating: example/wgas1.map \n", | |
| " inflating: example/plink.exe \n", | |
| " inflating: example/extra.map \n", | |
| " inflating: example/pop.cov \n", | |
| " inflating: example/Haploview.jar \n", | |
| " inflating: example/wgas1.ped \n", | |
| " inflating: example/extra.ped \n", | |
| " inflating: example/gPLINK.jar \n", | |
| " inflating: example/command-list.txt \n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 1 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "Y-AmH6g9apn0", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 306 | |
| }, | |
| "outputId": "c8c1f859-eb53-4c68-a545-346b45351d32" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# install plink\n", | |
| "wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20200616.zip\n", | |
| "unzip plink_linux_x86_64_20200616.zip\n", | |
| "chmod +x plink\n", | |
| "mv plink /usr/local/bin/" | |
| ], | |
| "execution_count": 2, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "--2020-07-30 05:51:05-- http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20200616.zip\n", | |
| "Resolving s3.amazonaws.com (s3.amazonaws.com)... 52.217.82.102\n", | |
| "Connecting to s3.amazonaws.com (s3.amazonaws.com)|52.217.82.102|:80... connected.\n", | |
| "HTTP request sent, awaiting response... 200 OK\n", | |
| "Length: 8916236 (8.5M) [application/zip]\n", | |
| "Saving to: ‘plink_linux_x86_64_20200616.zip’\n", | |
| "\n", | |
| "plink_linux_x86_64_ 100%[===================>] 8.50M 10.1MB/s in 0.8s \n", | |
| "\n", | |
| "2020-07-30 05:51:06 (10.1 MB/s) - ‘plink_linux_x86_64_20200616.zip’ saved [8916236/8916236]\n", | |
| "\n", | |
| "Archive: plink_linux_x86_64_20200616.zip\n", | |
| " inflating: plink \n", | |
| " inflating: LICENSE \n", | |
| " inflating: toy.ped \n", | |
| " inflating: toy.map \n", | |
| " inflating: prettify \n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 2 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "Lv4iDXGUbqaS", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 408 | |
| }, | |
| "outputId": "8ecc7cf3-6750-4a9c-ea18-920c6f336160" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# convert the example/gwas1.ped to tped and tfam for mpi3snp\n", | |
| "PREFIX=\"example/wgas1\"\n", | |
| "plink --file \"$PREFIX\" --recode transpose --out \"$PREFIX\"" | |
| ], | |
| "execution_count": 3, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "PLINK v1.90b6.18 64-bit (16 Jun 2020) www.cog-genomics.org/plink/1.9/\n", | |
| "(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3\n", | |
| "Logging to example/wgas1.log.\n", | |
| "Options in effect:\n", | |
| " --file example/wgas1\n", | |
| " --out example/wgas1\n", | |
| " --recode transpose\n", | |
| "\n", | |
| "13021 MB RAM detected; reserving 6510 MB for main workspace.\n", | |
| "Scanning .ped file... 0%\b\b1%\b\b2%\b\b3%\b\b4%\b\b5%\b\b6%\b\b7%\b\b8%\b\b10%\b\b\b11%\b\b\b12%\b\b\b13%\b\b\b14%\b\b\b15%\b\b\b16%\b\b\b17%\b\b\b18%\b\b\b20%\b\b\b21%\b\b\b22%\b\b\b23%\b\b\b24%\b\b\b25%\b\b\b26%\b\b\b27%\b\b\b28%\b\b\b30%\b\b\b31%\b\b\b32%\b\b\b33%\b\b\b34%\b\b\b35%\b\b\b36%\b\b\b37%\b\b\b38%\b\b\b40%\b\b\b41%\b\b\b42%\b\b\b43%\b\b\b44%\b\b\b45%\b\b\b46%\b\b\b47%\b\b\b48%\b\b\b50%\b\b\b51%\b\b\b52%\b\b\b53%\b\b\b54%\b\b\b55%\b\b\b56%\b\b\b57%\b\b\b58%\b\b\b60%\b\b\b61%\b\b\b62%\b\b\b63%\b\b\b64%\b\b\b65%\b\b\b66%\b\b\b67%\b\b\b68%\b\b\b70%\b\b\b71%\b\b\b72%\b\b\b73%\b\b\b74%\b\b\b75%\b\b\b76%\b\b\b77%\b\b\b78%\b\b\b80%\b\b\b81%\b\b\b82%\b\b\b83%\b\b\b84%\b\b\b85%\b\b\b86%\b\b\b87%\b\b\b88%\b\b\b90%\b\b\b91%\b\b\b92%\b\b\b93%\b\b\b94%\b\b\b95%\b\b\b96%\b\b\b97%\b\b\b98%\b\b\b100%\r.ped scan complete (for binary autoconversion).\n", | |
| "Performing single-pass .bed write (228694 variants, 90 people).\n", | |
| "0%\b\b1%\b\b2%\b\b3%\b\b4%\b\b5%\b\b6%\b\b7%\b\b8%\b\b9%\b\b10%\b\b\b11%\b\b\b12%\b\b\b13%\b\b\b14%\b\b\b15%\b\b\b16%\b\b\b17%\b\b\b18%\b\b\b19%\b\b\b20%\b\b\b21%\b\b\b22%\b\b\b23%\b\b\b24%\b\b\b25%\b\b\b26%\b\b\b27%\b\b\b28%\b\b\b29%\b\b\b30%\b\b\b31%\b\b\b32%\b\b\b33%\b\b\b34%\b\b\b35%\b\b\b36%\b\b\b37%\b\b\b38%\b\b\b39%\b\b\b40%\b\b\b41%\b\b\b42%\b\b\b43%\b\b\b44%\b\b\b45%\b\b\b46%\b\b\b47%\b\b\b48%\b\b\b49%\b\b\b50%\b\b\b51%\b\b\b52%\b\b\b53%\b\b\b54%\b\b\b55%\b\b\b56%\b\b\b57%\b\b\b58%\b\b\b59%\b\b\b60%\b\b\b61%\b\b\b62%\b\b\b63%\b\b\b64%\b\b\b65%\b\b\b66%\b\b\b67%\b\b\b68%\b\b\b69%\b\b\b70%\b\b\b71%\b\b\b72%\b\b\b73%\b\b\b74%\b\b\b75%\b\b\b76%\b\b\b77%\b\b\b78%\b\b\b79%\b\b\b80%\b\b\b81%\b\b\b82%\b\b\b83%\b\b\b84%\b\b\b85%\b\b\b86%\b\b\b87%\b\b\b88%\b\b\b89%\b\b\b90%\b\b\b91%\b\b\b92%\b\b\b93%\b\b\b94%\r--file: example/wgas1-temporary.bed + example/wgas1-temporary.bim +\n", | |
| "example/wgas1-temporary.fam written.\n", | |
| "228694 variants loaded from .bim file.\n", | |
| "90 people (45 males, 45 females) loaded from .fam.\n", | |
| "90 phenotype values loaded from .fam.\n", | |
| "Using 1 thread (no multithreaded calculations invoked).\n", | |
| "Before main variant filters, 90 founders and 0 nonfounders present.\n", | |
| "Calculating allele frequencies... 0%\b\b1%\b\b2%\b\b3%\b\b4%\b\b5%\b\b6%\b\b7%\b\b8%\b\b9%\b\b10%\b\b\b11%\b\b\b12%\b\b\b13%\b\b\b14%\b\b\b15%\b\b\b16%\b\b\b17%\b\b\b18%\b\b\b19%\b\b\b20%\b\b\b21%\b\b\b22%\b\b\b23%\b\b\b24%\b\b\b25%\b\b\b26%\b\b\b27%\b\b\b28%\b\b\b29%\b\b\b30%\b\b\b31%\b\b\b32%\b\b\b33%\b\b\b34%\b\b\b35%\b\b\b36%\b\b\b37%\b\b\b38%\b\b\b39%\b\b\b40%\b\b\b41%\b\b\b42%\b\b\b43%\b\b\b44%\b\b\b45%\b\b\b46%\b\b\b47%\b\b\b48%\b\b\b49%\b\b\b50%\b\b\b51%\b\b\b52%\b\b\b53%\b\b\b54%\b\b\b55%\b\b\b56%\b\b\b57%\b\b\b58%\b\b\b59%\b\b\b60%\b\b\b61%\b\b\b62%\b\b\b63%\b\b\b64%\b\b\b65%\b\b\b66%\b\b\b67%\b\b\b68%\b\b\b69%\b\b\b70%\b\b\b71%\b\b\b72%\b\b\b73%\b\b\b74%\b\b\b75%\b\b\b76%\b\b\b77%\b\b\b78%\b\b\b79%\b\b\b80%\b\b\b81%\b\b\b82%\b\b\b83%\b\b\b84%\b\b\b85%\b\b\b86%\b\b\b87%\b\b\b88%\b\b\b89%\b\b\b90%\b\b\b91%\b\b\b92%\b\b\b93%\b\b\b94%\b\b\b95%\b\b\b96%\b\b\b97%\b\b\b98%\b\b\b99%\b\b\b\b done.\n", | |
| "Total genotyping rate is 0.993346.\n", | |
| "228694 variants and 90 people pass filters and QC.\n", | |
| "Among remaining phenotypes, 49 are cases and 41 are controls.\n", | |
| "--recode transpose to example/wgas1.tped + example/wgas1.tfam ... 0%\b\b1%\b\b2%\b\b3%\b\b4%\b\b5%\b\b6%\b\b7%\b\b8%\b\b9%\b\b10%\b\b\b11%\b\b\b12%\b\b\b13%\b\b\b14%\b\b\b15%\b\b\b16%\b\b\b17%\b\b\b18%\b\b\b19%\b\b\b20%\b\b\b21%\b\b\b22%\b\b\b23%\b\b\b24%\b\b\b25%\b\b\b26%\b\b\b27%\b\b\b28%\b\b\b29%\b\b\b30%\b\b\b31%\b\b\b32%\b\b\b33%\b\b\b34%\b\b\b35%\b\b\b36%\b\b\b37%\b\b\b38%\b\b\b39%\b\b\b40%\b\b\b41%\b\b\b42%\b\b\b43%\b\b\b44%\b\b\b45%\b\b\b46%\b\b\b47%\b\b\b48%\b\b\b49%\b\b\b50%\b\b\b51%\b\b\b52%\b\b\b53%\b\b\b54%\b\b\b55%\b\b\b56%\b\b\b57%\b\b\b58%\b\b\b59%\b\b\b60%\b\b\b61%\b\b\b62%\b\b\b63%\b\b\b64%\b\b\b65%\b\b\b66%\b\b\b67%\b\b\b68%\b\b\b69%\b\b\b70%\b\b\b71%\b\b\b72%\b\b\b73%\b\b\b74%\b\b\b75%\b\b\b76%\b\b\b77%\b\b\b78%\b\b\b79%\b\b\b80%\b\b\b81%\b\b\b82%\b\b\b83%\b\b\b84%\b\b\b85%\b\b\b86%\b\b\b87%\b\b\b88%\b\b\b89%\b\b\b90%\b\b\b91%\b\b\b92%\b\b\b93%\b\b\b94%\b\b\b95%\b\b\b96%\b\b\b97%\b\b\b98%\b\b\b99%\b\b\bdone.\n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 3 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "IqQUU38dadvc", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 221 | |
| }, | |
