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Issue when building the docker image (ERROR [30/39]) #65

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avp65 opened this issue Jun 19, 2024 · 10 comments
Open

Issue when building the docker image (ERROR [30/39]) #65

avp65 opened this issue Jun 19, 2024 · 10 comments

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@avp65
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avp65 commented Jun 19, 2024 •
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Hello

I am a beginner in bioinformatic and the use of command line tools.
I am trying to build the image docker using the Dockerfile. The process failed at that step :

RUN cd $clinsv_path &&
git clone --branch latest-stable https://github.com/root-project/root.git root_src &&
mkdir root_build root_install && cd root_build &&
cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src && \

Here is a copy of all the process and the error message that I got.
What should I do to solve this problems ? Thank you.

(base) av65@ML22-1060 Downloads % docker build . -f Dockerfile.txt
[+] Building 1868.1s (34/43)                                                                    docker:desktop-linux
 => [internal] load build definition from Dockerfile.txt                                                        0.0s
 => => transferring dockerfile: 5.89kB                                                                          0.0s
 => [internal] load metadata for docker.io/library/ubuntu:20.04                                                 0.9s
 => [internal] load .dockerignore                                                                               0.0s
 => => transferring context: 2B                                                                                 0.0s
 => [ 1/39] FROM docker.io/library/ubuntu:20.04@sha256:0b897358ff6624825fb50d20ffb605ab0eaea77ced0adb8c6a4b756  0.0s
 => [internal] load build context                                                                               0.0s
 => => transferring context: 710B                                                                               0.0s
 => CACHED [ 2/39] WORKDIR /app                                                                                 0.0s
 => CACHED [ 3/39] RUN mkdir clinsv                                                                             0.0s
 => CACHED [ 4/39] ADD clinsvScripts.tar.gz /app                                                                0.0s
 => CACHED [ 5/39] ADD installKNITR.r /app                                                                      0.0s
 => CACHED [ 6/39] RUN mv clinsvScripts/* clinsv/                                                               0.0s
 => CACHED [ 7/39] RUN rm -r clinsvScripts                                                                      0.0s
 => CACHED [ 8/39] RUN apt-get update                                                                           0.0s
 => CACHED [ 9/39] RUN apt-get -y install build-essential                                                       0.0s
 => CACHED [10/39] RUN apt-get -y install wget curl git nano                                                    0.0s
 => CACHED [11/39] RUN apt-get -y install zlib1g-dev                                                            0.0s
 => CACHED [12/39] RUN apt-get -y install libbz2-dev liblzma-dev libcurl4-openssl-dev libncurses5-dev           0.0s
 => CACHED [13/39] RUN apt-get -y install python3.8 python3-pip                                                 0.0s
 => CACHED [14/39] RUN apt-get -y install dpkg-dev cmake g++ gcc binutils libx11-dev libxpm-dev libxft-dev lib  0.0s
 => CACHED [15/39] RUN apt-get -y install dh-autoreconf                                                         0.0s
