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jhangyu

bcbio_nextgen_install

jhangyu
Jul 19th, 2017
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  1. python bcbio_nextgen_install.py /home/jhangyu --tooldir=/home/jhangyu/anaconda --cores 22
  2. Checking required dependencies
  3. Installing isolated base python installation
  4. Installing bcbio-nextgen
  5. --2017-07-20 00:47:38--  https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements-conda.txt
  6. Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.40.133
  7. Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.40.133|:443... connected.
  8. HTTP request sent, awaiting response... 200 OK
  9. Length: 20 [text/plain]
  10. Saving to: ‘requirements-conda.txt’
  11.  
  12. requirements-conda. 100%[===================>]      20  --.-KB/s    in 0s      
  13.  
  14. 2017-07-20 00:47:39 (5.00 MB/s) - ‘requirements-conda.txt’ saved [20/20]
  15.  
  16. Fetching package metadata ...............
  17. Solving package specifications: .
  18.  
  19. # All requested packages already installed.
  20. # packages in environment at /home/jhangyu/anaconda:
  21. #
  22. nomkl                     1.0                           0    anaconda
  23. Fetching package metadata ...............
  24. Solving package specifications: .
  25.  
  26. # All requested packages already installed.
  27. # packages in environment at /home/jhangyu/anaconda:
  28. #
  29. bcbio-nextgen             1.0.4                    py27_0    bioconda
  30. Installing data and third party dependencies
  31. Upgrading bcbio
  32. Upgrading third party tools to latest versions
  33. --2017-07-20 00:49:36--  https://github.com/chapmanb/cloudbiolinux/archive/master.tar.gz
  34. Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113
  35. Connecting to github.com (github.com)|192.30.253.112|:443... connected.
  36. HTTP request sent, awaiting response... 302 Found
  37. Location: https://codeload.github.com/chapmanb/cloudbiolinux/tar.gz/master [following]
  38. --2017-07-20 00:49:37--  https://codeload.github.com/chapmanb/cloudbiolinux/tar.gz/master
  39. Resolving codeload.github.com (codeload.github.com)... 192.30.253.121, 192.30.253.120
  40. Connecting to codeload.github.com (codeload.github.com)|192.30.253.121|:443... connected.
  41. HTTP request sent, awaiting response... 200 OK
  42. Length: unspecified [application/x-gzip]
  43. Saving to: ‘STDOUT’
  44.  
  45.      0K ........ ........ ........ ........ ........ ........ 1.80M
  46.   3072K ........ ........ ........ ......                     66.5M=1.7s
  47.  
  48. 2017-07-20 00:49:40 (2.91 MB/s) - written to stdout [5163679]
  49.  