| "outputId": "7794ecdf-8d19-4b83-fac5-ae8361a45a56" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# downgrade cmake to 3.10\n", | |
| "# due to error: nvcc fatal : Unknown option 'pthread'\n", | |
| "# https://peter.bloomfield.online/workaround-nvcc-pthread-issue/\n", | |
| "sudo apt install cmake\n", | |
| "mv /usr/local/bin/cmake /usr/local/bin/cmake3.12\n", | |
| "mv /usr/bin/cmake /usr/bin/cmake3.10\n", | |
| "ln -s /usr/bin/cmake3.10 /usr/local/bin/cmake\n", | |
| "ln -s /usr/bin/cmake3.10 /usr/bin/cmake\n", | |
| "which cmake\n", | |
| "cmake --version # <<< should be 3.10" | |
| ], | |
| "execution_count": 4, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "Reading package lists... Done\n", | |
| "Building dependency tree \n", | |
| "Reading state information... Done\n", | |
| "cmake is already the newest version (3.10.2-1ubuntu2.18.04.1).\n", | |
| "The following package was automatically installed and is no longer required:\n", | |
| " libnvidia-common-440\n", | |
| "Use 'sudo apt autoremove' to remove it.\n", | |
| "0 upgraded, 0 newly installed, 0 to remove and 35 not upgraded.\n", | |
| "/usr/local/bin/cmake\n", | |
| "cmake version 3.10.2\n", | |
| "\n", | |
| "CMake suite maintained and supported by Kitware (kitware.com/cmake).\n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 4 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "sdMul-97a7NI", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 1000 | |
| }, | |
| "outputId": "b57f8021-b07d-41c3-b789-0818d42694d5" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# download mpi3snp\n", | |
| "wget -q https://github.com/UDC-GAC/mpi3snp/archive/master.zip\n", | |
| "unzip master.zip" | |
| ], | |
| "execution_count": 5, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "Archive: master.zip\n", | |
| "f03aecf46bb5256a46c9f67acf490d80882e2940\n", | |
| " creating: mpi3snp-master/\n", | |
| " extracting: mpi3snp-master/.gitignore \n", | |
| " inflating: mpi3snp-master/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/LICENSE.md \n", | |
| " inflating: mpi3snp-master/README.md \n", | |
| " creating: mpi3snp-master/src/\n", | |
| " inflating: mpi3snp-master/src/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/src/Definitions.h.in \n", | |
| " creating: mpi3snp-master/src/dataset/\n", | |
| " inflating: mpi3snp-master/src/dataset/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/src/dataset/Dataset.cpp \n", | |
| " inflating: mpi3snp-master/src/dataset/Dataset.h \n", | |
| " inflating: mpi3snp-master/src/dataset/Individual.h \n", | |
| " inflating: mpi3snp-master/src/dataset/SNP.h \n", | |
| " creating: mpi3snp-master/src/engine/\n", | |
| " inflating: mpi3snp-master/src/engine/CMakeLists.txt \n", | |
| " creating: mpi3snp-master/src/engine/cpu/\n", | |
| " inflating: mpi3snp-master/src/engine/cpu/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/src/engine/cpu/CPUEngine.cpp \n", | |
| " inflating: mpi3snp-master/src/engine/cpu/CPUEngine.h \n", | |
| " inflating: mpi3snp-master/src/engine/cpu/ContTable.h \n", | |
| " inflating: mpi3snp-master/src/engine/cpu/MutualInformation.cpp \n", | |
| " inflating: mpi3snp-master/src/engine/cpu/MutualInformation.h \n", | |
| " inflating: mpi3snp-master/src/engine/cpu/ThreadError.h \n", | |
| " creating: mpi3snp-master/src/engine/distributor/\n", | |
| " inflating: mpi3snp-master/src/engine/distributor/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/src/engine/distributor/Distributor.h \n", | |
| " creating: mpi3snp-master/src/engine/gpu/\n", | |
| " inflating: mpi3snp-master/src/engine/gpu/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/CUDAError.cu \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/CUDAError.h \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/GPUContTable.h \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/GPUEngine.cu \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/GPUEngine.h \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/Gpu_node_information.cpp \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/Gpu_node_information.h \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/MutualInformation.cu \n", | |
| " inflating: mpi3snp-master/src/engine/gpu/MutualInformation.h \n", | |
| " creating: mpi3snp-master/src/engine/interface/\n", | |
| " inflating: mpi3snp-master/src/engine/interface/Algorithm.h \n", | |
| " inflating: mpi3snp-master/src/engine/interface/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/src/engine/interface/Engine.h \n", | |
| " inflating: mpi3snp-master/src/engine/interface/Position.h \n", | |
| " creating: mpi3snp-master/src/engine/search/\n", | |
| " inflating: mpi3snp-master/src/engine/search/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/src/engine/search/Search.cpp \n", | |
| " inflating: mpi3snp-master/src/engine/search/Search.h \n", | |
| " inflating: mpi3snp-master/src/main.cpp \n", | |
| " creating: mpi3snp-master/src/utils/\n", | |
| " inflating: mpi3snp-master/src/utils/Arg_parser.cpp \n", | |
| " inflating: mpi3snp-master/src/utils/Arg_parser.h \n", | |
| " inflating: mpi3snp-master/src/utils/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/src/utils/Cpu_node_information.cpp \n", | |
| " inflating: mpi3snp-master/src/utils/Cpu_node_information.h \n", | |
| " inflating: mpi3snp-master/src/utils/IOMpi.cpp \n", | |
| " inflating: mpi3snp-master/src/utils/IOMpi.h \n", | |
| " inflating: mpi3snp-master/src/utils/Node_information.cpp \n", | |
| " inflating: mpi3snp-master/src/utils/Node_information.h \n", | |
| " inflating: mpi3snp-master/src/utils/Statistics.cpp \n", | |
| " inflating: mpi3snp-master/src/utils/Statistics.h \n", | |
| " creating: mpi3snp-master/thirdparty/\n", | |
| " inflating: mpi3snp-master/thirdparty/CMakeLists.txt \n", | |
| " creating: mpi3snp-master/thirdparty/args/\n", | |
| " inflating: mpi3snp-master/thirdparty/args/CMakeLists.txt \n", | |
| " inflating: mpi3snp-master/thirdparty/args/LICENSE \n", | |
| " inflating: mpi3snp-master/thirdparty/args/args.hxx \n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 5 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "fkPy2ANmaRR8", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 1000 | |
| }, | |
| "outputId": "0981bb80-7133-42ca-b578-cdd89c20319c" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# compile\n", | |
| "cd mpi3snp-master\n", | |
| "mkdir -p build\n", | |
| "cd build/\n", | |
| "cmake ..\n", | |
| "make -j4" | |
| ], | |
| "execution_count": 6, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "-- The C compiler identification is GNU 7.5.0\n", | |
| "-- The CXX compiler identification is GNU 7.5.0\n", | |
| "-- Check for working C compiler: /usr/bin/cc\n", | |
| "-- Check for working C compiler: /usr/bin/cc -- works\n", | |
| "-- Detecting C compiler ABI info\n", | |
| "-- Detecting C compiler ABI info - done\n", | |
| "-- Detecting C compile features\n", | |
| "-- Detecting C compile features - done\n", | |
| "-- Check for working CXX compiler: /usr/bin/c++\n", | |
| "-- Check for working CXX compiler: /usr/bin/c++ -- works\n", | |
| "-- Detecting CXX compiler ABI info\n", | |
| "-- Detecting CXX compiler ABI info - done\n", | |
| "-- Detecting CXX compile features\n", | |