 => CACHED [16/39] RUN ln -sf ../bin/bash ../bin/sh                                                             0.0s
 => CACHED [17/39] RUN curl -L https://cpanmin.us | perl - App::cpanminus                                       0.0s
 => CACHED [18/39] RUN mkdir clinsv/perl                                                                        0.0s
 => [19/39] RUN cd /app/clinsv/perl &&     git clone https://github.com/dpryan79/libBigWig &&     cd libBig  1305.1s
 => [20/39] RUN cd /app/clinsv &&     mkdir samtools &&     cd samtools &&     wget https://github.com/samto  126.0s
 => [21/39] RUN cd /app/clinsv/bin &&     ln -s ../samtools/bin/bcftools bcftools &&     ln -s ../samtools/bin  0.1s
 => [22/39] RUN mkdir /app/clinsv/bigWigTools &&     cd /app/clinsv/bigWigTools &&     wget http://hgdownloa  131.9s 
 => [23/39] RUN cd /app/clinsv/bin &&     ln -s ../bigWigTools/bigWigToWig bigWigToWig &&     ln -s ../bigWigT  0.1s 
 => [24/39] RUN mkdir /app/clinsv/python                                                                        0.1s 
 => [25/39] RUN cd /app/clinsv/python &&     wget https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tgz   60.1s 
 => [26/39] RUN cd /app/clinsv/python &&     rm -r Python-2.7.18*                                               0.3s 
 => [27/39] RUN cd /app/clinsv/bin &&     ln -s ../python/bin/python python &&     ln -s ../python/bin/python   0.1s 
 => [28/39] RUN pip3 install numpy                                                                              2.5s 
 => [29/39] RUN pip3 install pysam                                                                            149.1s 
 => ERROR [30/39] RUN cd /app/clinsv &&     git clone --branch latest-stable https://github.com/root-project/  91.6s 
------                                                                                                               
 > [30/39] RUN cd /app/clinsv &&     git clone --branch latest-stable https://github.com/root-project/root.git root_src &&     mkdir root_build root_install && cd root_build &&     cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src &&     cmake --build . -- install:                                                                               
0.120 Cloning into 'root_src'...
Updating files: 100% (24200/24200), done.
89.40 -- The C compiler identification is GNU 9.4.0
89.43 -- The CXX compiler identification is GNU 9.4.0
89.44 -- Check for working C compiler: /usr/bin/cc
89.47 -- Check for working C compiler: /usr/bin/cc -- works
89.47 -- Detecting C compiler ABI info
89.49 -- Detecting C compiler ABI info - done
89.50 -- Detecting C compile features
89.50 -- Detecting C compile features - done
89.50 -- Check for working CXX compiler: /usr/bin/c++
89.53 -- Check for working CXX compiler: /usr/bin/c++ -- works
89.53 -- Detecting CXX compiler ABI info
89.57 -- Detecting CXX compiler ABI info - done
89.57 -- Detecting CXX compile features
89.57 -- Detecting CXX compile features - done
89.57 -- Found Git: /usr/bin/git (found version "2.25.1") 
89.58 CMake Warning at cmake/modules/SetROOTVersion.cmake:85 (message):
89.58   GIT_DESCRIBE_ALL is `heads/latest-stable`·with a format unexpected for
89.58   tags.  Not setting the commit.
89.58 Call Stack (most recent call first):
89.58   cmake/modules/SetROOTVersion.cmake:99 (SET_ROOT_VERSION)
89.58   CMakeLists.txt:75 (include)
89.58 
89.58 
89.58 -- Building ROOT version 6.32.02
89.58 -- Checking internet connectivity
89.74 -- Checking internet connectivity - found
89.74 -- Looking for a CUDA compiler
89.77 -- Looking for a CUDA compiler - NOTFOUND
89.77 -- Found GCC. Major version 9, minor version 4
89.77 -- The default C++ standard in use by the detected compiler (/usr/bin/c++) is lower than C++17. Setting C++17 as the minimum standard.
89.78 -- Looking for pthread.h
89.81 -- Looking for pthread.h - found
89.81 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