  50. mv: cannot stat 'master': No such file or directory
  51. Setting up virtual machine
  52. INFO: <cloudbio.flavor.Flavor instance at 0x7fc219ef3830>
  53. INFO: This is a ngs_pipeline_minimal flavor
  54. INFO: Reading default fabricrc.txt
  55. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../config/fabricrc.txt
  56. INFO: Distribution __auto__
  57. INFO: Get local environment
  58. [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d =
  59. INFO: Ubuntu setup
  60. DBG [distribution.py]: Debian-shared setup
  61. DBG [distribution.py]: Source=zesty
  62. DBG [distribution.py]: NixPkgs: Ignored
  63. [localhost] local: echo $HOME
  64. [localhost] local: uname -m
  65. INFO: Now, testing connection to host...
  66. INFO: Connection to host appears to work!
  67. DBG [utils.py]: Expand paths
  68. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml
  69. INFO: Meta-package information from /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml
  70. - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen
  71. - Libraries: r-libs
  72. [localhost] local: whoami
  73. [localhost] local: echo $PATH
  74. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/custom.yaml
  75. INFO: Reading /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/custom.yaml
  76. DBG [shared.py]: Packages to install:
  77. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml
  78. INFO: Reading /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml
  79. DBG [shared.py]: Packages to install:
  80. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml
  81. INFO: Reading /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml
  82. DBG [shared.py]: Packages to install:
  83. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml
  84. INFO: Meta-package information from /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml
  85. - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen
  86. - Libraries: r-libs
  87. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml
  88. INFO: Reading /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml
  89. DBG [shared.py]: Packages to install:
  90. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml
  91. INFO: Meta-package information from /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml
  92. - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen
  93. - Libraries: r-libs
  94. DBG [config.py]: Using config file /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
  95. INFO: Reading /home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
  96. DBG [shared.py]: Packages to install: age-metasv,bamtools,bamutil,bcbio-prioritize,bcbio-rnaseq,bcbio-variation,bcbio-variation-recall,bcbreport,bcftools,bedtools=2.26.0,bio-vcf,biobambam,bowtie,bowtie2=2.2.8,bwa,bwakit,cage,cancerit-allelecount,cnvkit,cpat,cramtools,crossmap,cufflinks,cutadapt,cyvcf2,delly,dkfz-bias-filter,ensembl-vep=89.*,express,extract-sv-reads,fastqc,fgbio,freebayes=1.1.0,gatk,gatk-framework,gatk4,gemini,geneimpacts,genesplicer,glpk=4.57,goleft,grabix,gridss,gsort,gvcf-regions,hap.py,hisat2,hmmlearn,htseq,htslib,impute2,kallisto,kraken,lofreq,lumpy-sv,macs2,manta,maxentscan,mbuffer,metasv,mirdeep2=2.0.0.7,moreutils,multiqc,multiqc-bcbio,ngs-disambiguate,novoalign,oncofuse,optitype,parallel,pbgzip,perl-sanger-cgp-battenberg,phylowgs,picard,pindel,platypus-variant,pyloh,pytabix,pythonpy,qsignature,qualimap,rapmap,razers3,rtg-tools,sailfish,salmon,sambamba,samblaster,samtools,scalpel,sentieon,seq2c,seqbuster,seqtk,sickle-trim,simple_sv_annotation,snap-aligner=1.0dev.97,snpeff=4.3i,spades,star,stringtie,subread,svtools,svtyper,tdrmapper,theta2,tophat,tophat-recondition,ucsc-bedgraphtobigwig,ucsc-bedtobigbed,ucsc-bigbedinfo,ucsc-bigbedsummary,ucsc-bigbedtobed,ucsc-bigwiginfo,ucsc-bigwigsummary,ucsc-bigwigtobedgraph,ucsc-bigwigtowig,ucsc-fatotwobit,ucsc-gtftogenepred,ucsc-liftover,ucsc-wigtobigwig,umis,vardict,vardict-java,variantbam,varscan,vawk,vcf2db,vcfanno,vcflib,vt,wham