install error

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Ashley S Doane

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Apr 2, 2017, 11:10:51 AM4/2/17
to biovalidation
Hi,

I'm getting an install error I can't seem to figure out, related to conda linking packages. Seems related to an IOerror (see below).  I have anaconda installed in ~/ and removed this from my PATH (this hasn't caused problems before).  

Here is output after the listing of "NEW packages to be INSTALLED"...


The following packages will be UPDATED:

    numpy:                             1.12.1-py27_0                          --> 1.12.1-py27_nomkl_0               [nomkl] (soft-link)
    scipy:                             0.19.0-np112py27_0                     --> 0.19.0-np112py27_nomkl_0          [nomkl] (soft-link)

The following packages will be DOWNGRADED due to dependency conflicts:

    samtools:                          1.4-0                      bioconda    --> 1.3.1-5                  bioconda (soft-link)

Unlinking packages ...
[      COMPLETE      ]|####################################################################################################################################################| 100%
Linking packages ...
An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:




Current conda install:

               platform : linux-64
          conda version : 4.2.13
       conda is private : False
      conda-env version : 4.2.13
    conda-build version : not installed
         python version : 2.7.13.final.0
       requests version : 2.12.4
       root environment : /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda  (writable)
    default environment : /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda
       envs directories : /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/envs
          package cache : /athena/elementolab/scratch/asd2007/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



`$ /athena/elementolab/scratch/asd2007/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=2.2.8 bwa bwakit cage cancerit-allelecount cnvkit cpat cramtools crossmap cufflinks cutadapt cyvcf2 delly dkfz-bias-filter express extract-sv-reads fastqc fgbio freebayes=1.1.0 gatk gatk-framework gemini geneimpacts genesplicer glpk=4.57 goleft grabix gridss gsort gvcf-regions hap.py hisat2 hmmlearn htseq htslib=1.3 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 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=1.3.1 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 variant-effect-predictor=87 variantbam varscan vawk vcf2db vcfanno vcflib viennarna vt wham anaconda-client awscli nodejs 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 "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/exceptions.py", line 479, in conda_exception_handler
        return_value = func(*args, **kwargs)
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 145, in _main
        exit_code = args.func(args, p)
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/cli/main_install.py", line 80, in execute
        install(args, parser, 'install')
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/cli/install.py", line 405, in install
        execute_actions(actions, index, verbose=not context.quiet)
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/plan.py", line 643, in execute_actions
        inst.execute_instructions(plan, index, verbose)
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 135, in execute_instructions
        cmd(state, arg)
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 78, in LINK_CMD
        link(state['prefix'], dist, lt, index=state['index'])
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/install.py", line 986, in link
        _link(src, dst, lt)
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/conda/install.py", line 171, in _link
        shutil.copy2(src, dst)
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/shutil.py", line 130, in copy2
        copyfile(src, dst)
      File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/shutil.py", line 82, in copyfile
        with open(src, 'rb') as fsrc:
    IOError: [Errno 2] No such file or directory: u'/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/pkgs/kraken-0.10.6_eaf8fb68-pl5.22.0_3/bin/activate.bak'

[kraken              ]|                                                                                                                                                    |   0%
Fatal error: local() encountered an error (return code 1) while executing '/athena/elementolab/scratch/asd2007/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=2.2.8 bwa bwakit cage cancerit-allelecount cnvkit cpat cramtools crossmap cufflinks cutadapt cyvcf2 delly dkfz-bias-filter express extract-sv-reads fastqc fgbio freebayes=1.1.0 gatk gatk-framework gemini geneimpacts genesplicer glpk=4.57 goleft grabix gridss gsort gvcf-regions hap.py hisat2 hmmlearn htseq htslib=1.3 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 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=1.3.1 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 variant-effect-predictor=87 variantbam varscan vawk vcf2db vcfanno vcflib viennarna vt wham anaconda-client awscli nodejs 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 248, in <module>
    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 "/home/asd2007/anaconda2/lib/python2.7/subprocess.py", line 186, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/athena/elementolab/scratch/asd2007/local']' returned non-zero exit status 1


Please let me know if you have any advice.

Thanks again for bcbio! 
Best,
Ashley

Brad Chapman

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Apr 3, 2017, 6:42:38 AM4/3/17
to Ashley S Doane, biovalidation

Ashley;
Thanks much for the report and sorry about the issue. It looks like the
recently updated kraken bioconda package is broken. I pushed a fixed version
(0.10.6_eaf8fb68-pl5.22.0_4) that should work correctly if you re-try the
update. You shouldn't have to change anything, hopefully it'll just pick up
the new version and work. Hope this resolves the problem for you,
Brad

> [ text/plain ]
> Hi,
>
> I'm getting an install error I can't seem to figure out, related to conda
> linking packages. Seems related to an IOerror (see below). I have anaconda
> installed in ~/ and removed this from my PATH (this hasn't caused problems
> before).
>
> Here is output *after* the listing of "NEW packages to be INSTALLED"...
> --
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Ashley S Doane

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Apr 3, 2017, 5:20:31 PM4/3/17
to biovalidation, ashley...@gmail.com
Dear Brad:

Excellent thanks so much, install was successful.