89.84 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
89.84 -- Looking for pthread_create in pthreads
89.86 -- Looking for pthread_create in pthreads - not found
89.86 -- Looking for pthread_create in pthread
89.89 -- Looking for pthread_create in pthread - found
89.89 -- Found Threads: TRUE  
89.89 -- Performing Test GLIBCXX_USE_CXX11_ABI
90.00 -- Performing Test GLIBCXX_USE_CXX11_ABI - Success
90.00 -- ROOT default compression algorithm: zlib
90.00 -- Cannot enable cudnn without enabling cuda or tmva-gpu: cudnn is disabled.
90.01 -- Looking for ZLib
90.01 -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11") 
90.01 -- Looking for nlohmann/json.hpp
90.02 -- nlohmann/json.hpp not found. Switching on builtin_nlohmannjson option
90.02 -- Looking for Freetype
90.03 -- Found Freetype: /usr/lib/aarch64-linux-gnu/libfreetype.so (found version "2.10.1") 
90.03 -- Looking for PCRE
90.04 -- Could NOT find PCRE2 (missing: PCRE2_INCLUDE_DIR PCRE2_PCRE2_LIBRARY) 
90.04 -- Could NOT find PCRE (missing: PCRE_INCLUDE_DIR PCRE_PCRE_LIBRARY) 
90.04 -- PCRE not found. Switching on builtin_pcre option
90.05 -- Looking for LZMA
90.06 -- Looking for lzma_auto_decoder in /usr/lib/aarch64-linux-gnu/liblzma.so
90.08 -- Looking for lzma_auto_decoder in /usr/lib/aarch64-linux-gnu/liblzma.so - found
90.08 -- Looking for lzma_easy_encoder in /usr/lib/aarch64-linux-gnu/liblzma.so
90.11 -- Looking for lzma_easy_encoder in /usr/lib/aarch64-linux-gnu/liblzma.so - found
90.11 -- Looking for lzma_lzma_preset in /usr/lib/aarch64-linux-gnu/liblzma.so
90.13 -- Looking for lzma_lzma_preset in /usr/lib/aarch64-linux-gnu/liblzma.so - found
90.13 -- Found LibLZMA: /usr/lib/aarch64-linux-gnu/liblzma.so (found version "5.2.4") 
90.13 -- Looking for xxHash
90.14 -- Could NOT find xxHash (missing: xxHash_LIBRARY xxHash_INCLUDE_DIR) (Required is at least version "0.8")
90.14 -- xxHash not found. Switching on builtin_xxhash option
90.14 -- Looking for ZSTD
90.14 -- Could NOT find ZSTD (missing: ZSTD_LIBRARIES ZSTD_INCLUDE_DIR ZSTD_VERSION) 
90.14 -- ZSTD not found. Switching on builtin_zstd option
90.15 -- Performing Test CXX_FLAG_STD_CPLUSPLUS11
90.18 -- Performing Test CXX_FLAG_STD_CPLUSPLUS11 - Success
90.18 -- Performing Test C_FLAG_STD_C99
90.20 -- Performing Test C_FLAG_STD_C99 - Success
90.20 -- Performing Test C_FLAG_WALL
90.23 -- Performing Test C_FLAG_WALL - Success
90.23 -- Performing Test CXX_FLAG_WALL
90.26 -- Performing Test CXX_FLAG_WALL - Success
90.26 -- Performing Test C_FLAG_WEXTRA
90.29 -- Performing Test C_FLAG_WEXTRA - Success
90.29 -- Performing Test CXX_FLAG_WEXTRA
90.32 -- Performing Test CXX_FLAG_WEXTRA - Success
90.32 -- Performing Test C_FLAG_WUNDEF
90.34 -- Performing Test C_FLAG_WUNDEF - Success
90.34 -- Performing Test CXX_FLAG_WUNDEF
90.37 -- Performing Test CXX_FLAG_WUNDEF - Success
90.37 -- Performing Test C_FLAG_WSHADOW
90.40 -- Performing Test C_FLAG_WSHADOW - Success
90.40 -- Performing Test CXX_FLAG_WSHADOW
90.42 -- Performing Test CXX_FLAG_WSHADOW - Success
90.43 -- Performing Test C_FLAG_WCAST_ALIGN
90.45 -- Performing Test C_FLAG_WCAST_ALIGN - Success
90.45 -- Performing Test CXX_FLAG_WCAST_ALIGN
90.48 -- Performing Test CXX_FLAG_WCAST_ALIGN - Success
90.48 -- Performing Test C_FLAG_WCAST_QUAL
90.51 -- Performing Test C_FLAG_WCAST_QUAL - Success
90.51 -- Performing Test CXX_FLAG_WCAST_QUAL
90.54 -- Performing Test CXX_FLAG_WCAST_QUAL - Success
90.54 -- Performing Test C_FLAG_WSTRICT_PROTOTYPES
90.56 -- Performing Test C_FLAG_WSTRICT_PROTOTYPES - Success
90.56 -- Looking for LZ4
90.57 -- Could NOT find LZ4 (missing: LZ4_LIBRARY LZ4_INCLUDE_DIR) 
90.57 -- LZ4 not found. Switching on builtin_lz4 option
90.57 -- Looking for X11
90.60 -- Found X11: /usr/include   
90.60 -- Looking for XOpenDisplay in /usr/lib/aarch64-linux-gnu/libX11.so;/usr/lib/aarch64-linux-gnu/libXext.so