,anaconda-client,awscli,bzip2,ncurses,nodejs,nomkl,p7zip,readline,s3gof3r,xz,perl-app-cpanminus,perl-archive-extract,perl-archive-zip,perl-bio-db-sam,perl-cgi,perl-dbi,perl-encode-locale,perl-file-fetch,perl-file-sharedir,perl-file-sharedir-install,perl-ipc-system-simple,perl-lwp-protocol-https,perl-lwp-simple,perl-statistics-descriptive,perl-time-hires,perl-vcftools-vcf,bioconductor-annotate,bioconductor-biocgenerics,bioconductor-biocinstaller,bioconductor-biocstyle,bioconductor-biostrings,bioconductor-biovizbase,bioconductor-bubbletree,bioconductor-cn.mops,bioconductor-degreport,bioconductor-deseq2,bioconductor-dexseq,bioconductor-dnacopy,bioconductor-genomicranges,bioconductor-iranges,bioconductor-limma,bioconductor-rtracklayer,r-cghflasso,r-chbutils,r-devtools,r-dplyr,r-dt,r-ggdendro,r-ggplot2,r-gplots,r-gsalib,r-knitr,r-pheatmap,r-plyr,r-pscbs,r-reshape,r-rmarkdown,r-rsqlite,r-sleuth,r-snow,r-stringi,r-wasabi,r=3.3.2
  97. [localhost] local: /home/jhangyu/anaconda/bin/conda info --json
  98. [localhost] local: /home/jhangyu/anaconda/bin/conda list --json r-tximport
  99. [localhost] local: /home/jhangyu/anaconda/bin/conda install --quiet -y -c conda-forge -c bioconda age-metasv bamtools bamutil bcbio-prioritize bcbio-rnaseq bcbio-variation bcbio-variation-recall bcbreport bcftools bedtools=2.26.0 bio-vcf biobambam bowtie bowtie2=2.2.8 bwa bwakit cage cancerit-allelecount cnvkit cpat cramtools crossmap cufflinks cutadapt cyvcf2 delly dkfz-bias-filter ensembl-vep=89.* express extract-sv-reads fastqc fgbio freebayes=1.1.0 gatk gatk-framework gatk4 gemini geneimpacts genesplicer glpk=4.57 goleft grabix gridss gsort gvcf-regions hap.py hisat2 hmmlearn htseq htslib impute2 kallisto kraken lofreq lumpy-sv macs2 manta maxentscan mbuffer metasv mirdeep2=2.0.0.7 moreutils multiqc multiqc-bcbio ngs-disambiguate novoalign oncofuse optitype parallel pbgzip perl-sanger-cgp-battenberg phylowgs picard pindel platypus-variant pyloh pytabix pythonpy qsignature qualimap rapmap razers3 rtg-tools sailfish salmon sambamba samblaster samtools scalpel sentieon seq2c seqbuster seqtk sickle-trim simple_sv_annotation snap-aligner=1.0dev.97 snpeff=4.3i spades star stringtie subread svtools svtyper tdrmapper theta2 tophat tophat-recondition ucsc-bedgraphtobigwig ucsc-bedtobigbed ucsc-bigbedinfo ucsc-bigbedsummary ucsc-bigbedtobed ucsc-bigwiginfo ucsc-bigwigsummary ucsc-bigwigtobedgraph ucsc-bigwigtowig ucsc-fatotwobit ucsc-gtftogenepred ucsc-liftover ucsc-wigtobigwig umis vardict vardict-java variantbam varscan vawk vcf2db vcfanno vcflib vt wham anaconda-client awscli bzip2 ncurses nodejs nomkl p7zip readline s3gof3r xz perl-app-cpanminus perl-archive-extract perl-archive-zip perl-bio-db-sam perl-cgi perl-dbi perl-encode-locale perl-file-fetch perl-file-sharedir perl-file-sharedir-install perl-ipc-system-simple perl-lwp-protocol-https perl-lwp-simple perl-statistics-descriptive perl-time-hires perl-vcftools-vcf bioconductor-annotate bioconductor-biocgenerics bioconductor-biocinstaller bioconductor-biocstyle bioconductor-biostrings bioconductor-biovizbase bioconductor-bubbletree bioconductor-cn.mops bioconductor-degreport bioconductor-deseq2 bioconductor-dexseq bioconductor-dnacopy bioconductor-genomicranges bioconductor-iranges bioconductor-limma bioconductor-rtracklayer r-cghflasso r-chbutils r-devtools r-dplyr r-dt r-ggdendro r-ggplot2 r-gplots r-gsalib r-knitr r-pheatmap r-plyr r-pscbs r-reshape r-rmarkdown r-rsqlite r-sleuth r-snow r-stringi r-wasabi r=3.3.2
  100. Fetching package metadata ...............
  101. Solving package specifications: .
  102. Warning: 4 possible package resolutions (only showing differing packages):
  103.   - bioconda::glpk-4.57-0, bioconda::perl-archive-zip-1.55-3
  104.   - bioconda::glpk-4.57-_0, bioconda::perl-archive-zip-1.55-3
  105.   - bioconda::glpk-4.57-0, bioconda::perl-archive-zip-1.55-pl5.22.0_3
  106.   - bioconda::glpk-4.57-_0, bioconda::perl-archive-zip-1.55-pl5.22.0_3
  107.  