| "-- Detecting CXX compile features - done\n", | |
| "-- Looking for pthread.h\n", | |
| "-- Looking for pthread.h - found\n", | |
| "-- Looking for pthread_create\n", | |
| "-- Looking for pthread_create - not found\n", | |
| "-- Looking for pthread_create in pthreads\n", | |
| "-- Looking for pthread_create in pthreads - not found\n", | |
| "-- Looking for pthread_create in pthread\n", | |
| "-- Looking for pthread_create in pthread - found\n", | |
| "-- Found Threads: TRUE \n", | |
| "-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version \"3.1\") \n", | |
| "-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version \"3.1\") \n", | |
| "-- Found MPI: TRUE (found version \"3.1\") \n", | |
| "-- Looking for a CUDA compiler\n", | |
| "-- Looking for a CUDA compiler - /usr/local/cuda/bin/nvcc\n", | |
| "-- The CUDA compiler identification is NVIDIA 10.1.243\n", | |
| "-- Check for working CUDA compiler: /usr/local/cuda/bin/nvcc\n", | |
| "-- Check for working CUDA compiler: /usr/local/cuda/bin/nvcc -- works\n", | |
| "-- Detecting CUDA compiler ABI info\n", | |
| "-- Detecting CUDA compiler ABI info - done\n", | |
| "-- Setting build type to Release as none was specified.\n", | |
| "-- Configuring done\n", | |
| "-- Generating done\n", | |
| "-- Build files have been written to: /content/mpi3snp-master/build\n", | |
| "\u001b[35m\u001b[1mScanning dependencies of target dataset\u001b[0m\n", | |
| "\u001b[35m\u001b[1mScanning dependencies of target utils\u001b[0m\n", | |
| "[ 5%] \u001b[32mBuilding CXX object src/dataset/CMakeFiles/dataset.dir/Dataset.cpp.o\u001b[0m\n", | |
| "[ 10%] \u001b[32mBuilding CXX object src/utils/CMakeFiles/utils.dir/Cpu_node_information.cpp.o\u001b[0m\n", | |
| "[ 15%] \u001b[32mBuilding CXX object src/utils/CMakeFiles/utils.dir/Arg_parser.cpp.o\u001b[0m\n", | |
| "[ 20%] \u001b[32mBuilding CXX object src/utils/CMakeFiles/utils.dir/Node_information.cpp.o\u001b[0m\n", | |
| "[ 25%] \u001b[32mBuilding CXX object src/utils/CMakeFiles/utils.dir/IOMpi.cpp.o\u001b[0m\n", | |
| "[ 30%] \u001b[32mBuilding CXX object src/utils/CMakeFiles/utils.dir/Statistics.cpp.o\u001b[0m\n", | |
| "[ 35%] \u001b[32m\u001b[1mLinking CXX static library libdataset.a\u001b[0m\n", | |
| "[ 35%] Built target dataset\n", | |
| "[ 40%] \u001b[32m\u001b[1mLinking CXX static library libutils.a\u001b[0m\n", | |
| "[ 40%] Built target utils\n", | |
| "\u001b[35m\u001b[1mScanning dependencies of target engine_gpu\u001b[0m\n", | |
| "\u001b[35m\u001b[1mScanning dependencies of target engine_cpu\u001b[0m\n", | |
| "[ 45%] \u001b[32mBuilding CUDA object src/engine/gpu/CMakeFiles/engine_gpu.dir/GPUEngine.cu.o\u001b[0m\n", | |
| "[ 50%] \u001b[32mBuilding CUDA object src/engine/gpu/CMakeFiles/engine_gpu.dir/CUDAError.cu.o\u001b[0m\n", | |
| "[ 55%] \u001b[32mBuilding CUDA object src/engine/gpu/CMakeFiles/engine_gpu.dir/MutualInformation.cu.o\u001b[0m\n", | |
| "[ 60%] \u001b[32mBuilding CXX object src/engine/cpu/CMakeFiles/engine_cpu.dir/CPUEngine.cpp.o\u001b[0m\n", | |
| "[ 65%] \u001b[32mBuilding CXX object src/engine/cpu/CMakeFiles/engine_cpu.dir/MutualInformation.cpp.o\u001b[0m\n", | |
| "[ 70%] \u001b[32m\u001b[1mLinking CXX static library libengine_cpu.a\u001b[0m\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:\u001b[m\u001b[K In destructor ‘\u001b[01m\u001b[Kvirtual MutualInformation::~MutualInformation()\u001b[m\u001b[K’:\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2176:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kthrow will always call terminate() [\u001b[01;35m\u001b[K-Wterminate\u001b[m\u001b[K]\n", | |
| " throw CU\u001b[01;35m\u001b[KD\u001b[m\u001b[KAError();\n", | |
| " \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2176:17:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kin C++11 destructors default to noexcept\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2178:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kthrow will always call terminate() [\u001b[01;35m\u001b[K-Wterminate\u001b[m\u001b[K]\n", | |
| " throw CU\u001b[01;35m\u001b[KD\u001b[m\u001b[KAError();\n", | |
| " \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2178:17:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kin C++11 destructors default to noexcept\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2180:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kthrow will always call terminate() [\u001b[01;35m\u001b[K-Wterminate\u001b[m\u001b[K]\n", | |
| " throw CU\u001b[01;35m\u001b[KD\u001b[m\u001b[KAError();\n", | |
| " \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2180:17:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kin C++11 destructors default to noexcept\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2182:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kthrow will always call terminate() [\u001b[01;35m\u001b[K-Wterminate\u001b[m\u001b[K]\n", | |
| " throw CU\u001b[01;35m\u001b[KD\u001b[m\u001b[KAError();\n", | |
| " \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2182:17:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kin C++11 destructors default to noexcept\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2184:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kthrow will always call terminate() [\u001b[01;35m\u001b[K-Wterminate\u001b[m\u001b[K]\n", | |
| " throw CU\u001b[01;35m\u001b[KD\u001b[m\u001b[KAError();\n", | |
| " \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2184:17:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kin C++11 destructors default to noexcept\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2186:17:\u001b[m\u001b[K \u001b[01;35m\u001b[Kwarning: \u001b[m\u001b[Kthrow will always call terminate() [\u001b[01;35m\u001b[K-Wterminate\u001b[m\u001b[K]\n", | |
| " throw CU\u001b[01;35m\u001b[KD\u001b[m\u001b[KAError();\n", | |
| " \u001b[01;35m\u001b[K^\u001b[m\u001b[K\n", | |
| "\u001b[01m\u001b[K/content/mpi3snp-master/src/engine/gpu/MutualInformation.cu:2186:17:\u001b[m\u001b[K \u001b[01;36m\u001b[Knote: \u001b[m\u001b[Kin C++11 destructors default to noexcept\n", | |
| "[ 70%] Built target engine_cpu\n", | |
| "[ 75%] \u001b[32m\u001b[1mLinking CXX static library libengine_gpu.a\u001b[0m\n", | |
| "[ 75%] Built target engine_gpu\n", | |
| "\u001b[35m\u001b[1mScanning dependencies of target engine_search\u001b[0m\n", | |
| "[ 80%] \u001b[32mBuilding CXX object src/engine/search/CMakeFiles/engine_search.dir/Search.cpp.o\u001b[0m\n", | |
| "[ 85%] \u001b[32m\u001b[1mLinking CXX static library libengine_search.a\u001b[0m\n", | |
| "[ 85%] Built target engine_search\n", | |
| "\u001b[35m\u001b[1mScanning dependencies of target MPI3SNP\u001b[0m\n", | |
| "[ 90%] \u001b[32mBuilding CXX object src/CMakeFiles/MPI3SNP.dir/main.cpp.o\u001b[0m\n", | |
| "[ 95%] \u001b[32m\u001b[1mLinking CUDA device code CMakeFiles/MPI3SNP.dir/cmake_device_link.o\u001b[0m\n", | |
| "[100%] \u001b[32m\u001b[1mLinking CXX executable ../MPI3SNP\u001b[0m\n", | |
| "[100%] Built target MPI3SNP\n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 6 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "YuFcbPiKbBcS", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 34 | |
| }, | |