90.63 -- Looking for XOpenDisplay in /usr/lib/aarch64-linux-gnu/libX11.so;/usr/lib/aarch64-linux-gnu/libXext.so - found
90.63 -- Looking for gethostbyname
90.66 -- Looking for gethostbyname - found
90.66 -- Looking for connect
90.68 -- Looking for connect - found
90.68 -- Looking for remove
90.71 -- Looking for remove - found
90.71 -- Looking for shmat
90.73 -- Looking for shmat - found
90.73 -- X11_INCLUDE_DIR: /usr/include
90.73 -- X11_LIBRARIES: /usr/lib/aarch64-linux-gnu/libX11.so;/usr/lib/aarch64-linux-gnu/libXext.so
90.73 -- X11_Xpm_INCLUDE_PATH: /usr/include
90.73 -- X11_Xpm_LIB: /usr/lib/aarch64-linux-gnu/libXpm.so
90.73 -- X11_Xft_INCLUDE_PATH: /usr/include
90.73 -- X11_Xft_LIB: /usr/lib/aarch64-linux-gnu/libXft.so
90.73 -- X11_Xext_INCLUDE_PATH: /usr/include
90.73 -- X11_Xext_LIB: /usr/lib/aarch64-linux-gnu/libXext.so
90.74 -- Could NOT find GIF (missing: GIF_LIBRARY GIF_INCLUDE_DIR) 
90.74 -- Could NOT find TIFF (missing: TIFF_LIBRARY TIFF_INCLUDE_DIR) 
90.75 -- Found PNG: /usr/lib/aarch64-linux-gnu/libpng.so (found version "1.6.37") 
90.75 -- Could NOT find JPEG (missing: JPEG_LIBRARY JPEG_INCLUDE_DIR) 
90.75 -- Building AfterImage library included in ROOT itself
90.76 -- Looking for Python
90.81 -- Could NOT find Python3 (missing: Python3_EXECUTABLE Interpreter NumPy) (found suitable version "3.8", minimum required is "3.8")
90.81 -- Looking for OpenGL
90.82 -- Could NOT find OpenGL (missing: OPENGL_opengl_LIBRARY OPENGL_glx_LIBRARY OPENGL_INCLUDE_DIR) 
90.82 -- OpenGL (with GLU) not found. Switching off opengl option
90.82 -- Looking for LibXml2
90.82 -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARY LIBXML2_INCLUDE_DIR) 
90.82 -- LibXml2 not found. Switching off xml option
90.84 -- Found OpenSSL: /usr/lib/aarch64-linux-gnu/libcrypto.so (found version "1.1.1f")  
90.84 -- Looking for MySQL
90.84 -- Could NOT find MySQL (missing: MYSQL_INCLUDE_DIR MYSQL_LIBRARIES) 
90.84 -- MySQL not found. Switching off mysql option
90.84 -- Looking for PostgreSQL
90.85 -- Could NOT find PostgreSQL (missing: PostgreSQL_LIBRARY PostgreSQL_INCLUDE_DIR) 
90.85 -- PostgreSQL not found. Switching off pgsql option
90.85 -- Looking for SQLite
90.85 -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") 
90.85 -- Could NOT find Sqlite (missing: SQLITE_INCLUDE_DIR SQLITE_LIBRARIES) 
90.85 -- SQLite not found. Switching off sqlite option
90.85 -- Looking for CFITSIO
90.86 -- Could NOT find CFITSIO (missing: CFITSIO_LIBRARY CFITSIO_INCLUDE_DIR) 
90.86 -- CFITSIO not found. You can enable the option 'builtin_cfitsio' to build the library internally'
90.86 --                    For the time being switching off 'fitsio' option
90.86 -- Looking for XROOTD
90.86 CMake Warning at cmake/modules/SearchInstalledSoftware.cmake:18 (_find_package):
90.86   By not providing "FindXRootD.cmake" in CMAKE_MODULE_PATH this project has
90.86   asked CMake to find a package configuration file provided by "XRootD", but
90.86   CMake did not find one.
90.86 
90.86   Could not find a package configuration file provided by "XRootD" with any
90.86   of the following names:
90.86 
90.86     XRootDConfig.cmake
90.86     xrootd-config.cmake
90.86 
90.86   Add the installation prefix of "XRootD" to CMAKE_PREFIX_PATH or set
90.86   "XRootD_DIR" to a directory containing one of the above files.  If "XRootD"
90.86   provides a separate development package or SDK, be sure it has been
90.86   installed.
90.86 Call Stack (most recent call first):
90.86   cmake/modules/SearchInstalledSoftware.cmake:922 (find_package)
90.86   CMakeLists.txt:297 (include)
90.86 
90.86 
90.86 -- XROOTD not found, enabling 'builtin_xrootd' option
90.87 -- Downloading and building XROOTD version 5.5.2
90.88 -- Checking for module 'davix>=0.6.4'
90.88 --   No package 'davix' found
90.88 -- Looking for uuid_generate_random in uuid
