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Xingyu-Liao / LongRepMarker_v2.0

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There is a problem of installation #3

Open helan-1997 opened 2 years ago

helan-1997 commented 2 years ago

I met the error when installing the SPAdes. Log is here log.txt .

Xingyu-Liao commented 2 years ago

Hi,

Please paste the installation log of spades [location: /home/helang/biosoft/LongRepMarker_v2.0-master/log/SPAdes_Install.log]. Thanks!

Best,

Xingyu Liao

helan-1997 commented 2 years ago

the log is `-- The C compiler identification is GNU 7.5.0

-- The CXX compiler identification is GNU 7.5.0

-- Check for working C compiler: /usr/bin/cc

-- Check for working C compiler: /usr/bin/cc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Detecting C compile features

-- Detecting C compile features - done

-- Check for working CXX compiler: /usr/bin/c++

-- Check for working CXX compiler: /usr/bin/c++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Configuring incomplete, errors occurred!`

Xingyu-Liao commented 2 years ago

Hi,

Thanks for your feedback. The correct log should look like the following. I think the problem may be caused by the OpenMP_C module, please check the system configuration.

Best,

Xingyu Liao

-- The C compiler identification is GNU 7.5.0 -- The CXX compiler identification is GNU 7.5.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc - works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ - works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done _-- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMPCXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so - found -- Found Boost: /home/xingyu_liao/.linuxbrew/lib/cmake/Boost-1.78.0/BoostConfig.cmake (found version "1.78.0")
-- Override standard malloc (MI_OVERRIDE=ON) -- Enable abort() calls on memory allocation failure (MI_XMALLOC=ON) -- Enable printing of error and warning messages by default (MI_SHOW_ERRORS=ON) -- Use the C++ compiler to compile (MI_USE_CXX=ON) -- Library base name: mimalloc -- Build type : relwithdebinfo -- Compiler : /usr/bin/c++ -- Install directory: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/lib/mimalloc-1.6 -- Build targets : object -- Looking for open -- Looking for open - found -- Looking for execinfo.h -- Looking for execinfo.h - found -- Looking for signal.h -- Looking for signal.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for cxxabi.h -- Looking for cxxabi.h - not found -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- Looking for mach/mach.h -- Looking for mach/mach.h - not found -- Looking for link.h -- Looking for link.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for sys/mman.h -- Looking for sys/mman.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for malloc/malloc.h -- Looking for malloc/malloc.h - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for sys/resource.h -- Looking for sys/resource.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include
-- Looking for futimens -- Looking for futimens - found -- Looking for futimes -- Looking for futimes - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for mallinfo -- Looking for mallinfo - found -- Looking for mallctl -- Looking for mallctl - not found -- Looking for malloc_zone_statistics -- Looking for malloc_zone_statistics - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Looking for pthread_getspecific in pthread -- Looking for pthread_getspecific in pthread - found -- Looking for pthread_rwlock_init in pthread -- Looking for pthread_rwlock_init in pthread - found -- Looking for pthread_mutex_lock in pthread -- Looking for pthread_mutex_lock in pthread - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE
-- Looking for shm_open -- Looking for shm_open - not found -- Looking for shm_open in rt -- Looking for shm_open in rt - found -- Looking for include file endian.h -- Looking for include file endian.h - found -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file strings.h -- Looking for include file strings.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file sys/param.h -- Looking for include file sys/param.h - found -- Looking for include file sys/sysctl.h -- Looking for include file sys/sysctl.h - found -- Looking for include file emmintrin.h -- Looking for include file emmintrin.h - found -- Looking for include file pmmintrin.h -- Looking for include file pmmintrin.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for chmod -- Looking for chmod - found -- Looking for fseeko -- Looking for fseeko - found -- Looking for fstat -- Looking for fstat - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for getpid -- Looking for getpid - found -- Looking for mkstemp -- Looking for mkstemp - found -- Looking for popen -- Looking for popen - found -- Looking for putenv -- Looking for putenv - found -- Looking for stat -- Looking for stat - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for sysctl -- Looking for sysctl - found -- Looking for times -- Looking for times - found -- Looking for erfc -- Looking for erfc - not found -- Found PythonInterp: /home/xingyu_liao/miniconda3/bin/python (found version "3.9.5") -- Configuring done -- Generating done -- Build files have been written to: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/build_spades Scanning dependencies of target ssw Scanning dependencies of target format 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../../bin/spades-gsimplifier [100%] Built target spades-gsimplifier [100%] Linking CXX executable ../../bin/mag-improve [100%] Built target mag-improve [ 5%] Built target nlopt [ 8%] Built target ConsensusCore [ 15%] Built target BamTools [ 19%] Built target samtools [ 20%] Built target format [ 20%] Built target ssw [ 20%] Built target getopt_pp [ 30%] Built target llvm-support [ 33%] Built target bwa [ 37%] Built target spades-bwa [ 38%] Built target gqf [ 39%] Built target edlib [ 39%] Built target gfa1 [ 52%] Built target easel [ 65%] Built target hmmer [ 65%] Built target gtest [ 65%] Built target gtest_main [ 66%] Built target teamcity_gtest [ 66%] Built target coverage_model [ 67%] Built target mimalloc-obj [ 67%] Built target binary_io [ 68%] Built target version [ 69%] Built target utils [ 71%] Built target assembly_graph [ 74%] Built target path_extend [ 76%] Built target input [ 77%] Built target pipeline [ 77%] Built target sequence [ 79%] Built target modules [ 80%] Built target paired_info [ 81%] Built target stages [ 81%] Built target common_modules [ 82%] Built target graphio [ 83%] Built target hmmercpp [ 86%] Built target spades-stages [ 87%] Built target spades-core [ 89%] Built target spades-hammer [ 92%] Built target spades-ionhammer [ 94%] Built target spades-corrector-core [ 94%] Built target spades-truseq-scfcorrection [ 94%] Built target spades-kmercount [ 94%] Built target spades-kmer-estimating [ 95%] Built target spades-read-filter [ 95%] Built target spades-convert-bin-to-fasta [ 95%] Built target spades-gbuilder [ 95%] Built target spades-gmapper [ 96%] Built target unitig-coverage [ 96%] Built target mapping_printer [ 97%] Built target spaligner [ 97%] Built target form_truealignments [ 98%] Built target spades-gsimplifier [ 99%] Built target cds-mapping-stats [100%] Built target cds-subgraphs [100%] Built target mag-improve Install the project... -- Install configuration: "RelWithDebInfo" -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/bin/spades.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/bin/metaspades.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/bin/plasmidspades.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/bin/rnaspades.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/bin/metaviralspades.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/bin/metaplasmidspades.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/bin/rnaviralspades.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/bin/coronaspades.py -- Installing: 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/home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//stages/terminating_stage.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/init.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/id_generation.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/break_by_coverage.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/string_dist_utils.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/launch_options.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/barcode_extraction.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/generate_quality.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/moleculo_filter_contigs.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//truspades/reference_construction.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//common -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//common/SeqIO.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//common/init.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//common/parallel_launcher.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//common/alignment.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//common/sam_parser.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//executors -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//executors/executors.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//executors/executor_save_yaml.py -- Installing: /home/xingyu_liao/Test/google/LongRepMarker_v2.0-master/programs/SPAdes-3.15.3/share/spades/spades_pipeline//executors/executor_local.py