| "outputId": "4b8dee1a-6eb5-440c-d5b2-f361c62eeda6" | |
| }, | |
| "source": [ | |
| "# verify compile completion\n", | |
| "!ls ./mpi3snp-master/build/MPI3SNP" | |
| ], | |
| "execution_count": 7, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "./mpi3snp-master/build/MPI3SNP\n" | |
| ], | |
| "name": "stdout" | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "gDhpTU9OaOFj", | |
| "colab_type": "code", | |
| "colab": {} | |
| }, | |
| "source": [ | |
| "#%%shell\n", | |
| "#PREFIX=\"example/wgas1\"\n", | |
| "#PREFIX=\"t9a-zalloua2012-data/version-plink1.9-snpMajor/sample835\"\n", | |
| "#echo ./mpi3snp-master/build/MPI3SNP \"$PREFIX.tped\" \"$PREFIX.tfam\" \"$PREFIX.mpi3snp\"\n", | |
| "\n", | |
| "# Yields error: Error in example/wgas1.tped:1: invalid nucleotide value '0' at position 265\n", | |
| "#./mpi3snp-master/build/MPI3SNP \"$PREFIX.tped\" \"$PREFIX.tfam\" \"$PREFIX.mpi3snp\"" | |
| ], | |
| "execution_count": 8, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "1Yfb58SwR9PJ", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 187 | |
| }, | |
| "outputId": "50c073f6-ddd5-4aea-c8b9-a847d3cfda71" | |
| }, | |
| "source": [ | |
| "!grep \" 0 \" example/wgas1.tped |head|cut -d' ' -f 101-200" | |
| ], | |
| "execution_count": 26, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "A A G A A A G A G A G A A A A A A A A A G A 0 0 G A A A G A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A G A A A A A G A A A A A A A A A G A\n", | |
| "G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G 0 0 G G G G G G G G G G G G G G A G G G G G G G G G G G G G G G G G G G G G G G G G\n", | |
| "G G T G T G G G T G G G G G G G T G G G T G T T T T G G T G G G G G T G T G T T T T T G G G G G T G G G T G G G T G T G G G T G T T T G T G G G T T T G T G G G 0 0 G G\n", | |
| "G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G 0 0\n", | |
| "G G G G A G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G 0 0 G G G G G G 0 0 G G G G G G\n", | |
| "T T T T C T T T T T T T T T T T C C T T C C T T T T T T T T C C C T T T T T C T C C T T T T C C C T T T C T T T T T C C T T C T T T T T C T C C C T C T C T T T T T 0 0\n", | |
| "C T T T T T C T C T C C T T C T T T T T T T T T T T T T C T T T C T C T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T 0 0 T T\n", | |
| "C C A C C C C C C C C C A C A C A C C C C C C C C C C C C C A C C C C C C C C C A A A C C C C C C C C C C C A C A C C C C C C C C C C C C C C C C C C C C C C C C C 0 0\n", | |
| "T T C T T T T T T T T T C T C T C T T T T T C T C T T T T T C T T T T T T T T T C C C T T T T T T T T T T T C T C T T T T T T T T T T T T T T T T T T T T T T T T T C T\n", | |
| "A A G A G A A A A A G A G A G A G A G G G A G A G A G A G A G A G A G A G A G G A A A A G G G G 0 0 G A G A A A G A G G G G A A A A G A G G G G G A G A G G G A G A G A\n" | |
| ], | |
| "name": "stdout" | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "Ahw9HoVmQ7-r", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 224 | |
| }, | |
| "outputId": "ec2fc33b-f7ec-4f85-e7f1-c0a24918dd2b" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# Based on author reply that missing genotypes are not supported: https://github.com/UDC-GAC/mpi3snp/issues/7\n", | |
| "# replacing all 0 with A (would have prefered something like homozygous wild type)\n", | |
| "\n", | |
| "PREFIX=\"example/wgas1\"\n", | |
| "sed \"s/ 0 / A /g\" \"$PREFIX.tped\" > \"$PREFIX-fillna.tped\"\n", | |
| "sed -i \"s/ 0 / A /g\" \"$PREFIX-fillna.tped\" # consecutive 0's not replaced in previous step\n", | |
| "sed -i \"s/ 0$/ A/g\" \"$PREFIX-fillna.tped\" # final-column 0's not replaced in previous step\n", | |
| "wc -l \"$PREFIX-fillna.tped\"\n", | |
| "head \"$PREFIX-fillna.tped\"|cut -f 1-20" | |
| ], | |
| "execution_count": 49, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "228694 example/wgas1-fillna.tped\n", | |
| "1 rs3094315 0.792429 792429 A A A A G A A A A A A A G A G A A A A A A A G A A A A A A A A A A A G A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A G A A A G A A A G A G A G A A A A A A A A A G A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A G A A A A A G A A A A A A A A A G A\n", | |
| "1 rs6672353 0.817376 817376 G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G A A G G G G G G G G G G G G G G A G G G G G G G G G G G G G G G G G G G G G G G G G\n", | |
| "1 rs4040617 0.819185 819185 A A A A G A A A A A A A G A G A A A A A A A G A A A A A A A A A A A G A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A G A A A G A G A G A A A A A A A A A G A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A G A A A A A G A A A A A A A A A G A\n", | |
| "1 rs2905036 0.832343 832343 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T\n", | |
| "1 rs4245756 0.839326 839326 C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C\n", | |
| "1 rs4075116 1.04355 1043552 T T T T T T T T C T T T T T T T T T T T T T T T C T T T T T C T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T C T T T T T T T T T T T T T C T C T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T\n", | |
| "1 rs9442385 1.13726 1137258 T G T G T G T G T T T G G G G G T G T G T G T G T T G G G G G G G G T T T G T G G G G G T G G G T T G G T T G G G G G G G G T T T G G G T T T T G G G G T G G G T G T G T T T T T G T T T G G G G G T G T G G G T G G G G G G G T G G G T G T T T T G G T G G G G G T G T G T T T T T G G G G G T G G G T G G G T G T G G G T G T T T G T G G G T T T G T G G G A A G G\n", | |
| "1 rs6603781 1.19855 1198554 G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G A A\n", | |
| "1 rs11260562 1.20523 1205233 G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G A G G G G G G G G G G G A G G G G G G G G G G G G G G G G G A G G G G G G G G G G G G G G G G G G G G G A G G G G G G G G G G G G G A G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G A A G G G G G G A A G G G G G G\n", | |
| "1 rs6685064 1.25121 1251215 T T C T T T T T C T C C C T C T T T C T C C C C C T C T C T C C T T T T C T T T C T C C C T C C C C C T T T T T C T C T C T T T C C T T C T C C C C C C T T C T C C C C C T C C C T T T C T C T T T T T C T T T T T T T T T T T C C T T C C T T T T T T T T C C C T T T T T C T C C T T T T C C C T T T C T T T T T C C T T C T T T T T C T C C C T C T C T T T T T A A\n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 49 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "RXtB-gOWXbl8", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 119 | |
| }, | |
| "outputId": "7fe12d12-56e6-4b8e-b53e-f2d3fa7dace2" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "set -x\n", | |
| "grep \" 0 \" example/wgas1-fillna.tped |head|cut -d' ' -f 101-200\n", | |
| "grep \" 0$\" example/wgas1-fillna.tped |head|cut -d' ' -f 101-200" | |
| ], | |
| "execution_count": 50, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "+ grep ' 0 ' example/wgas1-fillna.tped\n", | |
| "+ head\n", | |
| "+ cut '-d ' -f 101-200\n", | |
| "+ cut '-d ' -f 101-200\n", | |
| "+ head\n", | |
| "+ grep ' 0$' example/wgas1-fillna.tped\n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 50 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "W5PNVsapRTG6", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 306 | |