  108. Package plan for installation in environment /home/jhangyu/anaconda:
  109.  
  110. The following packages will be UPDATED:
  111.  
  112.     bcbio-prioritize:       0.0.8-0        bioconda --> 0.0.8-1        bioconda
  113.     bcbio-rnaseq:           1.2.0-r3.3.2_2 bioconda --> 1.2.0-r3.3.2_3 bioconda
  114.     bcbio-variation:        0.2.6-1        bioconda --> 0.2.6-2        bioconda
  115.     bcbio-variation-recall: 0.1.7-0        bioconda --> 0.1.7-1        bioconda
  116.     cramtools:              3.0.b127-0     bioconda --> 3.0.b127-1     bioconda
  117.     gatk:                   3.7-py27_0     bioconda --> 3.7-py27_1     bioconda
  118.     oncofuse:               1.1.0-1        bioconda --> 1.1.0-2        bioconda
  119.     qualimap:               2.2.2a-0       bioconda --> 2.2.2a-1       bioconda
  120.     seqbuster:              3.1-1          bioconda --> 3.1-2          bioconda
  121.     subread:                1.5.2-0        bioconda --> 1.5.3-0        bioconda
  122.     varscan:                2.4.2-0        bioconda --> 2.4.2-1        bioconda
  123.  
  124. [localhost] local: /home/jhangyu/anaconda/bin/conda list --json -f age-metasv
  125. Traceback (most recent call last):
  126.   File "/home/jhangyu/anaconda/bin/bcbio_nextgen.py", line 215, in <module>
  127.     install.upgrade_bcbio(kwargs["args"])
  128.   File "/home/jhangyu/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 80, in upgrade_bcbio
  129.     upgrade_thirdparty_tools(args, REMOTES)
  130.   File "/home/jhangyu/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 433, in upgrade_thirdparty_tools
  131.     cbl_deploy.deploy(s)
  132.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 65, in deploy
  133.     _setup_vm(options, vm_launcher, actions)
  134.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 110, in _setup_vm
  135.     configure_instance(options, actions)
  136.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 257, in configure_instance
  137.     install_biolinux(options)
  138.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 281, in install_biolinux
  139.     _perform_install(target=target, flavor=flavor, more_custom_add=options.get("custom_add", None))
  140.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/fabfile.py", line 120, in _perform_install
  141.     install_conda(flavor=flavor, automated=True)
  142.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/fabfile.py", line 321, in install_conda
  143.     conda.install_packages(env, to_install=pkg_install)
  144.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/package/conda.py", line 42, in install_packages
  145.     _link_bin(package, env, conda_info, conda_bin)
  146.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/package/conda.py", line 76, in _link_bin
  147.     os.path.join(final_bindir, "%s%s" % (prefix, fname)))
  148.   File "/home/jhangyu/tmpbcbio-install/cloudbiolinux/cloudbio/package/conda.py", line 88, in _do_link
  149.     orig_file == os.path.normpath(os.path.join(os.path.dirname(final_file), os.readlink(final_file)))):
  150. OSError: [Errno 22] Invalid argument: '/home/jhangyu/anaconda/bin/age_align'
  151. Traceback (most recent call last):
  152.   File "bcbio_nextgen_install.py", line 251, in <module>
  153.     main(parser.parse_args(), sys.argv[1:])
  154.   File "bcbio_nextgen_install.py", line 44, in main
  155.     subprocess.check_call([bcbio, "upgrade"] + _clean_args(sys_argv, args))
  156.   File "/home/jhangyu/anaconda/lib/python2.7/subprocess.py", line 186, in check_call
  157.     raise CalledProcessError(retcode, cmd)
  158. subprocess.CalledProcessError: Command '['/home/jhangyu/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/home/jhangyu/anaconda', '--cores', '22', '--data']' returned non-zero exit status 1
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