1. Andrew Doxey Avatar Andrew Doxey
  2. Untitled project
  3. metannotate
  4. Issues

base_installation.sh install failures

Issue #1 new
Lee Bergstrand created an issue

Bug Report:

Operating Systems Tested: Ubuntu 14.04.2 LTS

Details:

Digital Ocean Ubuntu 14.04.2 LTS Virtual Machine (Clean Install)

  • 8 ?GB RAM
  • 4 Core
  • 80 GB SSD

Steps to reproduce:

  1. Boot VM

  2. Install apt-get install requirements:

    • python-dev
    • build-essential
    • default-jre
    • git

  3. Run recommended base Installation commands:

git clone https://bitbucket.org/doxeylab/metannotate.git
cd metannotate
bash base_installation.sh

List of Errors (See attached log file for further analysis):

Installation Error #1:

Installing EMBOSS transeq.\n
--2015-08-04 18:15:45--  ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz
           => ‘emboss-latest.tar.gz’
Resolving emboss.open-bio.org (emboss.open-bio.org)... 54.243.166.98
Connecting to emboss.open-bio.org (emboss.open-bio.org)|54.243.166.98|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/EMBOSS ... done.
==> SIZE emboss-latest.tar.gz ... done.
==> PASV ... done.    ==> RETR emboss-latest.tar.gz ... 
No such file ‘emboss-latest.tar.gz’.

tar (child): emboss-latest.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
base_installation.sh: line 20: cd: EMBOSS*: No such file or directory
base_installation.sh: line 21: ./configure: No such file or directory
make: *** No targets specified and no makefile found.  Stop.
cp: cannot stat ‘emboss/’: No such file or directory
ln: failed to create symbolic link ‘/home/syntax/.local/bin/transeq’: File exists
Installing python packages through pip.\n
Requirement already satisfied (use --upgrade to upgrade): celery in ./.local/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): pytz>dev in ./.local/lib/python2.7/site-packages (from celery)
Requirement already satisfied (use --upgrade to upgrade): billiard<3.4,>=3.3.0.20 in ./.local/lib/python2.7/site-packages (from celery)
Requirement already satisfied (use --upgrade to upgrade): kombu<3.1,>=3.0.25 in ./.local/lib/python2.7/site-packages (from celery)
Requirement already satisfied (use --upgrade to upgrade): amqp<2.0,>=1.4.5 in ./.local/lib/python2.7/site-packages (from kombu<3.1,>=3.0.25->celery)
Requirement already satisfied (use --upgrade to upgrade): anyjson>=0.3.3 in ./.local/lib/python2.7/site-packages (from kombu<3.1,>=3.0.25->celery)
Requirement already satisfied (use --upgrade to upgrade): taxtastic in ./.local/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): sqlalchemy>=0.7 in ./.local/lib/python2.7/site-packages (from taxtastic)
Requirement already satisfied (use --upgrade to upgrade): decorator in ./.local/lib/python2.7/site-packages (from taxtastic)
Requirement already satisfied (use --upgrade to upgrade): biopython in ./.local/lib/python2.7/site-packages (from taxtastic)
Requirement already satisfied (use --upgrade to upgrade): xlrd in ./.local/lib/python2.7/site-packages (from taxtastic)
Exception:
Traceback (most recent call last):
  File "/home/syntax/.local/lib/python2.7/site-packages/pip/basecommand.py", line 223, in main
    status = self.run(options, args)
  File "/home/syntax/.local/lib/python2.7/site-packages/pip/commands/install.py", line 270, in run
    wheel_cache
  File "/home/syntax/.local/lib/python2.7/site-packages/pip/basecommand.py", line 275, in populate_requirement_set
    wheel_cache=wheel_cache
  File "/home/syntax/.local/lib/python2.7/site-packages/pip/req/req_install.py", line 212, in from_line
    wheel_cache=wheel_cache, constraint=constraint)
  File "/home/syntax/.local/lib/python2.7/site-packages/pip/req/req_install.py", line 66, in __init__
    req = pkg_resources.Requirement.parse(req)
  File "/home/syntax/.local/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 2980, in parse
    reqs = list(parse_requirements(s))
  File "/home/syntax/.local/lib/python2.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 2911, in parse_requirements
    raise RequirementParseError("Missing distribution spec", line)
RequirementParseError: Missing distribution spec —-user