| }, | |
| "outputId": "fcb4ff8f-e4fd-4253-c0fb-a03c9e0dcf48" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# run mpi3snp again on fillna-version of genotypes\n", | |
| "\n", | |
| "PREFIX=\"example/wgas1\"\n", | |
| "\n", | |
| "# Runs out of 12 GB memory on colab as of 2020-07-30\n", | |
| "date\n", | |
| "time ./mpi3snp-master/build/MPI3SNP --debug \"$PREFIX-fillna.tped\" \"$PREFIX.tfam\" \"$PREFIX.mpi3snp\"\n", | |
| "date" | |
| ], | |
| "execution_count": 53, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "Thu Jul 30 06:31:38 UTC 2020\n", | |
| "*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*\n", | |
| "Hostname: 1c76726d9c67\n", | |
| "CPU: Intel(R) Xeon(R) CPU @ 2.00GHz\n", | |
| "Memory: 13021 MB\n", | |
| "MPI Library: Open MPI v2.1.1, package: Open MPI buildd@lcy01-amd64-009 Distribution, ident: 2.1.1, repo rev: v2.1.0-100-ga2fdb5b, May 10, 2017\n", | |
| "Processes: [0] \n", | |
| "*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*\n", | |
| "\n", | |
| "tcmalloc: large alloc 3044442112 bytes == 0x55d99da3c000 @ 0x7fd4e31fb887 0x55d997c26368 0x55d997c227dc 0x55d997c1d8bd 0x7fd4e1980b97 0x55d997c1e43a\n", | |
| "tcmalloc: large alloc 6088876032 bytes == 0x55da531a4000 @ 0x7fd4e31fb887 0x55d997c27344 0x55d997c254e3 0x55d997c227dc 0x55d997c1d8bd 0x7fd4e1980b97 0x55d997c1e43a\n", | |
| "tcmalloc: large alloc 12177752064 bytes == 0x55dbbe8e4000 @ 0x7fd4e31fb887 0x55d997c27344 0x55d997c254e3 0x55d997c227dc 0x55d997c1d8bd 0x7fd4e1980b97 0x55d997c1e43a\n", | |
| "\n", | |
| "real\t0m18.130s\n", | |
| "user\t0m8.366s\n", | |
| "sys\t0m7.978s\n", | |
| "Thu Jul 30 06:31:56 UTC 2020\n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 53 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "yQ8lo_IWXSGO", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 17 | |
| }, | |
| "outputId": "45962d52-9500-4b79-ea9b-4f951aee2c89" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# download mpi3snp's sample files\n", | |
| "wget -q https://dl.dropboxusercontent.com/s/qkz7osu1fccpbvq/test10000-1600.tfam\n", | |
| "wget -q https://dl.dropboxusercontent.com/s/8mt3jo6crvypio9/test10000-1600.tped # 60MB\n", | |
| "#wget -q https://dl.dropboxusercontent.com/s/7kaqr4eaoo61ejf/test400006400.tfam\n", | |
| "#wget -q https://dl.dropboxusercontent.com/s/bwum12mpescadpm/test400006400.tped # 1GB" | |
| ], | |
| "execution_count": 37, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 37 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "SjoUMUYbYRNW", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 664 | |
| }, | |
| "outputId": "0b2cfd78-0334-4861-f56e-cc5fef848151" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "# run on sample file 10k-1600. ETA 09:20 .. 09:26 .. ??:?? (aborted)\n", | |
| "PREFIX=test10000-1600\n", | |
| "./mpi3snp-master/build/MPI3SNP --debug \"$PREFIX.tped\" \"$PREFIX.tfam\" \"$PREFIX.mpi3snp\"" | |
| ], | |
| "execution_count": 38, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*\n", | |
| "Hostname: 1c76726d9c67\n", | |
| "CPU: Intel(R) Xeon(R) CPU @ 2.00GHz\n", | |
| "Memory: 13021 MB\n", | |
| "MPI Library: Open MPI v2.1.1, package: Open MPI buildd@lcy01-amd64-009 Distribution, ident: 2.1.1, repo rev: v2.1.0-100-ga2fdb5b, May 10, 2017\n", | |
| "Processes: [0] \n", | |
| "*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*\n", | |
| "\n", | |
| "[1c76726d9c67:01361] *** Process received signal ***\n", | |
| "[1c76726d9c67:01361] Signal: Segmentation fault (11)\n", | |
| "[1c76726d9c67:01361] Signal code: Address not mapped (1)\n", | |
| "[1c76726d9c67:01361] Failing at address: 0x7f38fee3020d\n", | |
| "[1c76726d9c67:01361] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7f39018d58a0]\n", | |
| "[1c76726d9c67:01361] [ 1] /lib/x86_64-linux-gnu/libc.so.6(getenv+0xa5)[0x7f3901514835]\n", | |
| "[1c76726d9c67:01361] [ 2] /usr/lib/x86_64-linux-gnu/libtcmalloc.so.4(_ZN13TCMallocGuardD1Ev+0x34)[0x7f3901d7fe44]\n", | |
| "[1c76726d9c67:01361] [ 3] /lib/x86_64-linux-gnu/libc.so.6(__cxa_finalize+0xf5)[0x7f39015156c5]\n", | |
| "[1c76726d9c67:01361] [ 4] /usr/lib/x86_64-linux-gnu/libtcmalloc.so.4(+0x13cb3)[0x7f3901d7dcb3]\n", | |
| "[1c76726d9c67:01361] *** End of error message ***\n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "error", | |
| "ename": "CalledProcessError", | |
| "evalue": "ignored", | |
| "traceback": [ | |
| "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", | |
| "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)", | |
| "\u001b[0;32m<ipython-input-38-1d148ad131af>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_cell_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'shell'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'# run on sample file 10k-1600\\nPREFIX=test10000-1600\\n./mpi3snp-master/build/MPI3SNP --debug \"$PREFIX.tped\" \"$PREFIX.tfam\" \"$PREFIX.mpi3snp\"'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", | |
| "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/IPython/core/interactiveshell.py\u001b[0m in \u001b[0;36mrun_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m 2115\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvar_expand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2116\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2117\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2118\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2119\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", | |
| "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/google/colab/_system_commands.py\u001b[0m in \u001b[0;36m_shell_cell_magic\u001b[0;34m(args, cmd)\u001b[0m\n\u001b[1;32m 110\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_run_command\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcmd\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclear_streamed_output\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 111\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mparsed_args\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mignore_errors\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 112\u001b[0;31m \u001b[0mresult\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcheck_returncode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 113\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 114\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", | |
| "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/google/colab/_system_commands.py\u001b[0m in \u001b[0;36mcheck_returncode\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 136\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreturncode\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 137\u001b[0m raise subprocess.CalledProcessError(\n\u001b[0;32m--> 138\u001b[0;31m returncode=self.returncode, cmd=self.args, output=self.output)\n\u001b[0m\u001b[1;32m 139\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 140\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_repr_pretty_\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcycle\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;31m# pylint:disable=unused-argument\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", | |