Best,
Ashley

Ashley S Doane

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Apr 7, 2017, 10:05:50 PM4/7/17
to biovalidation, ashley...@gmail.com
Hi,

Hi,
Sorry to report more issues, but I haven't been able to sort out this error installing genomes (just GRCh37 for now).  The tools seem to be installing ok. Aside from the error 404, it also seems to be looking for java in /opt/anaconda1anaconda2anaconda3/bin/java, which definitely doesn't exist.  I've done the standard unset PYTHONPATH commands.

 Here is output before error, after calling:
bcbio_nextgen.py upgrade -u stable --data --genomes GRCh37

bcbio_nextgen.py upgrade -u stable --data --genomes GRCh37
Upgrading bcbio
--2017-04-07 21:59:36--  https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements-conda.txt
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.20.133
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.20.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 37 [text/plain]
Saving to: ‘bcbio-update-requirements.txt’


100%[================================================================================================================================================>] 37          --.-K/s   in 0s


2017-04-07 21:59:36 (7.59 MB/s) - ‘bcbio-update-requirements.txt’ saved [37/37]


Fetching package metadata .............
Solving package specifications: ..........


# All requested packages already installed.
# packages in environment at /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda:
#
bcbio-nextgen             1.0.2                    py27_0    bioconda
htslib                    1.3.2                         0    bioconda
Upgrade of bcbio-nextgen code complete.
Upgrading bcbio-nextgen data files
Setting up virtual machine
INFO: <cloudbio.flavor.Flavor instance at 0x7f09d6c99170>
INFO: This is a ngs_pipeline_minimal flavor
INFO: Reading default fabricrc.txt
DBG [config.py]: Using config file /athena/elementolab/scratch/asd2007/local/share/tmpbcbio-install/cloudbiolinux/cloudbio/../config/fabricrc.txt
INFO: Distribution __auto__
INFO: Get local environment
INFO: CentOS setup
DBG [distribution.py]: NixPkgs: Ignored
[localhost] local: echo $HOME
[localhost] local: uname -m
INFO: Now, testing connection to host...
INFO: Connection to host appears to work!
DBG [utils.py]: Expand paths
INFO: List of genomes to get (from the config file at '{'install_liftover': False, 'genome_indexes': ['bwa', 'star', 'rtg'], 'genomes': [{'annotations': ['GA4GH_problem_regions', 'capture_regions', 'MIG', 'prioritize', 'dbsnp', 'hapmap', '1000g_omni_snps', 'ACMG56_genes', '1000g_snps', 'mills_indels', 'clinvar', 'cosmic', 'ancestral', 'qsignature', 'genesplicer', 'effects_transcripts', 'vcfanno', 'viral', 'transcripts', 'RADAR', 'mirbase'], 'validation': ['giab-NA12878', 'giab-NA24385', 'giab-NA24631', 'dream-syn3', 'dream-syn4'], 'name': 'Human (GRCh37)', 'dbkey': 'GRCh37'}], 'install_uniref': False}'): Human (GRCh37)
INFO: Genome preparation method ggd failed, trying next
INFO: Downloading genome from s3: GRCh37 rtg
[localhost] local: pwd
[localhost] local: echo $HOME
[localhost] local: wget --continue --no-check-certificate -O GRCh37-rtg.tar.xz 'https://s3.amazonaws.com/biodata/genomes/GRCh37-rtg.tar.xz'
--2017-04-07 21:59:59--  https://s3.amazonaws.com/biodata/genomes/GRCh37-rtg.tar.xz
Resolving s3.amazonaws.com (s3.amazonaws.com)... 52.216.225.147
Connecting to s3.amazonaws.com (s3.amazonaws.com)|52.216.225.147|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2017-04-07 21:59:59 ERROR 404: Not Found.