helan-1997 commented 2 years ago

Expect simpler installation steps.

Xingyu-Liao commented 2 years ago

Hi,

I have updated the source code of LongRepMarker_v2.0. Please refer to the following steps to install LongRepMarker_v2.0 with conda..

1> Download the source file of LongRepMarker_v2.0 from tencent cloud drive (https://share.weiyun.com/zAVtLByF ，Extraction code：202264)

2> Decompress the "LongRepMarker_v2.0.zip" file. cd /data/zip      # for example, the compressed file is stored in the directory of "/data/zip". unzip ./LongRepMarker_v2.0.zip      # decompresses the file named "LongRepMarker_v2.0.zip".

3> Create a conda virtual environment. conda create -n TE python=3.8 pip=20.0.2 perl=5.32.1 make=4.2 unzip gcc=10.3.0 zlib pysam cmake

4> Activate the conda environment. conda activate TE

5> Enter the working directory of LongRepMarker from the conda environment. (TE)xingyu_liao@kw60204: cd /data/zip/LongRepMarker_v2.0      #TE is the name of conda virtual environment.

6> Install LongRepMarker_v2.0. (TE)xingyu_liao@kw60204:/data/zip/LongRepMarker_v2.0: ./Makefile.sh

Please download the latest version of LongRepMarker_v2.0 and rebuild it with conda. I think this is an easy way for installation. Thanks!

Best,

Xingyu Liao

helan-1997 commented 2 years ago

there is a new issue 05)Installing gfatools. gfatools installation failed, please check the installation log [ /home/helang/biosoft/LongRepMarker_v2.0-master/log/paf2gfa_Install.log ].

helan-1997 commented 2 years ago

And I have successfully installed it before, so I can't install it after updating. You can confirm that my system is OK.

Xingyu-Liao commented 2 years ago

Please run the following commands and paste the output.