| "\u001b[0;31mCalledProcessError\u001b[0m: Command '# run on sample file 10k-1600\nPREFIX=test10000-1600\n./mpi3snp-master/build/MPI3SNP --debug \"$PREFIX.tped\" \"$PREFIX.tfam\" \"$PREFIX.mpi3snp\"' died with <Signals.SIGINT: 2>." | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "AMK7aQS2YeSV", | |
| "colab_type": "code", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 377 | |
| }, | |
| "outputId": "35777e4a-5e39-4f5f-cf80-5da54822c2ff" | |
| }, | |
| "source": [ | |
| "%%shell\n", | |
| "set -x\n", | |
| "# compare mpi3snp sample files with plink example files\n", | |
| "head -n3 test10000-1600.tfam\n", | |
| "head -n3 example/wgas1.tfam\n", | |
| "\n", | |
| "head -n3 test10000-1600.tped|cut -f 1-20\n", | |
| "head -n3 example/wgas1.tped|cut -f 1-20\n", | |
| "head -n3 example/wgas1-fillna.tped|cut -f 1-20" | |
| ], | |
| "execution_count": 41, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": [ | |
| "+ head -n3 test10000-1600.tfam\n", | |
| "case0\tcase0\t0\t0\t1\t2\n", | |
| "control1\tcontrol1\t0\t0\t1\t1\n", | |
| "case2\tcase2\t0\t0\t1\t2\n", | |
| "+ head -n3 example/wgas1.tfam\n", | |
| "CH18526 NA18526 0 0 2 1\n", | |
| "CH18524 NA18524 0 0 1 1\n", | |
| "CH18529 NA18529 0 0 2 1\n", | |
| "+ head -n3 test10000-1600.tped\n", | |
| "+ cut -f 1-20\n", | |
| "0\trs0\t0\t0 C C A A A A A C A A A C A A A A C C A A A C A C A A A C A A A C A A A C A A A C A A A C A C C C A A A C A C A C C C A C A A A C A C A A A C C C A C A C A A C C C C A A A C A A A C C C A C A A A C A C A C A A C C A A A A A C A A A C A A A C A C A C A A A C A C A A A A C C A A A C C C A A A C A C A C A A A C A A A C A A A C A A A A A A A C A A A A C C A C A A A C A C A A A A A A A A A C A C A A C C A C A A A C A A A C A C A A A A A A C C A C A C A A A A A A A C A C A A A A A A A A A C A C A C A A A A A A A A A C A C A A A A C C A C A A A A A C A C A C A C C C A C C C A C A C A C A A A A A A A A A C A C C C A C A C A A A C C C A A A C A A A A A A A C A C A A A A C C A C A C C C A A A A A A A A A A A A A C A C A A A A A C A C A C A A A C A C A C A C A C A A A C A A A A A C A A C C A C A A A A A A A A A A A A A C A C A C A C A A A C A C A A A A A A A C A C A C A A A A A C A A A A A C A C A A A C A C A C A C A C A C A C A C A A A A C C A C A A A C A C A C A A A A A C A A A C C C A C A A A A A A A A A A C C A A A C A A A C A C A C A A A C A C A C A A A C A A A A A C C C A A A C A C C C A A A C A A A C A A A C A A A A A A A C A A A A A A A A A C A A A C A C A C A C A A A A C C A C A C C C A A A A A A A C A A A A A C A C A C A A C C A C A C A A A C A C A A A C A C A A A A A A A C C C A A A A A C A A A A A C A C A C A C A A A C A A A A A A A C A C A C A A A A A A A A C C A C A A A A A A A A A C A C A C A C A C A C A C A A A C A C C C A A A C A A A A A A A A C C A C A C A A A A A A C C A A C C A A A C A C A A A C A C A A A A A C A C A C A A A C A A C C A C A A A C A A A C A C A A A A A A A A A A A A A C A C A C A A A A A C A A A A A A C C A C A A A A C C C C A A A C A A A A A A A A A A A A A A A C A A A C C C A A A A A C A C A A A C A C A C A C A C A C A C A C C C A A A A C C A A A A A A A A A C A A A C C C A C A A A A A C A A A A A C A A A A A C A A A A A A A A A A A C A A A A C C A C A C A C A C A A A C A A A A A A A A A A A A A A A C A A C C A A A C A C A A C C A C A C A C A A A C A A A A A C A C A A A C A A A C A A A C A C A C A A A C A C A C A A A C A A A A A A C C A A A A A C A A A A A C A A A C A A A A A A C C A C A C A A A A A C A C A A A A A A A C A A C C A A A A A C A A A A A A A A A C A C A A A A A A A A A C A C A C A C A C A A A C A A C C A A A C A C A C A C A A A C A C A A A A C C A A A C A A A C A C A C C C A C A A A C A C C C A C C C A A A A A A A C C C A C C C A C A A A A A A A A A C A A A A A A A A A A A A A C A C C C A C A C A C A C A A A C A C A C A A A C A A A C A C A C A C A C A A A C A A A A A A A C A C A A A C A A A A A C A C A A A A A C C C A C A C A A A C C C C C A A A A A C A C C C A C A A A A A A A A A A A A A A A C A A C C A A A C A A A C A C A A A C A A A A A A A C A A A C A A A C A C A A A A A C A C A A A C C C A C A C A A A A A C A C A C A A A C A A A A A A C C A A A A A A A A A C A A A A A A A C A C A C A A A C A C A A A A A C C C A C A C A C C C C C C C A C A C A A A C A C A A C C A A A C A C A C A A A C A C A C A A A C A A A C A C A A A C A A A A A A A C A A A C A C A C A C A C A C A A A A A C A C A A A A A C A C A C A A C C A C A A A C C C A C A A A A A C A C A A A A A C A C A A A C A C A A A A A C A A A C A C A A A A A C A A A A A C A A A C A A A A A C A A A A A C A C A A A C A A A C A C A C A A A A C C A C A C C C A C A A A C A A A C A C A A A A A C A C A C A A A A A C A A A C A A A A A A A C A C A C A C A A A A A A A C A C A C A C A A A C A C A C A A A A A C A C A C A A A C A C A C A A A C A A A C A A A A A C A A C C A C A A A A A C A C A A A A A A A C A C C C A A A C A A A A A A A C A C A C A C A A A C A C A A A A A A A A A C A A A C A C A C A A A C A A A C A C A C A C A A A A C C C C A C C C A A A A A C A A A A A A A A A A A C A A C C A C A C A C A A A C A A C C A C A C A C A A A A A A A C A C A C A C A A A C A C A C A C A C A C A C C C A A A C A A A A A A A A A A A A A A A A C C A A A A A A A A A C A C A C A A A C A C A C A C A C A C C C A C A A A C A C A A A A A A A A A C A A A C C C A C A C A C A A C C C C C C A A A A A C A C A A A C A A A C A A A A A A A C A A A A A A C C A A A C A A A A A A A C A C A C A C A A A A A C A A A A A C A A A A A A A A A A A C A C A A A C C C A C A C A C A A A C A C C C A C A A A A A A A C A A A C A C A C A C A A A C A C A A A A A A A A A A A C A C A C A C A A A C A A A C A C A C A C A A A C A C A A A C A A A A A C C C A A A A A C A C A A A A C C A A A A A A A C A C A A A C A C A C A C A C A C A C A C A A A A A C A C A C A C A A A A A A A A A A A A A C A A A A C C A A C C A C A A A A A C A A A C A C A C A C A C A A A C A C A C A C A A A C A C A C C C A C A C A A A C A A A C A A A C A C A C A C A A C C A C C C A C A C A C A C A A A C A C A C A A A A A C A A A C A C A A A A A C C C C C A C A A A C A A A C A A A A C C A A A A A C A C A A A A A C C C A C A C C C A A A A A A A A C C A A A A A A A A A A A A A A A A A A A A A C A C C C A C A C A C C C A A A A C C A A A A A A A A A A A A A C A A A A A A A A C C A A A A A A A A C C A A A A A C A C A C A C A A A A A A A A A C A C A A C C A A A A A C A C A A A A C C A A A C A A A A A A A C A C A A A C A A A C A C A C A A A C A A A A C C A A A C A C A A A A A A A A A A A A A A A A A C A A A C C C C C A C C C C C A C A A A C C C A A A A A A A A A C A A A A C C A A A A A A A C A A A A A A A C A C A C A C C C A A A A A C A A A C A A A C A C A A A C A A A A A A A C A A A C A A A A A C A C A A A A A C A C A A A C A A A C A C A A A A A A A A A C A C C C A A A A A A A C A C A A A C A C A C A C A A A C A C A C A A A C A C A C A A A A A C A A A A C C A C A A A A A C A A A C A C A A A A A C A A A A A A A C C C A C A C A A A C A C A C A C A C A A A C A A A C A C A A A C C C C C C C A A A C C C A A A A A C A C A A A C A C A C C C A C A C A C A A A C A A A A A C A C A C A A A C A C A C A C A A A C A C A A A A A A A C A A A C A C A C A C A A A C A A A A C C A C A A A A A A C C A A A A A A A C A A A C A A A A A A A C A C A A A A A A A C A A A C A C A C A A A C A A A A A C A C A A A C A A A C A C A C A A A C A A A A A A A C C C A A C C C C C C C C A C A C A C A A A A C C C C A A A A C C A C A C A A A C A C C C C C A A A C C C A A A C A C A A A A A C C C A A A C A A A C A A A A A A A C A A C C A C C C A C A C A C A C A C A A A C A A A A A A A C A A A A A A C C A C A C A C A A A A A C A A A A A A A A A C A A A A A C A A A A A C A A A C A C A C A A A C A A A A A C A C A A A A A A A A A C A A A A A A\n", | |