Warning: local() encountered an error (return code 8) while executing 'wget --continue --no-check-certificate -O GRCh37-rtg.tar.xz 'https://s3.amazonaws.com/biodata/genomes/GRCh37-rtg.tar.xz''


INFO: Genome preparation method s3 failed, trying next
INFO: Preparing genome GRCh37 with index rtg
[localhost] local: export PATH=/athena/elementolab/scratch/asd2007/local/share/bin:$PATH && export RTG_JAVA_OPTS='-Xms1g' && export RTG_MEM=2g && rtg format -o rtg/GRCh37.sdf /athena/elementolab/scratch/asd2007/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa
Unable to execute /opt/anaconda1anaconda2anaconda3/bin/java


Fatal error: local() encountered an error (return code 1) while executing 'export PATH=/athena/elementolab/scratch/asd2007/local/share/bin:$PATH && export RTG_JAVA_OPTS='-Xms1g' && export RTG_MEM=2g && rtg format -o rtg/GRCh37.sdf /athena/elementolab/scratch/asd2007/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa'


Aborting.
INFO: Genome preparation method raw failed, trying next

Traceback (most recent call last):

  File "/athena/elementolab/scratch/asd2007/local/share/bin/bcbio_nextgen.py", line 4, in <module>
    __import__('pkg_resources').run_script('bcbio-nextgen==1.0.2', 'bcbio_nextgen.py')
  File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script
  File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1499, in run_script
  File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-1.0.2-py2.7.egg-info/scripts/bcbio_nextgen.py", line 215, in <module>
    install.upgrade_bcbio(kwargs["args"])
  File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 95, in upgrade_bcbio
    upgrade_bcbio_data(args, REMOTES)
  File "/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 290, in upgrade_bcbio_data
    cbl_deploy.deploy(s)
  File "/athena/elementolab/scratch/asd2007/local/share/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 65, in deploy
    _setup_vm(options, vm_launcher, actions)
  File "/athena/elementolab/scratch/asd2007/local/share/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 110, in _setup_vm
    configure_instance(options, actions)
  File "/athena/elementolab/scratch/asd2007/local/share/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 268, in configure_instance
    setup_biodata(options)
  File "/athena/elementolab/scratch/asd2007/local/share/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 250, in setup_biodata
    install_proc(options["genomes"], ["ggd", "s3", "raw"])
  File "/athena/elementolab/scratch/asd2007/local/share/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 339, in install_data
    _prep_genomes(env, genomes, genome_indexes, ready_approaches)
  File "/athena/elementolab/scratch/asd2007/local/share/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 479, in _prep_genomes
    raise IOError("Could not prepare index {0} for {1} by any method".format(idx, gid))
IOError: Could not prepare index rtg for GRCh37 by any method

Brad Chapman

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Apr 8, 2017, 5:53:03 AM4/8/17
to Ashley S Doane, biovalidation, ashley...@gmail.com

Ashley;
Thanks much for the report and apologies about the issues. I'm not sure what
is happening here, it looks like something went wrong with your rtg
installation but I can't seem to reproduce here.
`/opt/anaconda1anaconda2anaconda3/bin/java` is an internal path used in conda
as a placeholder but looking at the rtg wrapper scripts I can't see how it
gets introduced. Could you try removing and re-installing rtg?

bcbio_conda uninstall rtg-tools
rm -rf /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/pkgs/rtg-tools-3.*
bcbio_conda install -c bioconda rtg-tools

then running `rtg` to see if that fixes it? Sorry to not have a better idea
but hope this gets a clean working install,
Brad

> [ text/plain ]
> Hi,
>
> Hi,
> Sorry to report more issues, but I haven't been able to sort out this error
> installing genomes (just GRCh37 for now). The tools seem to be installing
> ok. Aside from the error 404, it also seems to be looking for java in /opt/
> anaconda1anaconda2anaconda3/bin/java, which definitely doesn't exist. I've

Ashley S Doane

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Apr 9, 2017, 2:10:29 AM4/9/17
to biovalidation, ashley...@gmail.com
Thanks Brad, reinstalling rtg solved that issue and that part of the genome setup completed, but similar error came up soon after:
 Running GGD recipe: GRCh37 RADAR 5
tabix: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):

  File "/athena/elementolab/scratch/asd2007/local/bin/bcbio_nextgen.py", line 4, in <module>    __import__('pkg_resources').run_script('bcbio-nextgen==1.0.2', 'bcbio_nextgen.py')

I ran the test scripts in bcbio_nextgen and it also looks like a number of errors related to an openSSL library, for example:

/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/bin/tabix: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
' returned non-zero exit status 127

I started with a clean install of bcbio, and unset the python variables per documentation.   
tabix seems to be linking to system libraries as well (not sure if that's supposed to be the case).  I'm on centos7.

ldd /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/bin/tabix
 linux-vdso.so.1 =>  (0x00007fff6f7aa000)
 libz.so.1 => /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/bin/../lib/libz.so.1 (0x00007f6b3228a000)
 libcurl.so.4 => /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/bin/../lib/libcurl.so.4 (0x00007f6b32023000)
 libcrypto.so.1.0.0 => /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/bin/../lib/libcrypto.so.1.0.0 (0x00007f6b31bec000)
 libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007f6b319d0000)
 libc.so.6 => /usr/lib64/libc.so.6 (0x00007f6b3160e000)
 libssl.so.1.0.0 => /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/bin/../lib/./libssl.so.1.0.0 (0x00007f6b31397000)
 librt.so.1 => /usr/lib64/librt.so.1 (0x00007f6b3118e000)
 libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f6b30f8a000)
 /lib64/ld-linux-x86-64.so.2 (0x00007f6b324a1000)

Hopefully this narrow's down the problem a bit.  I haven't tried using my system libraries and trying to let conda do what it wants.

thanks for your help, really appreciate it.