(TE)@kw60204: conda activate TE (TE)@kw60204: conda list

helan-1997 commented 2 years ago

(TE) helang@lenovo-ThinkStation-P920:~/biosoft/LongRepMarker_v2.0-master$ conda list

packages in environment at /home/helang/miniconda3/envs/TE:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge https://mirrors.aliyun.com/anaconda/cloud/conda-forge _openmp_mutex 4.5 2_gnu https://mirrors.aliyun.com/anaconda/cloud/conda-forge binutils_impl_linux-64 2.36.1 h193b22a_2 https://mirrors.aliyun.com/anaconda/cloud/conda-forge bzip2 1.0.8 h7f98852_4 https://mirrors.aliyun.com/anaconda/cloud/conda-forge c-ares 1.18.1 h7f98852_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge ca-certificates 2022.5.18.1 ha878542_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge cmake 3.23.2 h5432695_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge expat 2.4.8 h27087fc_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge gcc 10.3.0 he2824d0_10 https://mirrors.aliyun.com/anaconda/cloud/conda-forge gcc_impl_linux-64 10.3.0 hf2f2afa_16 https://mirrors.aliyun.com/anaconda/cloud/conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 https://mirrors.aliyun.com/anaconda/cloud/conda-forge keyutils 1.6.1 h166bdaf_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge krb5 1.19.3 h3790be6_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libcurl 7.83.1 h7bff187_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libdeflate 1.10 h7f98852_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libedit 3.1.20191231 he28a2e2_2 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libev 4.33 h516909a_1 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libffi 3.4.2 h7f98852_5 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libgcc-devel_linux-64 10.3.0 he6cfe16_16 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libgcc-ng 12.1.0 h8d9b700_16 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libgomp 12.1.0 h8d9b700_16 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libnghttp2 1.47.0 h727a467_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libnsl 2.0.0 h7f98852_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libsanitizer 10.3.0 h26c7422_16 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libssh2 1.10.0 ha56f1ee_2 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libstdcxx-ng 12.1.0 ha89aaad_16 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libuuid 2.32.1 h7f98852_1000 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libuv 1.43.0 h7f98852_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge libzlib 1.2.12 h166bdaf_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge lz4-c 1.9.3 h9c3ff4c_1 https://mirrors.aliyun.com/anaconda/cloud/conda-forge make 4.2.1 h14c3975_2004 https://mirrors.aliyun.com/anaconda/cloud/conda-forge ncurses 6.3 h27087fc_1 https://mirrors.aliyun.com/anaconda/cloud/conda-forge openssl 1.1.1o h166bdaf_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge perl 5.32.1 2_h7f98852_perl5 https://mirrors.aliyun.com/anaconda/cloud/conda-forge pip 20.0.2 py_2 https://mirrors.aliyun.com/anaconda/cloud/conda-forge pysam 0.19.1 py38h8bf8b8d_0 https://mirrors.aliyun.com/anaconda/cloud/bioconda python 3.8.13 h582c2e5_0_cpython https://mirrors.aliyun.com/anaconda/cloud/conda-forge python_abi 3.8 2_cp38 https://mirrors.aliyun.com/anaconda/cloud/conda-forge readline 8.1 h46c0cb4_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge rhash 1.4.1 h7f98852_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge setuptools 62.3.2 py38h578d9bd_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge sqlite 3.38.5 h4ff8645_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge sysroot_linux-64 2.12 he073ed8_15 https://mirrors.aliyun.com/anaconda/cloud/conda-forge tk 8.6.12 h27826a3_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge unzip 6.0 h7f98852_3 https://mirrors.aliyun.com/anaconda/cloud/conda-forge wheel 0.37.1 pyhd8ed1ab_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge xz 5.2.5 h516909a_1 https://mirrors.aliyun.com/anaconda/cloud/conda-forge zlib 1.2.12 h166bdaf_0 https://mirrors.aliyun.com/anaconda/cloud/conda-forge zstd 1.5.2 h8a70e8d_1 https://mirrors.aliyun.com/anaconda/cloud/conda-forge

helan-1997 commented 2 years ago

image

Xingyu-Liao commented 2 years ago

The only difference is zstd. Please recreate the conda environment by the following command. conda create -n TE python=3.8 pip=20.0.2 perl=5.32.1 make=4.2 unzip gcc=10.3.0 zlib pysam cmake zstd

@Q@LMK@W`30DOAL68A8Q$P

helan-1997 commented 2 years ago

The only difference is zstd. Please recreate the conda environment by the following command. conda create -n TE python=3.8 pip=20.0.2 perl=5.32.1 make=4.2 unzip gcc=10.3.0 zlib pysam cmake zstd

@Q@LMK@W`30DOAL68A8Q$P

It's all installed, but there are no screenshots.