90.91 -- Looking for uuid_generate_random in uuid - found
90.91 -- Found libuuid: /usr/include  
90.92 -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARY LIBXML2_INCLUDE_DIR) 
90.92 -- Davix dependency libxml2 not found, switching OFF 'davix' option.
90.92 -- Looking for TBB
90.92 -- Could NOT find TBB (missing: TBB_ROOT_DIR TBB_INCLUDE_DIR TBB_LIBRARY) (Required is at least version "2020")
90.92 -- TBB not found, enabling 'builtin_tbb' option
90.93 -- Looking for VDT
90.93 -- Could NOT find Vdt (missing: VDT_INCLUDE_DIR VDT_LIBRARY) (Required is at least version "0.4")
90.93 -- VDT not found. Ensure that the installation of VDT is in the CMAKE_PREFIX_PATH
90.93 --                Switching ON 'builtin_vdt' option
90.94 -- Looking for BLAS for optional parts of TMVA
90.94 -- Looking for sgemm_
90.97 -- Looking for sgemm_ - not found
90.98 -- Could NOT find BLAS (missing: BLAS_LIBRARIES) 
90.98 -- TMVA: Numpy or Python development package not found for python _Python3_EXECUTABLE-NOTFOUND. Switching off tmva-pymva option
90.98 -- PyROOT: development package found. Building for version 3.8
90.99 -- Performing Test ROOT_HAVE_CXX_ATOMICS_WITHOUT_LIB
91.04 -- Performing Test ROOT_HAVE_CXX_ATOMICS_WITHOUT_LIB - Success
91.14 -- Building LLVM in 'Release' mode.
91.14 -- The ASM compiler identification is GNU
91.14 -- Found assembler: /usr/bin/cc
91.15 -- bolt project is disabled
91.15 -- clang project is enabled
91.15 -- clang-tools-extra project is disabled
91.15 -- compiler-rt project is disabled
91.15 -- cross-project-tests project is disabled
91.15 -- libc project is disabled
91.15 -- libclc project is disabled
91.15 -- lld project is disabled
91.15 -- lldb project is disabled
91.15 -- mlir project is disabled
91.15 -- openmp project is disabled
91.15 -- polly project is disabled
91.15 -- pstl project is disabled
91.15 -- flang project is disabled
91.17 CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
91.17   Could NOT find Python3 (missing: Python3_EXECUTABLE Interpreter) (found
91.17   suitable version "3.8", minimum required is "3.0")
91.17 Call Stack (most recent call first):
91.17   /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
91.17   /usr/share/cmake-3.16/Modules/FindPython/Support.cmake:2214 (find_package_handle_standard_args)
91.17   /usr/share/cmake-3.16/Modules/FindPython3.cmake:300 (include)
91.17   cmake/modules/SearchInstalledSoftware.cmake:18 (_find_package)
91.17   interpreter/llvm-project/llvm/CMakeLists.txt:835 (find_package)
91.17 
91.17 
91.17 -- Configuring incomplete, errors occurred!
91.17 See also "/app/clinsv/root_build/CMakeFiles/CMakeOutput.log".
91.17 See also "/app/clinsv/root_build/CMakeFiles/CMakeError.log".
------
Dockerfile.txt:126
--------------------
 125 |     #installing root 6 (root 5 deprecated)
 126 | >>> RUN cd $clinsv_path && \
 127 | >>>     git clone --branch latest-stable https://github.com/root-project/root.git root_src && \
 128 | >>>     mkdir root_build root_install && cd root_build && \
 129 | >>>     cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src && \
 130 | >>> #add -j4 perhaps, means amount of cores available to build
 131 | >>>     cmake --build . -- install
 132 |     
--------------------
ERROR: failed to solve: process "/bin/sh -c cd $clinsv_path &&     git clone --branch latest-stable https://github.com/root-project/root.git root_src &&     mkdir root_build root_install && cd root_build &&     cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src &&     cmake --build . -- install" did not complete successfully: exit code: 1
@avp65 avp65 changed the title Issue when building the docker image (Building and testing Bio-DB-Big-v1.0.1 failed) Issue when building the docker image (ERROR [30/39]) Jun 19, 2024
@drmjc
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drmjc commented Jun 21, 2024