Brad Chapman

unread,
Apr 9, 2017, 4:29:04 PM4/9/17
to Ashley S Doane, biovalidation, ashley...@gmail.com

Ashley;
Glad re-installing rtg fixed that issue and thanks for the detailed report on
the new problems. A couple of thoughts:

- Is it possible that you have a different tabix, not installed by bcbio, on
your PATH? That might explain the error since ldd appears to report the
correct linking to libcrypto.so
- Does libcrypo appear to be correctly installed. You should have the shared
libraries here:

ls -lh /athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/libcrypto.*

If not, perhaps uninstalling and re-installing openssl in conda will fix
it?

You do expect to link to system libraries if present since they're dynamically
linked. Your ldd looks okay hence the thoughts about what might be
problematic.

Hope this helps,
Brad


> [ text/plain ]
>> an email to biovalidatio...@googlegroups.com <javascript:>.
>> > To post to this group, send email to bioval...@googlegroups.com
>> <javascript:>.

Ashley S Doane

unread,
Apr 10, 2017, 9:38:30 AM4/10/17
to biovalidation, Brad Chapman
Thanks Brad, I will try your suggestions. Conda didnt want to uninstall openssl before, but I could force it to then reinstall. 
A few other binaries in ../anaconda/bin seemed to be having issues with openssl libraries e.g. bgzip, so hopefully this solves it.  
Thanks

Ashley Stephen Doane
PhD Candidate
Tri-Institutional Computational Biology and Medicine
Weill Cornell Medicine
From: Brad Chapman <chap...@50mail.com>
Sent: Sunday, April 9, 2017 4:29:01 PM
To: Ashley S Doane; biovalidation
Cc: ashley...@gmail.com
Subject: Re: [biovalidation] install error
 

Ashley S Doane

unread,
May 11, 2017, 9:51:17 PM5/11/17
to biovalidation
Hi, Just an update on how I solved this and an additional minor bug (and possible solution).

The library errors were related to changes in centos 7.3 ssl libraries and were solved with system wide updates.

The other issue is related to icu versions and lxml, getting called by qualimap in an rnaseq run.

/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/qc/qualimap.pyc in _parse_rnaseq_qualimap_metrics(report_file='/scratchLocal/asd2007/RNAseq/ecyj3189/ecyjad3189.../qc/58CB/qualimap_rnaseq/58CB/qualimapReport.html')
    275     return out
    276
    277 def _parse_rnaseq_qualimap_metrics(report_file):
    278     """Extract useful metrics from the qualimap HTML report file.
    279     """
--> 280     import lxml.html
    281     out = {}
    282     parsers = ["Reads alignment", "Reads genomic origin", "Transcript coverage profile"]
    283     root = lxml.html.parse(report_file).getroot()
    284     for table in root.xpath("//div[@class='table-summary']"):


...........................................................................
/athena/elementolab/scratch/asd2007/local/share/bcbio/anaconda/lib/python2.7/site-packages/lxml/html/__init__.py in <module>()
     49     # while unnecessary, importing from 'collections.abc' is the right way to do it
     50     from collections.abc import MutableMapping, MutableSet
     51 except ImportError:
     52     from collections import MutableMapping, MutableSet
     53
---> 54 from .. import etree
     55 from . import defs
     56 from ._setmixin import SetMixin
     57
     58 try:


ImportError: libicui18n.so.58: cannot open shared object file: No such file or directory

The solution I found was to 
 bcbio_conda install icu=58


but this downgrades salmon from 0.8.2-0 to 8.1-0.   At this point in the run, I think all salmon functions have run, and I can revert to 0.8.2 after with a bcbio upgrade.

Thanks
Ashley

Brad Chapman

unread,
May 15, 2017, 10:17:03 AM5/15/17
to Ashley S Doane, biovalidation

Ashley;
Thanks for the details here and apologies about the problem. We pushed a fix
for the lxml/icu issues to the latest development and I'll follow up with more
details in the GitHub thread:

https://github.com/chapmanb/bcbio-nextgen/issues/1878

Thanks again,
Brad


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