| "1\trs1\t0\t1 A A A A A C A A A C A A A A A A A A A C A A A C A A C C A A A C A A A C A C A A A C A C A C A A A C A C A A A A A A A C A A A A A C A A A A A A A C A C A C A A A C A A C C A A A A A A A A A A A A A A A C A C A C A A A A A A A C A A A A A A C C A A A C A C A A A A C C A A A A A A A A A C A A A A A A A A A A A C A A A A A C C C A A A C A A A A A A A C A C A A A A A C A C A A C C A A A A A C A C A C A C A A A A A C A A A A A C A C A C A A A A A C A A A A A A A A A C A C A A C C A C A A A A A A A A A A A C A C A A A A A C A C A A A C A C A C A C A C A A A A A A A C A C A A A A A A A C A A A C A C A A A C A C C C A A A A A C A A A C A A A A A A A A C C A C A A A A A A A A A C A A A A A A A A A C A A A A A A A C A A A A A A A A A A A C A C A C A C A A A A A A A A A A A A A C A A A A A C A A A A A C C C A A A C A A A A A A A C A A A A A A A A A A A A A A A A A C A A A A A A A C A C A A A C A A A A A A C C A A A A A C A A A A A A A C A A A C A C A A A C A A A A A C A A A A A A A C A A A A A A A A A A A A A A A C C C A A A A A C A C A A A C A A C C A C A A A C A A A A A C A A A C A A A C A C A C A C A A A C A C A A A C C C A C A C A A A A A A A C A A A C A A A A A C A C A C A A A A A A A C A C A A A C A A A A A C A A A A A C A A A C A A A C A C A C A A A A A A A A A C A A A A A A A A A A A A A A A C A C C C A A A A A C A C A A A A A C A C A C A A A A A A A A A C A A A A A A A C A C A C A C A A A A C C A C A C A A C C A A A A A A A C A A A A A C A A A A A C A A A A A A A A A A A A A A A C A A A A A C A C A A A A A A A A A C A C A A A C C C A C A A A A A A A A A A A C A A A A A A A A A C A C A A A A A C A A A A A A A A A A A A A A C C A A A A A C A C A A A C A A A C A A A A A A C C A A A C A A A A A A A A A A A C A A A A A C A A A A A A A C A C A C A A A A C C A A A A A C A A A A A A A A A A A A A A A A A A A A A A A C A C A A A A A C A A A A A A A C A C A C A C A A A C A A A C A C A C A A A A A A A A A A A A A C A A A C A C A A A C A A A C A A C C A A A A A C A A A A A C A A A A A A A A A A A C A C A C A A A C A A A A A C A C A C A C A C A A A C A C A A A C A A A A A A C C A A A A A C A A A A A A A C A A A C A A A C A A A C A A A C A A A A A A A A A A A A A A A A A A A C A A A C A C A C A C A C A A A A A C A A A A A A A A A A A A A A A A A C A C A A A A A C A A A A A A A A A A A C A A A C A C A A A A A C A A A C A C A C A C A A A A A C A C A C A A A A A A A A A A A A A C C C A A A A A A A C A A A C A A A A A A A A C C A C A A A A A A A A A C A A A A A A A A A C A A A C A C A A A A A C A C A A A A A A A A A A A C A A A C A C A A A A A C A A A C A A A C C C A C A C C C A A A C C C A C A C A A A C A A A A A A A A C C A A C C A C A A A A A C A A A C A C A A A A A A C C A C A A A C A C A A C C A A A C A C A C A A A C A A A A A A A A A A A A A A A A A A A A A C A C A C A C A C A C A A A C A A A A A C A C A A A C A A A A A A A A A A A A A A A C A C A C A A A C A A C C A A A A A A A A A C A C A C A C A A A C A A A A A C C C A C A A A A A A C C A A A C A C A A A A A A A A A C A C A C A A A C A A A A A A A A A C C C C C A C A A A C A C A C A A A A A C A A A A A C A A A A A A C C A A A A A C C C A C A A A C A A A A A A A A A C A A A A A C A A A C A A A A A C A C A A A A A A A A C C A A A A A A A C A C A C A A A A A C A A A A A A A A A C A A A A A A A A A A A C A A A A A C A A A C A A A C A A A A A A A C A A A A A A A C A A A A A A A A A A C C A A A C A C A C A C A A A A A A A A A A A A A A A A A A A C A A A A A C A A C C A A A A A A A A A A A C A C A A A A A A A A A A A A A C C C A A A A A A A C A A A A A A A A A C A A A C A A A C A C A C A A A A A A A A A A A A A A A A A C A A A C A A A A A C A C A A A A A A A A A A A C A A A A A A A A A C A C A C A A A C A C A C A C A C A A A A A A A A A A A C A C A A A C C C A A A A A A A A A C A C A C A A A C A C A A A C A A A A A C A C A A A A A C A A A C A A A C A A A C A A A C C C A A A A A C A C A A C C C C A A A C A A A A A A A A A A A C A C A A A C C C A C A C A C A C A A A A A C C C A C A A A A A C A A A A A C A A A A A C A A A A A C A A A A A A A A A C A A A C A A A C A A A A A C A C A A A C A A A A A C A A A A A A A A A A A A A A C C A C C C A A A A A A A A A A A A A C A C A C A A A A A A A A C C A C A A A A A A A A A A A A A A A C A A A A A A A A A A A C A A A A A A A C A C A C A C A A A C A C A A A A A A A C A A A A A A A A A A A C A C A A A C A C A A A A A A A A A A A C A C A A A A A A A C A C A C A A A A A A A A A A A C A C A A A A A A A A A C A A A A A A A A A A A C A C A A A A A A A C A C A A A A A A A C A C A C A C A A A A A C A A C C A A A C C C A C A C A A A C A C A C A C A C A A A A A C A A A A A C A A A A A C A C A A C C A C A A A A A A A A A A A A C C A C A A A A A C A A A C C C A A A C A C A A A A A C A A A A A C C C A A A C A A A C A A A A A C A A C C A A A A A C A A A C A C A A A A A C A A A C A C A C A A A A A A C C A C A A A A C C A A A C A A C C A A A A A C A C A A A A A A A A A A A A A C C C A C A A C C C C A A A A A A C C A A A A A A A A A C A C A A C C A A A C A A A C A A A A A A A A A A A A A A C C A A A A A A A C A C A C A C A A A A A A A A A C A A A A A A A C A A A C A A A A A A A A A C A C A A A C A A A C A A A A A A A C A A A A A A A A A A A C C C A C A A A C A A A C A A C C A A A C A A A A A A A A A A A C A A A A A A A A A A A A C C A C A A A C A A A C A A A C A C A A A A A A A C A A A A A A A C A C A A A A A A A A A C C C A C A C A C A C A A A A A A A A A C A C A A A A A A A A A A A A A A A C A C A C C C A C A C A C A A A A A C A C A A A A A A A A A A A A A C C C C C A A C C A A A C C C A A A C A C A A A A A A A A A A A C A A A A A C A C A C C C A A A A A A A A A A A A A C A C A A A C A C A C A C A C A A C C A A A A A A A C A C A A A A A C A A A A A C A A A A A A A A A C A A A A A A A A A C A A A A A C A A A C A C A A A C A C A A A A A A A A A C A A A A A C A C A A A C A A A A A A A C A A C C A A A C A C A A A A A A A C A C A A A A A C A C A A A A A A A A A C A A A C A A A C A A A A A C A C A A A C A C A C A A A C A C A A A C A C A A A C A A A A A A A A C C A A A C A A A A A A A C A A A A A A A A A A A A A A A A A C A A C C A A A A A C A A A A C C A A A C A A A A A A A C A C A A A C A A A A A C A A A A A A A C A C A A A C A C A A A A C C A C A A A A A A C C A C A A A C A A C C A C C C A C A A A A A A A A A A A A A A A C A C A C A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A C A A A A A C\n", | |