Hi, it's quite painful to install these dependencies, so I'd recommend just use the prebuilt docker image

@avp65
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avp65 commented Jun 24, 2024 •
edited
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Hi thank you for your response.
Can you explain me how to find and use the prebuilt docker image?
I thought we have to use the file named Dockerfile to built it by ourselve that's why I run the command line:
docker build . -f Dockerfile.txt.
Sorry for my question, I begin in this field and I never used this way to run a tool.

@drmjc
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drmjc commented Jun 26, 2024 via email

@tollecr
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tollecr commented Jun 27, 2024

Readme has errors, try:

docker pull mrbradley2/clinsv:v1.0

not the readme's

docker pull mrbradley2/clinsv:v1.0.0

@avp65
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avp65 commented Jun 27, 2024 •
edited
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Thank you for your response, I tried it but it stops prematurely with this message :

***** error exist status != 0 (35072), please check /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e for more information

(base) av65@ml22-1 ClinSV_test % docker pull mrbradley2/clinsv:v1.0

refdata_path=$PWD/clinsv/refdata-b38
input_path=$PWD
project_folder=$PWD/test_run

docker run -v $refdata_path:/app/ref-data \
-v $project_folder:/app/project_folder  \
-v $input_path:/app/input  \
--entrypoint "perl" mrbradley2/clinsv:v1.0 /app/clinsv/bin/clinsv \
-r all \
-p /app/project_folder/ \
-i "/app/input/*.bam" \
-ref /app/ref-data/refdata-b38 \

v1.0: Pulling from mrbradley2/clinsv
Digest: sha256:17a0eae080654a21a74d1cd43b1c5f35dfcf57f99003ef9d77b46cad6acc0b0a
Status: Image is up to date for mrbradley2/clinsv:v1.0
docker.io/mrbradley2/clinsv:v1.0

What's Next?
  1. Sign in to your Docker account → docker login
  2. View a summary of image vulnerabilities and recommendations → docker scout quickview mrbradley2/clinsv:v1.0
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
 ### executing: sh /app/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.sh &> /app/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.e  ...  

##############################################
####                ClinSV                ####
##############################################
# 28/06/2024 23:11:26

# clinsv dir: /app/clinsv
# projectDir: /app/project_folder
# sampleInfoFile: /app/project_folder/sampleInfo.txt 
# name stem: project_folder
# lumpyBatchSize: 5
# genome reference: /app/ref-data/refdata-b38
# run steps: all
# number input bams: 1

# Read Sample Info from /app/project_folder/sampleInfo.txt
# use: FR05812606	H7LH3CCXX_6		/app/input/NA12878.grch38.subsampled.bam
# 1 samples to process
# If not, please exit make a copy of sampleInfo.txt, modify it and rerun with -s sampleInfo_mod.txt pointing to the new sample info file. 

###### Generate the commands and scripts ######

# bigwig

# lumpy

# cnvnator

# annotate

# prioritize

# qc

###### Run jobs ######


 ### finished after (hh:mm:ss): 06:16:34
 ### exist status: 0

 ### executing: sh /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh &> /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e  ...  

 ### finished after (hh:mm:ss): 00:17:26
 ### exist status: 35072



 ***** error exist status != 0 (35072), please check /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e for more information
```
Below is what is in the file 

```
+ export PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ cd /app/project_folder/alignments/FR05812606/bw/
+ wigToBigWig /app/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/FR05812606/bw/FR05812606.q0.bw
/app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh: line 7: 14088 Killed                  wigToBigWig /app/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/FR05812606/bw/FR05812606.q0.bw

```

@J-Bradlee
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This looks similar to issue #34 . ClinSV requires at least 60gb of ram. Have you looked at how much ram is being taken up before it gets shut down?

@tollecr
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tollecr commented Jul 27, 2024 via email

@J-Bradlee
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J-Bradlee commented Aug 1, 2024 via email

@tollecr
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tollecr commented Aug 1, 2024 via email

@J-Bradlee
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Samtools is throwing an error since it can't find the bai files or it wasn't indexed.

Run this samtools command on you bam file:

samtools index your.bam

The corresponding bai folder should be in your clinsv input folder with your bam

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@drmjc @tollecr @J-Bradlee @avp65