Installation Error #2:

make[1]: Leaving directory `/home/syntax/hmmer-3.1b1-linux-intel-x86_64/src'
     SUBDIR profmark
make[1]: Entering directory `/home/syntax/hmmer-3.1b1-linux-intel-x86_64/profmark'
     CC create-profmark.o
     GEN create-profmark
     CC rocplot.o
     GEN rocplot
make[1]: Leaving directory `/home/syntax/hmmer-3.1b1-linux-intel-x86_64/profmark'
ln: failed to create symbolic link ‘/home/syntax/.local/bin/hmmstat’: File exists
ln: failed to create symbolic link ‘/home/syntax/.local/bin/hmmsearch’: File exists
ln: failed to create symbolic link ‘/home/syntax/.local/bin/hmmalign’: File exists
ln: failed to create symbolic link ‘/home/syntax/.local/bin/esl-reformat’: File exists
ln: failed to create symbolic link ‘/home/syntax/.local/bin/esl-sfetch’: File exists
Installing USEARCH.\n
ln: failed to create symbolic link ‘/home/syntax/.local/bin/usearch’: File exists
Installing USEARCH.\n

Installation Error #3:

#!

base_installation.sh: line 56: cd: downloads: No such file or directory
--2015-08-04 18:17:08--  http://www.microbesonline.org/fasttree/FastTreeMP
Resolving www.microbesonline.org (www.microbesonline.org)... 128.32.126.165
Connecting to www.microbesonline.org (www.microbesonline.org)|128.32.126.165|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 373480 (365K) [text/plain]
FastTreeMP: Permission denied

Cannot write to ‘FastTreeMP’ (Permission denied).
mv: cannot stat ‘FastTreeMP’: No such file or directory
chmod: changing permissions of ‘/home/syntax/.local/bin/FastTreeMP’: Operation not permitted
Installing pplacer and guppy.\n
base_installation.sh: line 63: cd: downloads: No such file or directory
--2015-08-04 18:17:08--  http://matsen.fhcrc.org/pplacer/builds/pplacer-v1.1-Linux.tar.gz
Resolving matsen.fhcrc.org (matsen.fhcrc.org)... 140.107.135.113
Connecting to matsen.fhcrc.org (matsen.fhcrc.org)|140.107.135.113|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 12846368 (12M) [application/x-gzip]
pplacer-v1.1-Linux.tar.gz.1: Permission denied

Cannot write to ‘pplacer-v1.1-Linux.tar.gz.1’ (Permission denied).
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/pplacer: Cannot open: Permission denied
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/guppy: Cannot open: Permission denied
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/rppr: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/add_classifications.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/check_placements.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/classif_rect.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/classif_table.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/deduplicate_sequences.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/extract_taxonomy_from_biom.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/hrefpkg_query.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/multiclass_concat.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/pca_for_qiime.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/refpkg_align.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/setup.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/sort_placefile.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/split_qiime.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/test_refpkg_align.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts/update_refpkg.py: Cannot open: File exists
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0/scripts: Cannot utime: Operation not permitted
tar: pplacer-v1.1.alpha16-1-gf748c91-Linux-3.2.0: Cannot utime: Operation not permitted
tar: Exiting with failure status due to previous errors
mv: cannot stat ‘pplacer’: No such file or directory
mv: cannot stat ‘guppy’: No such file or directory
Downloading and indexing taxonomy info.\n
base_installation.sh: line 73: cd: precompute: No such file or directory

Installation Error #4:

--2015-08-04 18:17:09--  ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
           => ‘taxdump.tar.gz.1’
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.11, 2607:f220:41e:250::13
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.11|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/taxonomy ... done.
==> SIZE taxdump.tar.gz ... 32850137
==> PASV ... done.    ==> RETR taxdump.tar.gz ... done.
taxdump.tar.gz.1: Permission denied
tar: citations.dmp: Cannot open: File exists
tar: delnodes.dmp: Cannot open: File exists
tar: division.dmp: Cannot open: File exists
tar: gc.prt: Cannot open: File exists
tar: gencode.dmp: Cannot open: File exists
tar: merged.dmp: Cannot open: File exists
tar: names.dmp: Cannot open: File exists
tar: nodes.dmp: Cannot open: File exists
tar: readme.txt: Cannot open: File exists
tar: Exiting with failure status due to previous errors
base_installation.sh: line 76: trimmed.names.dmp: Permission denied
python: can't open file 'make_taxonomy_pickle.py': [Errno 2] No such file or directory
Downloading and indexing gi number to taxid mappings.\n
base_installation.sh: line 81: cd: precompute: No such file or directory

Installation Error #5:

--2015-08-04 18:17:11--  ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz
           => ‘gi_taxid_prot.dmp.gz’
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.11, 2607:f220:41e:250::13
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.11|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/taxonomy ... done.
==> SIZE gi_taxid_prot.dmp.gz ... 570212802
==> PASV ... done.    ==> RETR gi_taxid_prot.dmp.gz ... done.
gi_taxid_prot.dmp.gz: Permission denied
gzip: gi_taxid_prot.dmp.gz: No such file or directory
mv: cannot move ‘gi_taxid_prot.dmp’ to ‘../data/’: Not a directory
base_installation.sh: line 92: path.txt: Permission denied

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