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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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bcbio-nextgen install error on EC2 instance #1581

Closed PatrickJReed closed 7 years ago

PatrickJReed commented 7 years ago

unable to install on m4.4XL instance

"sudo python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local --genomes GRCh37 --aligners bwa" aborts see below:

Please consider posting the following information to the conda GitHub issue tracker at:

https://github.com/conda/conda/issues

Current conda install:

           platform : linux-64
      conda version : 4.2.9
   conda is private : False
  conda-env version : 4.2.9
conda-build version : not installed
     python version : 2.7.12.final.0
   requests version : 2.9.1
   root environment : /usr/local/share/bcbio/anaconda  (writable)
default environment : /usr/local/share/bcbio/anaconda
   envs directories : /usr/local/share/bcbio/anaconda/envs
      package cache : /usr/local/share/bcbio/anaconda/pkgs
       channel URLs : https://repo.continuum.io/pkgs/free/linux-64/
                      https://repo.continuum.io/pkgs/free/noarch/
                      https://repo.continuum.io/pkgs/pro/linux-64/
                      https://repo.continuum.io/pkgs/pro/noarch/
        config file : None
       offline mode : False

$ /usr/local/share/bcbio/anaconda/bin/conda install -y -c bioconda -c r -c conda-forge age-metasv bamtools bamutil bcbio-prioritize bcbio-rnaseq bcbio-variation bcbio-variation-recall bcbreport bcftools=1.3.0 bedtools=2.24.0 bio-vcf biobambam bowtie bowtie2 bwa bwakit cage cancerit-allelecount cnvkit cpat cramtools crossmap cufflinks cutadapt cyvcf2 delly express fastqc freebayes=1.0.2.29 gatk gatk-framework gemini geneimpacts glpk=4.57 grabix gsort gvcf-regions hap.py hisat2 hmmlearn htseq htslib impute2 kallisto kraken lofreq lumpy-sv macs2 manta mbuffer metasv mirdeep2 moreutils multiqc multiqc-bcbio novoalign oncofuse optitype pandoc 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 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 vardict vardict-java variant-effect-predictor variantbam varscan vawk vcf2db vcfanno vcflib viennarna vt wham anaconda-client awscli p7zip s3gof3r 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-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 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

Traceback (most recent call last):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/exceptions.py", line 473, in conda_exception_handler
    return_value = func(*args, **kwargs)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 144, in _main
    exit_code = args.func(args, p)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/cli/main_install.py", line 80, in execute
    install(args, parser, 'install')
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/cli/install.py", line 420, in install
    raise CondaRuntimeError('RuntimeError: %s' % e)
CondaRuntimeError: Runtime error: RuntimeError: Runtime error: Could not open u'/usr/local/share/bcbio/anaconda/pkgs/viennarna-2.2.10-0.tar.bz2.part' for writing (HTTPSConnectionPool(host='binstar-cio-packages-prod.s3.amazonaws.com', port=443): Read timed out.).

viennarna-2.2. 1% |### | Time: 0:00:02 189.50 kB/s Fatal error: local() encountered an error (return code 1) while executing '/usr/local/share/bcbio/anaconda/bin/conda install -y -c bioconda -c r -c conda-forge age-metasv bamtools bamutil bcbio-prioritize bcbio-rnaseq bcbio-variation bcbio-variation-recall bcbreport bcftools=1.3.0 bedtools=2.24.0 bio-vcf biobambam bowtie bowtie2 bwa bwakit cage cancerit-allelecount cnvkit cpat cramtools crossmap cufflinks cutadapt cyvcf2 delly express fastqc freebayes=1.0.2.29 gatk gatk-framework gemini geneimpacts glpk=4.57 grabix gsort gvcf-regions hap.py hisat2 hmmlearn htseq htslib impute2 kallisto kraken lofreq lumpy-sv macs2 manta mbuffer metasv mirdeep2 moreutils multiqc multiqc-bcbio novoalign oncofuse optitype pandoc 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 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 vardict vardict-java variant-effect-predictor variantbam varscan vawk vcf2db vcfanno vcflib viennarna vt wham anaconda-client awscli p7zip s3gof3r 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-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 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'

Aborting. Traceback (most recent call last): File "bcbio_nextgen_install.py", line 245, in main(parser.parse_args(), sys.argv[1:]) File "bcbio_nextgen_install.py", line 44, in main subprocess.check_call([bcbio, "upgrade"] + _clean_args(sys_argv, args)) File "/usr/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/usr/local/share/bcbio/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/usr/local', '--genomes', 'GRCh37', '--aligners', 'bwa', '--data']' returned non-zero exit status 1

PatrickJReed commented 7 years ago

It took multiple retries but I finally got a successful install. Looks like a network connection issue.