| "2\trs2\t0\t2 A A C C A C A A A C A A C C A A C C C C A C C C A A A C A C C C A C A C C C A C C C A A A A A C C C A A A C A A A C A A A C A C C C A C A C A C A A C C C C A C A C A A A A A A A C A C A C A C A C C C A A C C A A A C A A A C C C C C A C C C A C C C C C A A A A A C A C A C A C A C A C A C A A A A A C A C A A C C A C A C A C A A A A A A C C A A A A C C A C A C C C C C A A A C A C A C A C C C A C C C A C A C A C A A A C A C A C A C A C A C A C A A A C A C A A A C A C A C A A A C A C A C A C A A A C A C A C A C A C C C A C C C A C A A A C A A A C A C A A A C A A A A A A C C A C A C C C C C A A A A A A A C A C A C C C A C C C A C A C A A A C A A A C A C A C A A A C C C A C C C C C A C A C C C C C A A A A A C A C C C C C A C C C A C A A A A A A A C A C A C C C A C A A A C A A A A A A A A C C A A A C A C A A A A A C A C A C A C A A C C C C A A A A A C A C C C C C A C A A A C A C A C A C A C C C C C A C A C A C A C A C A C A C A C C C A C A C A A A C A C A C A A C C A A A A A C A A C C A C A C A C C C A A C C A C A A A C A A C C A C A A C C A C A C C C A A C C C C A A A C A A A A A C C C A C A C C C A A C C A C A A A C A A A A A A C C A C A C A C A C A C A C A A A A A C C C A C A A A C A A A A A A A C A A A C A A C C A A A C C C A C C C A C C C A C A C A C A C A C A A A C C C A C C C A C A C A C A C A C A C C C A A A A C C A C A A A C A C C C A C A A A A A A A C A A A C A A A A A C C C A C C C A C A C A A A C A C A A A C A C A C A C A A A C A C A A A A C C A C C C A C A C A C A A A C A A C C A C A C C C A C A A A C A A A C C C A A A C A C A C A C A A A A C C A C A C C C A C A C A A C C A A C C A C A C A C A A A A A C A C A C A A A A A A A C A C A C A A A C C C A C A A A A A C A A A C A C A A A A A A A C A C A C A C A C A C A A C C A A A C A C C C A A C C A C A C C C A C A C A C A C A A C C A A A A A A A A A C A A A C A C A A C C A C A C A A A A A C A A A A A C A C C C A C C C A C A A C C C C C C A C C C C C A A C C A C A C A C A C C C C C A C A C A C C C A C A C C C C C A C A A A A A C A C A C A C A A A A C C A C A A C C A C A C A C A C A C C C A A A C A C A A A C A C A A A C A C A C A C A A A A A C A C C C A C A A A C A C A C A A A C C C A A A C C C A C A C A A C C C C C C A A A C A A A A A C A C A A C C A A C C A A A C A C C C A A C C A C C C A C A A A A C C A C C C A C C C C C C C A C A C A C A C A A A C C C A A A C A C A C A A C C A C C C A C C C A C A C A C C C A C A A A A A A A A A C A C A C A C A C C C A C C C C C A A A A A C A C A C A C A C A C A C C C A C C C A C A A A C C C A A C C A C C C A C A C A A C C A C C C A A A C A A A A A C A C A C A C A C A C A C A C A C A C A C A A A A A C A A A A A C A C A A C C A A A C A A A A A C A C A C C C A C A A C C A C A C A A A C C C A A A A A C A C A A A C A A C C A A A C A C A A C C A A A C C C A A A A A C A A C C A C C C A C C C C C A C C C A C A C A C A A A A C C A C C C A A A A A C C C A C A C A C C C A C C C A C A C C C A C C C A C C C A A A C A C A A A C A C A A A A A C A A A A A C A A A C C C A C A C A C A C A C C C A C A A A A A A A C A C C C A A C C C C A C A A C C A C A C A C A C A C A C A C A C A A A C A C A C C C A A A C A C A C A C A C C C A A A C A C A C A C A C A A A C A C A C A A A A A C C C A C A C C C A C A C A A A C A A A C A A A C C C A A C C A C A C C C A C A A A A A C C C A A A C A C A C A A A A A C A A A C A C A C A A A C A C A C A C A C A A A C A A A A A A A C A C A A A C A A A C C C A C A A A A C C A C A A A C A C A C A A A A A C A C A C A C A C C C A A A C A C A C A C A A A A A C A A A A A A C C A C A A A C A A A C C C A C A A A A A A C C A A C C A C A C A C A A A C A A A A A C A C C C A C A C A C A C A A A A C C A C A C A C A C A C C C A C C C A C A A C C C C C C A A A A A A A C A C A A A A A A A C C C A A A C C C A C A C A C A C A C A A A C A A A C A A C C A C A A A C A A A A A C A A A C A C A C A A A C C C C C A C C C A C A A A C A A A C C C A A C C A C C C A A A C A A C C A C A C A A A A C C A C A C C C A C C C A A A C A C C C A C A C A C A A A A A C A C A C A C A A A A A A A C A C A C A C A C A A A C A A A C A C A A A A A C A C A A A A A C A C A C A A A C A A C C A C C C A A A A A C A C C C A A A C A C A C A A A C C C C C A C A A A C A C A C A C C C A C A C A C C C A A A A C C C C A C A C C C C C A C A C A A A A A A A C A A A C A A C C A C C C A A A A A A A C C C A C C C A C A C A A A A A A A A A A A C A C C C A C A C A C A A C C C C A C A A A A A C A A A C A C A C A C A A A C A C A C A C A A A A C C A C A C A A A C A C A C A A A A A C C C A C C C C C A C A A A A A C C C A C A C C C A C C C A A A C C C A C C C A C A C A C A C A C A A A C A A C C A A A C A C C C A C C C A A A A A A A A A C A C A C A C A C A C C C C C C C A C A C A C A A A A A A A C A C C C A C C C A C A C A A C C C C A C A C A A A C A C C C C C C C A A A A A C A C A A A A A A A C C C A A A A A A A C A A A A A A A A A C A A A A A C A C A C A C A C C C A A A C A C A C A A A A A A C C A C C C A A A A A C C C A A A C A C C C A C A C C C A C A C A C C C A C A C A C C C A A A C C C A C A A A C A C A C A C C C A A A C A A A C A C C C A A A A A C C C C C A A A C A C C C A A A A C C A C A C A A A A A C C C C C A C A C A A A C A A A C C C A A A A A C A C A C A A A C A A A A C C C C A C A C A C A A A C A A A A A C A C A C A C A C C C A C A C A C C C A A A A A C A A C C A C A C A C A A A A A C A C A C A C A C A C A C C C C C C C A A A A A A A C C C A A C C C C A C A A A A A C A A A A A A C C A C A A A C C C A A C C A C C C C C C C A C A A A C A C A A A C A C A C A C A A A A A C A C C C A C C C A C A A A A A C A C C C C C A C C C A C A C A C A C A C C C C C A C A C A C A A A C A C A C A A C C A A A C C C A C A C A C A C C C A C A A A C A A C C A A C C A A C C A C A C A A A C A C A C A C A A A A C C A C C C A A A C A C A A A C A A A C A A A C C C A A C C C C A C A A A C A C A C A C A C A C A A A C A A A A A A A C A A C C A A A C A A A C A C C C A A A A A C C C A C A C A A C C A A C C A C A A C C C C C C C C A C A C C C C C A A A A C C A C A C A C A C A A C C A C A A C C A C A C A A C C A A A C A C C C A C C C A A A A A A A C A C A A A C A C A A C C C C A C A C A C C C A A A A A C A A A C A A A C A C A C A C A C A C A C A C A A A A A C A C A C A A A C C C A C C C C C C C A A A A A C A A A C A C A A A C C C A C A C A C C C A A A A A A A A C C C C A C A A C C A C A C C C A A A A A C A C A C A C A C A C C C C C A C A C A C C C A C C C A A A C A C A C A A A C A A\n", | |
| "+ cut -f 1-20\n", | |
| "+ head -n3 example/wgas1.tped\n", | |
| "1 rs3094315 0.792429 792429 A A A A G A A A A A A A G A G A A A A A A A G A A A A A A A A A A A G A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A G A A A G A A A G A G A G A A A A A A A A A G A 0 0 G A A A G A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A G A A A A A G A A A A A A A A A G A\n", | |
| "1 rs6672353 0.817376 817376 G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G 0 0 G G G G G G G G G G G G G G A G G G G G G G G G G G G G G G G G G G G G G G G G\n", | |
| "1 rs4040617 0.819185 819185 A A A A G A A A A A A A G A G A A A A A A A G A A A A A A A A A A A G A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A G A A A G A G A G A A A A A A A A A G A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G A A A G A A A G A A A A A G A A A A A A A A A G A\n", | |
| "+ cut -f 1-20\n", | |
| "+ head -n3 example/wgas1-fillna.tped\n" | |
| ], | |
| "name": "stdout" | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "" | |
| ] | |
| }, | |
| "metadata": { | |
| "tags": [] | |
| }, | |
| "execution_count": 41 | |
| } | |
| ] | |
| } | |
| ] | |
| } |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment